A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

AA(int) - Method in class org.strbio.mol.Protein
returns the N'th residue in the sequence.
aaMolecularWeight - Static variable in class org.strbio.mol.Residue
molecular weight of each residue above
aapercent - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
aapercent_2 - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
aboutDialog - Variable in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
AboutDialog - Class in org.strbio.util.ui
A generic "about dialog" Version 1.0, 7/9/99 - original version, modified from Pred2ary 1.31
AboutDialog(GUIApp, String, int, String[]) - Constructor for class org.strbio.util.ui.AboutDialog
 
aboutDialog - Variable in class org.strbio.util.ui.GUIApp
 
accept(File) - Method in class org.strbio.mol.lib.ProteinFilter
 
Access - Class in org.strbio.local
Class to run access on a protein.
Access() - Constructor for class org.strbio.local.Access
 
ActionJButton - Class in org.strbio.util
In Swing 1.1.x and Java 1.2.x, a button can no longer be created for an Action using the "invisible toolbar" method.
ActionJButton(Action) - Constructor for class org.strbio.util.ActionJButton
 
actualAccuracy() - Method in class org.strbio.mol.Protein
The actual accuracy of the secondary structure prediction that's been done on this protein.
add(DMatrix) - Method in class org.strbio.math.DMatrix
Adds another DMatrix to this one.
add(double) - Method in class org.strbio.math.DMatrix
Adds a double to every value in this DMatrix.
add(DMatrix, DMatrix) - Static method in class org.strbio.math.DMatrix
Adds two DMatrix's and returns a new DMatrix containing the sum.
add(DVector) - Method in class org.strbio.math.DVector
Adds another DVector to this one.
add(DVector, DVector) - Static method in class org.strbio.math.DVector
Adds two DVector's and returns a new DVector containing the sum.
add(DVector) - Method in class org.strbio.math.DVectorSet
add in a single point to this set, without duplicating it.
add(DVectorSet) - Method in class org.strbio.math.DVectorSet
add in another set of DVectors, without duplicating them.
add(FMatrix) - Method in class org.strbio.math.FMatrix
Adds another FMatrix to this one.
add(float) - Method in class org.strbio.math.FMatrix
Adds a float to every value in this FMatrix.
add(FMatrix, FMatrix) - Static method in class org.strbio.math.FMatrix
Adds two FMatrix's and returns a new FMatrix containing the sum.
add(FVector) - Method in class org.strbio.math.FVector
Adds another FVector to this one.
add(FVector, FVector) - Static method in class org.strbio.math.FVector
Adds two FVector's and returns a new FVector containing the sum.
add(IMatrix) - Method in class org.strbio.math.IMatrix
Adds another IMatrix to this one.
add(IMatrix, IMatrix) - Static method in class org.strbio.math.IMatrix
Adds two IMatrix's and returns a new IMatrix containing the sum.
add(IVector) - Method in class org.strbio.math.IVector
Adds another IVector to this one.
add(IVector, IVector) - Static method in class org.strbio.math.IVector
Adds two IVector's and returns a new IVector containing the sum.
add(int[]) - Method in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea.ClickedArea
This adds a new area of interest.
add(Polymer) - Method in class org.strbio.mol.PolymerSet
add in a single Polymer to this set, without duplicating it.
add(PolymerSet) - Method in class org.strbio.mol.PolymerSet
add in another set of Polymers, without duplicating them.
add(String) - Method in class org.strbio.mol.PolymerSet
add in another set of Polymers from a file, without duplicating them.
addClassPred(double[]) - Method in class org.strbio.mol.lib.pred2ary.PCPSet
same functions for class pred
addClassPred(double[], int) - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
add class pred to that from an array.
addCompound(String) - Method in class org.strbio.util.db.PDBInfo
add a String to the compound records.
addCorrect(int) - Method in class org.strbio.math.CorrectMatrix
Add a correct guess for category A.
addFast(DVector) - Method in class org.strbio.math.DVectorSet
add in a single point, without checking dimensionality.
addGraph(Graphable2D) - Method in class org.strbio.util.graph.Graph2D
Add a graph to the view, setting its legend font to the current one.
addInfo(Info) - Method in class org.strbio.util.db.Data
Add some info to this set.
addKeySeq() - Method in class org.strbio.mol.Profile
Tell the profile to add the "key sequence"... another sequence with the sequence of this protein.
addMethod(FRParametersNode) - Method in class org.strbio.mol.lib.FRParameters
add a method to the list of parameters.
addPred(PCPSet) - Method in class org.strbio.mol.lib.pred2ary.PCPSet
add H and E stats together for 2 sets
addPred(double[]) - Method in class org.strbio.mol.lib.pred2ary.PCPSet
add H and E stats together for 2 sets, using array
addPred(PredClassProfile) - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
add H and E predictions together for 2 proteins.
addPred(double[], int) - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
add H and E from array.
addPrediction(int, int) - Method in class org.strbio.math.SimMatrix
Add a prediction, which was actually category a, but predicted to be in category b.
addPredToArray(double[]) - Method in class org.strbio.mol.lib.pred2ary.PCPSet
 
addPredToArray(double[], int) - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
add h, e to array
addReversedCopies() - Method in class org.strbio.mol.PolymerSet
Add reversed copies from the set.
addScoreFunction(ScoreFunction, double) - Method in class org.strbio.mol.lib.AlignmentParameters
Add new scoring function with specified weight.
addScoreFunction(ScoreFunction) - Method in class org.strbio.mol.lib.AlignmentParameters
Add new scoring function with default weight.
addSeq(String) - Method in class org.strbio.mol.Profile
Tell the profile to add a sequence with a given name.
addSeqsDirectlyFrom(Profile) - Method in class org.strbio.mol.Profile
Add additional sequences from another profile of the same length.
addSeqsFrom(Profile) - Method in class org.strbio.mol.Profile
add sequence info from another profile; aligns and copies.
addSM(TPSet) - Method in class org.strbio.mol.lib.pred2ary.TPSet
 
addSource(String) - Method in class org.strbio.util.db.PDBInfo
add a String to the source records.
addStrMatch(String, String, String, String) - Method in class org.strbio.mol.ThreadSet
add a single structural match to the set.
addStrMatch(AlignmentSet) - Method in class org.strbio.mol.ThreadSet
add a single structural match to the set, created by the user
addStrMatch(Polymer, Polymer) - Method in class org.strbio.mol.ThreadSet
add a single structural match to the set.
addTitle(String) - Method in class org.strbio.util.db.PDBInfo
add a String to the title records.
addTranslation(String, char) - Method in class org.strbio.raf.RAFResidue
add a custom translation
addWrong(int) - Method in class org.strbio.math.CorrectMatrix
Add a wrong guess for category A.
adjustSplitPane(boolean) - Method in class org.strbio.app.JThread
 
alAP - Static variable in class org.strbio.app.JThreadServer
 
Alces - Class in org.strbio.net
Class to access http://alces.med.umn.edu/rawtm.html Version 1.0, 9/18/1 - original version
Alces() - Constructor for class org.strbio.net.Alces
 
Align - Class in org.strbio.app
Shows alignment of a given sequence with a fold.
Align() - Constructor for class org.strbio.app.Align
 
aligned(int) - Method in class org.strbio.mol.Alignment
returns number of fold monomer alignmed to seq monomer i, or -1 if aligned to a gap.
Alignment - Class in org.strbio.mol
An Alignment is a simple representation of an alignment between two polymers.
Alignment() - Constructor for class org.strbio.mol.Alignment
making a new alignment sets everything to null.
Alignment(Polymer, Polymer) - Constructor for class org.strbio.mol.Alignment
make a new alignment with a seq and fold.
Alignment(int) - Constructor for class org.strbio.mol.Alignment
make a new alignment vector of a given length, setting all entries to unaligned.
Alignment(Polymer, Polymer, int[]) - Constructor for class org.strbio.mol.Alignment
make a new alignment from two polymers and an integer array.
Alignment(int[]) - Constructor for class org.strbio.mol.Alignment
make a new alignment from an integer array.
Alignment(Alignment) - Constructor for class org.strbio.mol.Alignment
make a new alignment from another one.
alignment - Variable in class org.strbio.mol.lib.MinareaResults
 
AlignmentDependent - Interface in org.strbio.mol.lib
Interface for scoring functions that are dependent on the rest of the alignment.
AlignmentParameters - Class in org.strbio.mol.lib
Alignment parameters.
AlignmentParameters(GapModel, ScoreList) - Constructor for class org.strbio.mol.lib.AlignmentParameters
Provide an initial gap model and score list.
AlignmentParameters() - Constructor for class org.strbio.mol.lib.AlignmentParameters
Default is everything null.
alignmentParameters - Variable in class org.strbio.mol.ThreadSet
Alignment parameters
alignmentParameters2 - Variable in class org.strbio.mol.ThreadSet
Alignment parameters for evaluating alignment goodness in FR tests; Null means use same one as that used to generate the alignment.
AlignmentParametersEA - Class in org.strbio.mol.lib
Parameters, with some statistical functions to tell you how accurate they are at alignment and/or fold recognition.
AlignmentParametersEA() - Constructor for class org.strbio.mol.lib.AlignmentParametersEA
 
AlignmentParametersEA(GapModel, ScoreList) - Constructor for class org.strbio.mol.lib.AlignmentParametersEA
 
AlignmentSet - Class in org.strbio.mol
Class to represent a set of alignments (i.e. correct, calculated) between two polymers.
AlignmentSet() - Constructor for class org.strbio.mol.AlignmentSet
making a new alignment sets everything to null.
AlignmentSet(Polymer, Polymer) - Constructor for class org.strbio.mol.AlignmentSet
make a new alignment with given seq, fold.
alignmentStats - Variable in class org.strbio.mol.AlignmentSet
alignment accuracy results; mostly cached values for things that can be calculated on the fly.
AlignmentStats - Class in org.strbio.mol
A class holding alignment statistics for a given alignment.
AlignmentStats() - Constructor for class org.strbio.mol.AlignmentStats
The default object has all stats undefined (Double.NaN), or -1 for integers.
alignmentStats(Printf) - Method in class org.strbio.mol.ThreadSet
compute stats on alignment.
alignStrMatches(Printf, boolean, boolean) - Method in class org.strbio.mol.ThreadSet
Aligns structural matches.
alignStrMatches() - Method in class org.strbio.mol.ThreadSet
Calculated alignment for all structural matches, without printing anything.
alignStrMatchesMinarea() - Method in class org.strbio.mol.ThreadSet
redo all structural matches using minarea, and save the results to a single file
alignToArray(int[]) - Method in class org.strbio.mol.Polymer
Adjust gaps in polymer to form one half of a given alignment.
alignToInverseArray(int[]) - Method in class org.strbio.mol.Polymer
Adjust gaps in polymer to match an array representation.
allElements - Variable in class org.strbio.util.db.Data.InfoEnumeration
 
allocSeqs(int) - Method in class org.strbio.mol.Profile
Tell the Profile to allocate space for at least N known sequences.
allocSeqs(int) - Method in class org.strbio.mol.ProfRes
Tell the ProfRes to allocate space for at least N sequences.
allocSeqsRes() - Method in class org.strbio.mol.Profile
Tell all residues in the profile to allocate space for at least as many sequences as we know about.
alpha() - Method in class org.strbio.mol.Residue
Alpha is the bond angle between CA(n-1), CA(n), CA(n+1).
alpha - Variable in class org.strbio.util.NeuralNet
user-dependent variables for SD BP method: momentum
altLoc - Variable in class org.strbio.mol.Atom
Here's where you store the Alternate Location Indicator character, which is right after the name in the PDB.
ap - Variable in class org.strbio.mol.lib.pred2ary.AppletJury
 
ap - Static variable in class org.strbio.raf.MakeRAF
 
appDataPath() - Method in class org.strbio.app.JThread
where is data for this app stored, relative to the app itself?
appDataPath() - Method in class org.strbio.app.JThreadText
where is data for this app stored, relative to the app itself?
appDataPath() - Method in class org.strbio.util.ui.GUIApp
where is data for this app stored, relative to the app itself?
append(DVector) - Method in class org.strbio.math.DVector
appends the contents of another DVector to this one.
append(DVector, DVector) - Static method in class org.strbio.math.DVector
Returns a new DVector containing the first argument appended to the second.
append(FVector) - Method in class org.strbio.math.FVector
appends the contents of another FVector to this one.
append(FVector, FVector) - Static method in class org.strbio.math.FVector
Returns a new FVector containing the first argument appended to the second.
applet - Variable in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
AppletJury - Class in org.strbio.mol.lib.pred2ary
This is a standard jury that is retrieved over the net using an applet's methods.
AppletJury(String, Pred2aryApplet, int, int) - Constructor for class org.strbio.mol.lib.pred2ary.AppletJury
Create a new jury, given the name of the binary input file.
AppletJury.LoadProgressIndicator - Interface in org.strbio.mol.lib.pred2ary
Indicator to update with verbose output, after every juror finishes.
arguments() - Method in class org.strbio.local.BlastClient
return arguments for the program.
arguments() - Method in class org.strbio.local.BlastP
return arguments for the program.
arguments() - Method in class org.strbio.local.PSIBlastP
return arguments for the program.
arguments() - Method in class org.strbio.local.PSIBlastP2
return the correct arguments, depending on whether this is the 1st or 2nd run.
arguments2() - Method in class org.strbio.local.PSIBlastP2
return arguments for the program, the second time it's run.
arrayToPolymers() - Method in class org.strbio.mol.Alignment
Sets up gaps in two Polymers to match this vector.
ASns(Alignment, int) - Method in class org.strbio.mol.Alignment
calculate alignment sensitivity, as in CASP2.
ASns(int) - Method in class org.strbio.mol.AlignmentSet
calculate alignment sensitivity, as in CASP2.
asns - Variable in class org.strbio.mol.AlignmentStats
alignment sensitivity, tolerance 0
ASns(int) - Method in class org.strbio.mol.ThreadSet
calculate alignment specificity, as in CASP2.
asns1 - Variable in class org.strbio.mol.AlignmentStats
alignment sensitivity, tolerance 1
asns1 - Variable in class org.strbio.mol.lib.AlignmentParametersEA
asns1 values for each match (there is no such thing for non-matches
asns4 - Variable in class org.strbio.mol.AlignmentStats
alignment sensitivity, tolerance 4
ASpc(Alignment, int) - Method in class org.strbio.mol.Alignment
calculate alignment specificity, as in CASP2.
ASpc(int) - Method in class org.strbio.mol.AlignmentSet
calculate alignment specificity, as in CASP2.
aspc - Variable in class org.strbio.mol.AlignmentStats
alignment specificity, tolerance 0
ASpc(int) - Method in class org.strbio.mol.ThreadSet
calculate alignment specificity, as in CASP2.
aspc1 - Variable in class org.strbio.mol.AlignmentStats
alignment specificity, tolerance 1
aspc4 - Variable in class org.strbio.mol.AlignmentStats
alignment specificity, tolerance 4
atod(String, int, int) - Static method in class org.strbio.util.StringUtil
Converts a string to a double, starting at 'offset', and continuing until just before character 'end'.
atod(String, int) - Static method in class org.strbio.util.StringUtil
 
atod(String) - Static method in class org.strbio.util.StringUtil
 
atof(String, int, int) - Static method in class org.strbio.util.StringUtil
Converts a string to a float, starting at 'offset', and continuing until just before character 'end'.
atof(String, int) - Static method in class org.strbio.util.StringUtil
 
atof(String) - Static method in class org.strbio.util.StringUtil
 
atoi(String, int, int) - Static method in class org.strbio.util.StringUtil
Converts a string to an int, starting at 'offset', and continuing until just before character 'end'.
atoi(String, int) - Static method in class org.strbio.util.StringUtil
 
atoi(String) - Static method in class org.strbio.util.StringUtil
 
atol(String, int, int) - Static method in class org.strbio.util.StringUtil
Converts a string to a long, starting at 'offset', and continuing until just before character 'end'.
atol(String, int) - Static method in class org.strbio.util.StringUtil
 
atol(String) - Static method in class org.strbio.util.StringUtil
 
Atom - Class in org.strbio.mol
Class to represent an atom.
Atom() - Constructor for class org.strbio.mol.Atom
Constructor makes ALI ' ' and coord and name null.
Atom(Atom) - Constructor for class org.strbio.mol.Atom
copies another atom, making its own copy of the data
AtomNode - Class in org.strbio.mol
Class to represent a node in a list of atoms.
AtomNode() - Constructor for class org.strbio.mol.AtomNode
constructor sets next, prev to null
AtomNode(Atom) - Constructor for class org.strbio.mol.AtomNode
when constructed from an Atom, it makes a new copy of the data in the Atom, but doesn't set next, prev.
atoms - Variable in class org.strbio.mol.Molecule
pointer to the atoms, if there are any (if not, this is null)
atoms - Variable in class org.strbio.mol.Monomer
pointer to the atoms, if there are any (if not, this is null).
atomSearch(String) - Method in class org.strbio.mol.Molecule
Search the atoms of this molecule for the first atom with a given name.
atomSearch(String) - Method in class org.strbio.mol.Monomer
Search the atoms of this monomer for the first atom with a given name.
autoSplit() - Method in class org.strbio.mol.Polymer
splits a polymer into several, if it has a break in the chain.
average() - Method in class org.strbio.math.Bin
Return the average of all values sampled.
average(int) - Method in class org.strbio.math.Bin2D
Average value sampled in a particular bin.
average() - Method in class org.strbio.math.DMatrix
Returns the average value in the matrix.
average() - Method in class org.strbio.math.DVector
Returns the average value in the array.
average() - Method in class org.strbio.math.FBin
Return the average of all values sampled.
average() - Method in class org.strbio.math.FMatrix
Returns the average value in the matrix.
average() - Method in class org.strbio.math.FVector
Returns the average value in the array.
averageRank() - Method in class org.strbio.mol.ThreadSet
average rank of structural matches
averageRankRW() - Method in class org.strbio.mol.ThreadSet
average rank with reciprocal weighting
averageRW() - Method in class org.strbio.math.DVector
Returns the average value in the array, weighting each value using reciprocal weighting.
averageRW() - Method in class org.strbio.math.FVector
Returns the average value in the array, weighting each value using reciprocal weighting.
averageScore(ScoreList) - Method in class org.strbio.mol.Alignment
Returns average score of all pairs of aligned monomers.
averageScore(ScoreList) - Method in class org.strbio.mol.AlignmentSet
Returns average score of all pairs of aligned monomers.
averageZ() - Method in class org.strbio.mol.ThreadSet
average z score of structural matches
AVG_RESIDUE - Static variable in class org.strbio.mol.lib.BackbonePotential
Reference state is average residue.
AVG_RESIDUE_SAME_TYPE - Static variable in class org.strbio.mol.lib.BackbonePotential
Reference state is average residue of the same type as the residue being tested (GPN only).
avgScoreMatch - Variable in class org.strbio.mol.lib.AlignmentParametersEA
scores for each match (gapped alignment score)
avgScoreNonMatch - Variable in class org.strbio.mol.lib.AlignmentParametersEA
scores for each non-match
avgScoreWithGaps(AlignmentParameters) - Method in class org.strbio.mol.Alignment
Returns average score for all pairs of aligned monomers.
avgScoreWithGaps - Variable in class org.strbio.mol.AlignmentStats
average score of the calculated alignment, including gaps, or NaN if not available.
avgScoreWithoutGaps(AlignmentParameters) - Method in class org.strbio.mol.Alignment
Returns average score for all pairs of aligned monomers.
avgScoreWithoutGaps - Variable in class org.strbio.mol.AlignmentStats
average score of the calculated alignment, not including gaps, or NaN if not available.
AxisScale - Interface in org.strbio.util.graph
A scale to go along an axis of a graph, i.e. x or y axes.

B

b_sets - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
back(double[]) - Method in class org.strbio.util.NeuralNet
propagate desired outputs backward through the net, computing interesting variables.
back - Variable in class org.strbio.util.ui.HelpFrame
button to go back 1 page in the history list.
BACKBONE_POTENTIAL - Static variable in class org.strbio.mol.PolymerProperties
ProfilePSI property: is there a local secondary structure prediction based potential?
BackbonePotential - Class in org.strbio.mol.lib
methods for handling the 2ary prediction dependent backbone pseudopotential.
BackbonePotential() - Constructor for class org.strbio.mol.lib.BackbonePotential
Create a new potential object with no data.
BackbonePotential(String) - Constructor for class org.strbio.mol.lib.BackbonePotential
Create and load in from a file.
banner() - Static method in class org.strbio.app.Model
 
BarLegend - Class in org.strbio.util
A legend for graphs, showing a bar indicating which ColorScale colors correspond to which numeric values.
BarLegend(double, double, ColorScale, String) - Constructor for class org.strbio.util.BarLegend
Initialize new legend.
BarPlot - Class in org.strbio.util.graph
A component that displays a bar graph.
BarPlot(DVector) - Constructor for class org.strbio.util.graph.BarPlot
initialize with a set of bars.
bars - Variable in class org.strbio.util.graph.BarPlot
This is a vector containint the y coordinates of the bars.
barWidth - Variable in class org.strbio.util.graph.BarPlot
What percent of the available width do the bars fill?
best_stop - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
bias - Variable in class org.strbio.mol.lib.FRParameters
Bias when computing composite scores
bias(int, int) - Method in class org.strbio.util.NeuralNet
return the bias of a given neuron.
Bin - Class in org.strbio.math
a class which does 1-D histogram-bins.
Bin(int, double, double) - Constructor for class org.strbio.math.Bin
to set up the histogram-bin, you need to know the number of bins you want, the minimum possible value, and the maximum possible value of the data.
Bin2D - Class in org.strbio.math
This saves samples pairs of data, and remembers some stats about the y values for each bin.
Bin2D(int, double, double) - Constructor for class org.strbio.math.Bin2D
to set up the histogram-bin, you need to know the number of bins you want, the minimum possible value, and the maximum possible value of the data.
Bin2D() - Constructor for class org.strbio.math.Bin2D
 
bin_stats - Variable in class org.strbio.math.Bin2D
 
binsize - Variable in class org.strbio.math.Bin
 
Blast - Interface in org.strbio.mol.lib
Interface for common Blast-related routines.
blast - Variable in class org.strbio.mol.lib.JMCThreadMethod
 
blast - Variable in class org.strbio.mol.lib.JMCThreadMethod2
 
blast(Printf, Blast) - Method in class org.strbio.mol.Profile
Run BLAST on this profile, using a specified server.
blast(Printf) - Method in class org.strbio.mol.Profile
Run BLAST on this profile, using NCBI's blast server.
blast(Printf, Blast) - Method in class org.strbio.mol.ProfilePSI
Run BLAST on this profile, using a specified server.
blast(Printf, Blast) - Method in class org.strbio.mol.ProfileSet
Run BLAST on all proteins in the set, using a specified blast server.
blast(Printf) - Method in class org.strbio.mol.ProfileSet
Run BLAST on all proteins in the set, using NCBI's blast server.
BlastAdapter - Class in org.strbio.mol.lib
Adapter class to implement the routines in Blast.
BlastAdapter() - Constructor for class org.strbio.mol.lib.BlastAdapter
 
blastAll(Printf) - Method in class org.strbio.local.BlastP
Return a profile containing responses to the blast query.
blastAll(Printf) - Method in class org.strbio.local.PSIBlastP
Blast, and get the checkpoint info.
blastAll(Printf) - Method in class org.strbio.local.PSIBlastP2
Blast, and get the checkpoint info.
blastAll(Printf) - Method in interface org.strbio.mol.lib.Blast
Return a profile containing responses to the blast query.
blastAll(Printf) - Method in class org.strbio.net.BlastWeb
Returns a profile with all responses to the query.
blastBits - Variable in class org.strbio.mol.Profile
Blast score for each sequence, if known... this should measure how close the sequence is to the key sequence.
BlastClient - Class in org.strbio.local
Runs a local copy of blastclient.
BlastClient() - Constructor for class org.strbio.local.BlastClient
Initialize with no information; you still have to call setQuery before starting Blast.
BlastClient(String) - Constructor for class org.strbio.local.BlastClient
Initialize with a given query sequence.
BlastClient(Protein) - Constructor for class org.strbio.local.BlastClient
Initialize with a given protein.
BlastConstants - Class in org.strbio.mol.lib
Some constants used in BLAST 2.0.6.
BlastConstants() - Constructor for class org.strbio.mol.lib.BlastConstants
 
blastGetInitial(Printf) - Method in class org.strbio.net.BlastWeb
Query the blast server for the queue data.
blastGetResult(Printf) - Method in class org.strbio.net.BlastWeb
Query the blast server for the queue data.
blastInitial(Printf) - Method in class org.strbio.net.PSIBlastWeb
Return a string containg initial results from the web server.
blastLog10E - Variable in class org.strbio.mol.Profile
E values for each sequence, if known... this should measure how close the sequence is to the key sequence, and how likely the match was in the database searched.
BlastNCBI - Class in org.strbio.net
Does a BlastP search in the NR database at NCBI, using the main web gateway.
BlastNCBI() - Constructor for class org.strbio.net.BlastNCBI
Initialize with no information; you still have to call setQuery before starting Blast.
BlastNCBI(String) - Constructor for class org.strbio.net.BlastNCBI
Initialize with a given query sequence.
BlastNCBI(Protein) - Constructor for class org.strbio.net.BlastNCBI
Initialize with a given protein.
BlastNCBI2 - Class in org.strbio.net
Does a BlastP search in the NR database at NCBI, using the "stable" web gateway.
BlastNCBI2() - Constructor for class org.strbio.net.BlastNCBI2
Initialize with no information; you still have to call setQuery before starting Blast.
BlastNCBI2(String) - Constructor for class org.strbio.net.BlastNCBI2
Initialize with a given query sequence.
BlastNCBI2(Protein) - Constructor for class org.strbio.net.BlastNCBI2
Initialize with a given protein.
BlastP - Class in org.strbio.local
Runs a local copy of blastp.
BlastP() - Constructor for class org.strbio.local.BlastP
Initialize with no information; you still have to call setQuery before starting Blast.
BlastP(String) - Constructor for class org.strbio.local.BlastP
Initialize with a given query sequence.
BlastP(Protein) - Constructor for class org.strbio.local.BlastP
Initialize with a given protein.
BlastPAdapter - Class in org.strbio.local
This is an adapter class for Blast which should extend both Program and BlastAdapter.
BlastPAdapter() - Constructor for class org.strbio.local.BlastPAdapter
 
blastPBlastAll(Printf) - Method in class org.strbio.local.BlastP
kludge to allow super.super() reference to blastAll method.
blastProfile(Printf) - Method in class org.strbio.local.BlastPAdapter
Return a profile containing responses to the blast query.
blastProfile(Printf) - Method in interface org.strbio.mol.lib.Blast
Return a profile containing responses to the blast query.
blastProfile(Printf) - Method in class org.strbio.mol.lib.BlastAdapter
Return a profile containing responses to the blast query.
BlastProtein - Class in org.strbio.app
Run Blast on a protein (or set).
BlastProtein() - Constructor for class org.strbio.app.BlastProtein
 
blastProteinSet(Printf) - Method in class org.strbio.local.BlastPAdapter
Returns a set of proteins in response to a blast query.
blastProteinSet(Printf) - Method in interface org.strbio.mol.lib.Blast
Returns a set of proteins in response to a blast query.
blastProteinSet(Printf) - Method in class org.strbio.mol.lib.BlastAdapter
Returns a set of proteins in response to a blast query.
blastRaw(Printf) - Method in class org.strbio.net.BlastNCBI2
Return a stream containing the raw HTML from the NCBI server.
blastRaw(Printf) - Method in class org.strbio.net.BlastWeb
Return a string containing the raw HTML from the server.
blastRaw(Printf) - Method in class org.strbio.net.PSIBlastWeb
Return a string containing the raw HTML from the server.
blastStepN(int, Printf) - Method in class org.strbio.net.PSIBlastWeb
Return a string containing the html from step N.
BlastWeb - Class in org.strbio.net
Does a BlastP search in the NR database at over the web.
BlastWeb() - Constructor for class org.strbio.net.BlastWeb
Initialize with no information; you still have to call setQuery before starting Blast.
BlastWeb(String) - Constructor for class org.strbio.net.BlastWeb
Initialize with a given query sequence.
BlastWeb(Protein) - Constructor for class org.strbio.net.BlastWeb
Initialize with a given protein.
blosum62() - Static method in class org.strbio.mol.lib.BlastConstants
The Blosum62 matrix, without the BZX* columns.
blueScale - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
 
bondAngle(Atom, Atom, Atom) - Static method in class org.strbio.mol.Atom
returns the bond angle in radians between three atoms, or Double.NaN if the coordinates of any are unknown.
BOX_ALL - Variable in class org.strbio.util.graph.Graph2D
Draw box completely around graph region (default).
BOX_BOTTOM - Variable in class org.strbio.util.graph.Graph2D
Draw line on bottom side of graph region.
BOX_LEFT - Variable in class org.strbio.util.graph.Graph2D
Draw line on left side of graph region.
BOX_NONE - Variable in class org.strbio.util.graph.Graph2D
Don't draw a box around the graph region.
BOX_RIGHT - Variable in class org.strbio.util.graph.Graph2D
Draw line on right side of graph region.
BOX_TOP - Variable in class org.strbio.util.graph.Graph2D
Draw line on top side of graph region.
boxHeight - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
 
boxOffset - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
 

C

c_hls - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
c_jackknife - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
c_lowerror - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
c_maxerror - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
c_sets - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
c_steps - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
c_test - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
calcMatchRank() - Method in class org.strbio.mol.ThreadSet
Calculate vector of ranks, showing one rank for each match.
calcMatchZ() - Method in class org.strbio.mol.ThreadSet
Calculate vector of z scores, showing one z score for each match.
calcMaxNameLength() - Method in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
Figure out the maximum name length in the set.
calcMaxX() - Method in class org.strbio.util.graph.Graph2D
Returns the maximum x value, from all the graphs.
calcMaxY() - Method in class org.strbio.util.graph.Graph2D
Returns the maximum y value, from all the graphs.
calcMinX() - Method in class org.strbio.util.graph.Graph2D
Returns the minimum x value, from all the graphs.
calcMinY() - Method in class org.strbio.util.graph.Graph2D
Returns the minimum y value, from all the graphs.
calcPctAligned - Variable in class org.strbio.mol.AlignmentStats
pct aligned, calculated.
calcPctAlignedLong - Variable in class org.strbio.mol.AlignmentStats
pct aligned, calculated, vs longest seq
calcPctID - Variable in class org.strbio.mol.AlignmentStats
pct ID, calculated
calcRMS - Variable in class org.strbio.mol.AlignmentStats
RMS, calculated alignment.
calcTm() - Method in class org.strbio.mol.Primer
calculate tm using Melting
calcTm() - Method in class org.strbio.mol.PrimerSet
calculate tm using Melting
calculate(Alignment, Alignment, MinareaResults) - Method in class org.strbio.mol.AlignmentStats
Calculate all results (that can be), given correct and calculated alignments, and minarea results (for RMS only; can be null to ignore).
calculateCorrect(Alignment) - Method in class org.strbio.mol.AlignmentStats
Only calculate the stats that depend on correct alignment
calculated - Variable in class org.strbio.mol.AlignmentSet
A vector containing the last alignment calculated with Align.
calculatedFoldToSeq() - Method in class org.strbio.mol.AlignmentSet
Return a vector of which sequence is related to which fold monomer, in the calculated alignment.
calculatedRMS() - Method in class org.strbio.mol.AlignmentSet
return calculated RMS; assume molecules already superimposed.
calculatedSeqToFold() - Method in class org.strbio.mol.AlignmentSet
return vector of calculated alignment; which seq monomer is related to which fold monomer.
calculateEstimated(Alignment) - Method in class org.strbio.mol.AlignmentStats
Only calculate the estimated stats.
calculateFirstPosition(float[][], int[][], int[][], Polymer, Polymer) - Method in class org.strbio.mol.lib.GapModelAdapter
 
calculateScores(Alignment, ScoreList) - Method in class org.strbio.mol.AlignmentStats
Calculate scores, given a score list.
calcWrapPos(int) - Method in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
returns the number of chars in the sequence that will fit on a page with a given width.
cAlpha - Variable in class org.strbio.mol.Residue
Pre-calculated alpha angle at this residue.
canEstimateAA() - Method in class org.strbio.mol.lib.AlignmentParametersEA
will this return valid results for estAsns1, etc?
canEstimateFR() - Method in class org.strbio.mol.lib.AlignmentParametersEA
will this return valid results for estFR*?
canEstimateFR() - Method in class org.strbio.mol.lib.FRParameters
will this return valid results for estFR*?
CATH - Class in org.strbio.net
Class to access CATH over the web.
CATH() - Constructor for class org.strbio.net.CATH
 
CATHInfo - Class in org.strbio.util.db
This is a class containing info that is found in CATH.
CATHInfo() - Constructor for class org.strbio.util.db.CATHInfo
Default initialization has -1 for start/end res, and null for everything else.
centerFrame(Frame) - Static method in class org.strbio.util.JMC
Center a frame on the screen.
centerOfMass() - Method in class org.strbio.mol.Monomer
Return a new DVector(3) containing the center of mass for the monomer.
centerOfMass(DVector) - Method in class org.strbio.mol.Monomer
Finds the center of mass for the monomer and puts in in the DVector(3) that you pass it.
centerOfMass() - Method in class org.strbio.mol.Polymer
Return a new DVector(3) containing the center of mass for the polymer.
centerOfMass(DVector) - Method in class org.strbio.mol.Polymer
Finds the center of mass for the monomer and puts in in the DVector(3) that you pass it.
CGOptimizer - Interface in org.strbio.util
This is a pretty generic interface for CJ optimizing routines.
CGOptimizer.Optimizable - Interface in org.strbio.util
This is the interface you have to implement if you want to optimize using NRMin.
chainID - Variable in class org.strbio.mol.Polymer
Chain ID, or space if none.
checkpointName - Variable in class org.strbio.local.PSIBlastP
 
choose(int) - Method in class org.strbio.mol.Profile
Make a profile based on this one, featuring one of the sub- sequences.
chooseSequence() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
chooseSequenceB - Variable in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
CirclePoint - Class in org.strbio.util.graph
A point type that paints circles.
CirclePoint(int) - Constructor for class org.strbio.util.graph.CirclePoint
need radius of the point to draw
cl - Variable in class org.strbio.util.db.Data.InfoEnumeration
 
CLASS_2ARY - Static variable in class org.strbio.mol.lib.pred2ary.TPSet
turn on the 3 inputs with predicted secondary structure percentages and predicted number of alternations between helix and sheet.
CLASS_AA - Static variable in class org.strbio.mol.lib.pred2ary.TPSet
set these to determine exactly what sort of class network to use note that the "sequence length" input is always on.
CLASS_STRONG - Static variable in class org.strbio.mol.lib.pred2ary.TPSet
turn on the 2 inputs with "strong" secondary structure predictions.
classifyFasta(String, String, int, int) - Static method in class org.strbio.util.HTML
This function adds markup around a given section of a FASTA sequence stored as a String.
classifyMSF(String, String, int, int) - Static method in class org.strbio.util.HTML
This function adds markup around a given section of a Profile stored in a MSF-formatted String.
classifyMSF(String, String, int, int, int) - Static method in class org.strbio.util.HTML
This function is just like the classifyMSF function that marks up an entire profile, but this one can mark up only a single sequence in a profile if you prefer.
className(int) - Static method in class org.strbio.mol.lib.pred2ary.PredClassProfile
Return the English name for class of type cl.
clean(String) - Method in class org.strbio.local.Malfe
malfe doesn't leave stuff lying around.
clean(String) - Method in class org.strbio.local.Minarea
Clean files left around by minarea.
clean(String) - Method in class org.strbio.local.Program
Clean up files left around after running the program with a given argument string.
clear() - Method in class org.strbio.math.DVectorSet
Delete all info on this set, but not the points themselves.
clear() - Method in class org.strbio.math.StatsMatrix
Clear all statistics.
clear() - Method in class org.strbio.mol.lib.BackbonePotential
delete all info
clear() - Method in class org.strbio.mol.lib.pred2ary.PredictionSet
 
clear() - Method in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea.ClickedArea
 
clear() - Method in class org.strbio.mol.lib.pred2ary.TPSet
Clear out all information in the set.
clear() - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
 
clear() - Method in class org.strbio.mol.Molecule
Forget everything you know about this molecule.
clear() - Method in class org.strbio.mol.Polymer
Forget everything you know about this Polymer.
clear() - Method in class org.strbio.mol.PolymerSet
Delete all info on this set, but not the polymers themselves.
clear() - Method in class org.strbio.util.db.Data
clear all info.
clearAlignments() - Method in class org.strbio.mol.lib.ThreadResults
clear all known alignments.
clearClassPred() - Method in class org.strbio.mol.lib.pred2ary.PCPSet
 
clearClassPred() - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
clear class pred to zero
clearEstAAStats() - Method in class org.strbio.mol.lib.AlignmentParametersEA
remove stats for estimating alignment accuracy
clearEstFRStats() - Method in class org.strbio.mol.lib.AlignmentParametersEA
remove stats for estimating fold recognition accuracy.
clearEstFRStats() - Method in class org.strbio.mol.lib.FRParameters
remove stats for estimating fold recognition accuracy.
clearInfo(Class) - Method in class org.strbio.util.db.Data
Removes all info of a certain type.
clearLog() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
clearPolymers() - Method in class org.strbio.mol.PolymerSet
Delete info on which polymers are in this set, but not the polymers themselves.
clearPred() - Method in class org.strbio.mol.lib.pred2ary.PCPSet
clear H and E to zero
clearPred() - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
clear H and E to zero
clearProperties() - Method in class org.strbio.mol.Polymer
clears all the properties.
clearProperties() - Method in class org.strbio.mol.PolymerSet
clears all the properties.
clearProperty(int) - Method in class org.strbio.mol.Polymer
clears (un-sets) one property.
clearProperty(int) - Method in class org.strbio.mol.PolymerSet
clears (un-sets) one property.
clearSame() - Method in class org.strbio.mol.ThreadSet
Forget that seq-fold pairs have the same name.
clearScores() - Method in class org.strbio.mol.ThreadSet
forget about any alignments done so far.
clearSeqs() - Method in class org.strbio.mol.Profile
Tell the Profile to forget any sequence information it knows.
clearSeqs() - Method in class org.strbio.mol.ProfRes
Tell the ProfRes to forget any sequence information it knows.
clearSM() - Method in class org.strbio.mol.lib.pred2ary.TPSet
 
clearStrMatches() - Method in class org.strbio.mol.ThreadSet
Deny all knowledge of structural matches.
ClickablePointPlot - Class in org.strbio.util.graph
A component that acts like it's displaying points, but only circles the one that's been clicked on.
ClickablePointPlot(DVectorSet, ClickablePointPlot.ClickListener) - Constructor for class org.strbio.util.graph.ClickablePointPlot
initialize with a set of points.
ClickablePointPlot.ClickListener - Interface in org.strbio.util.graph
This is an interface for things that are interested in knowing when the graph is clicked.
clicked(double, double) - Method in class org.strbio.util.graph.ClickablePointPlot
this method gets called by Graph2D when the graph is clicked on.
clicked(DVector) - Method in interface org.strbio.util.graph.ClickablePointPlot.ClickListener
This function gets called with the DVector that was clicked on, or null if nothing was clicked.
clicked(double, double) - Method in interface org.strbio.util.graph.Graph2D.ClickListener
This function gets called with the coordinates of the point that was clicked, in the frame of reference currently being displayed.
clickedArea - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
Keep track of interesting rectangles (where sequences are drawn)
clickedOn(int, int) - Method in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea.ClickedArea
this looks up which area corresponds to given x and y coordinates, or returns null if none do.
clickedProtein - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
 
clickedSequence - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
 
close() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.AboutDialog
 
close() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.LoadWindow
 
close() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.ProgressDialog
 
close() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.SaveWindow
 
close() - Method in class org.strbio.util.ui.ProfileGUIApp.LoadProgressDialog
 
ClustalW - Class in org.strbio.local
Class to run clustalw Version 1.0, 8/21/01 - original version
ClustalW() - Constructor for class org.strbio.local.ClustalW
 
cnet1 - Variable in class org.strbio.mol.lib.pred2ary.TrainingSet
 
cnet4 - Variable in class org.strbio.mol.lib.pred2ary.TrainingSet
 
code - Variable in class org.strbio.util.db.PDBInfo
PDB code for the file; i.e. 1abc.
colorOf(double) - Method in class org.strbio.util.ColorScale.BlackScale
 
colorOf(double) - Method in class org.strbio.util.ColorScale.BlendScale
 
colorOf(double) - Method in class org.strbio.util.ColorScale.BlueScale
 
colorOf(double) - Method in interface org.strbio.util.ColorScale
All color scales return a color corresponding to a double between 0.0 and 1.0; if the double is out of bounds, the color corresponding to the nearest endpoint of the scale should be returned.
colorOf(double) - Method in class org.strbio.util.ColorScale.GreenScale
 
colorOf(double) - Method in class org.strbio.util.ColorScale.RainbowScale
 
colorOf(double) - Method in class org.strbio.util.ColorScale.RainbowScale2
 
colorOf(double) - Method in class org.strbio.util.ColorScale.RedScale
 
colorOf(double) - Method in class org.strbio.util.ColorScale.WhiteScale
 
ColorScale - Interface in org.strbio.util
Color scales for use in graphical programs.
ColorScale.BlackScale - Class in org.strbio.util
A scale going from white to black.
ColorScale.BlackScale() - Constructor for class org.strbio.util.ColorScale.BlackScale
 
ColorScale.BlendScale - Class in org.strbio.util
A scale blending one color into another.
ColorScale.BlendScale(Color, Color) - Constructor for class org.strbio.util.ColorScale.BlendScale
 
ColorScale.BlueScale - Class in org.strbio.util
A scale going from black to blue.
ColorScale.BlueScale() - Constructor for class org.strbio.util.ColorScale.BlueScale
 
ColorScale.GreenScale - Class in org.strbio.util
A scale going from black to green.
ColorScale.GreenScale() - Constructor for class org.strbio.util.ColorScale.GreenScale
 
ColorScale.RainbowScale - Class in org.strbio.util
A ROYGBIV scale going from R(low) to V(high)
ColorScale.RainbowScale() - Constructor for class org.strbio.util.ColorScale.RainbowScale
 
ColorScale.RainbowScale2 - Class in org.strbio.util
A ROYGBIV scale going from V(low) to R(high)
ColorScale.RainbowScale2() - Constructor for class org.strbio.util.ColorScale.RainbowScale2
 
ColorScale.RedScale - Class in org.strbio.util
A scale going from black to red.
ColorScale.RedScale() - Constructor for class org.strbio.util.ColorScale.RedScale
 
ColorScale.WhiteScale - Class in org.strbio.util
A scale going from black to white.
ColorScale.WhiteScale() - Constructor for class org.strbio.util.ColorScale.WhiteScale
 
ColorScaleLegend - Class in org.strbio.util.graph
A legend for graphs, showing a bar indicating which ColorScale colors correspond to which numeric values.
ColorScaleLegend(double, double, ColorScale, Font, FontMetrics, String, String) - Constructor for class org.strbio.util.graph.ColorScaleLegend
Initialize new legend.
cols() - Method in class org.strbio.math.DHalfMatrix
Returns the number of columns (of the theoretical whole matrix, not just the upper triangular part.
cols() - Method in class org.strbio.math.DMatrix
returns the number of columns in the encapsulated array.
cols() - Method in class org.strbio.math.FHalfMatrix
Returns the number of columns (of the theoretical whole matrix, not just the upper triangular part.
cols() - Method in class org.strbio.math.FMatrix
returns the number of columns in the encapsulated array.
cols() - Method in class org.strbio.math.IMatrix
returns the number of columns in the encapsulated array.
combine() - Method in class org.strbio.mol.lib.pred2ary.PCPSet
Combine all proteins in this set into one Profile.
combine() - Method in class org.strbio.mol.ProfileSet
Combine all proteins in this set into one Profile.
compare(Alignment, int) - Method in class org.strbio.mol.Alignment
compares two alignments.
CompareFolds - Class in org.strbio.app
Computes comparison scores for sets of sequences and folds.
CompareFolds() - Constructor for class org.strbio.app.CompareFolds
 
CompileJuryScript - Class in org.strbio.app
Compile a jury script for Pred2aryJury.
CompileJuryScript() - Constructor for class org.strbio.app.CompileJuryScript
 
complement(char) - Static method in class org.strbio.mol.Nucleotide
complement of a dna base
complement(String) - Static method in class org.strbio.mol.Nucleotide
complement of a dna chain
CompliesWithLicense - Static variable in class org.strbio.util.Hooke
This is the original license on the software.
compound - Variable in class org.strbio.util.db.PDBInfo
Information from the PDB's COMPND records, one string per line (edges stripped off).
compute2arySM(int, int) - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
 
compute2arySM(int, int) - Method in class org.strbio.mol.lib.pred2ary.TPSet
compute SM for a set.
computeClassSM() - Method in class org.strbio.mol.lib.pred2ary.TPSet
compute CSM for a set
containsDigit(String) - Static method in class org.strbio.util.StringUtil
does the string contain a digit?
containsLetter(String) - Static method in class org.strbio.util.StringUtil
does the string contain a letter?
contentLength() - Method in class org.strbio.net.BlastNCBI2
Content length depends on the number of characters in the sequence, and what database you're searching.
ConvertProtein - Class in org.strbio.app
Convert proteins between file formats.
ConvertProtein() - Constructor for class org.strbio.app.ConvertProtein
 
coord - Variable in class org.strbio.mol.Atom
Atomic coordinates.
copy() - Method in class org.strbio.mol.Polymer
Return a copy of yourself.
copy() - Method in class org.strbio.mol.Profile
Return a copy of yourself.
copy() - Method in class org.strbio.mol.ProfilePSI
Return a copy of yourself.
copy() - Method in class org.strbio.mol.Protein
Return a copy of yourself.
copyAtoms(Molecule) - Method in class org.strbio.mol.Molecule
copy the atoms from another molecule.
copyAtoms(Monomer) - Method in class org.strbio.mol.Monomer
copy the atoms from another monomer.
copyAtoms(Polymer) - Method in class org.strbio.mol.Polymer
copy the atoms from another polymer.
copyCorrectFrom(ThreadSet) - Method in class org.strbio.mol.ThreadSet
Copy correct alignments from another threadSet to this one's calculated alignments.
copyDataFrom(Monomer) - Method in class org.strbio.mol.lib.pred2ary.PCPRes
Copy another PCPRes.
copyDataFrom(Monomer) - Method in class org.strbio.mol.Monomer
copy another monomer, including the atoms.
copyDataFrom(Monomer) - Method in class org.strbio.mol.ProfRes
Copy another ProfRes.
copyDataFrom(Monomer) - Method in class org.strbio.mol.ProfResPSI
Copy another ProfResPSI.
copyDataFrom(Monomer) - Method in class org.strbio.mol.Residue
copy another residue, including the atoms.
copyLvl1HE() - Method in class org.strbio.mol.lib.pred2ary.TPSet
copy lvl1 predictions for all proteins in set
copyNode() - Method in class org.strbio.mol.AtomNode
Return a node with a copy of the same atom.
copyNode() - Method in class org.strbio.mol.lib.pred2ary.PCPRes
copy contents of a residue
copyNode() - Method in class org.strbio.mol.Monomer
copy contents of a monomer.
copyNode() - Method in class org.strbio.mol.Nucleotide
copy contents of a residue
copyNode() - Method in class org.strbio.mol.ProfRes
copy contents of a residue
copyNode() - Method in class org.strbio.mol.ProfResPSI
copy contents of a ProfResPSI.
copyNode() - Method in class org.strbio.mol.Residue
copy contents of a residue
copyNode() - Method in interface org.strbio.util.DLinkedList.Node
This should return a copy of a node, without next and prev set.
copyPredSSFrom(Protein) - Method in class org.strbio.mol.Protein
Copy predicted secondary structure info from another protein.
copySeqsDirectlyFrom(Profile) - Method in class org.strbio.mol.Profile
Copy additional sequences from another profile of the same length, eliminating current sequences.
copySeqsFrom(Profile) - Method in class org.strbio.mol.Profile
copy sequence info from another profile; aligns and copies, replacing current sequence info.
copyUnreducedStats(int) - Method in class org.strbio.mol.lib.pred2ary.TPSet
copy unreduced predictions for all proteins in set
correct - Variable in class org.strbio.mol.AlignmentSet
A vector of correct sequence-fold monomer pairs.
correctAlignFold(int[]) - Method in class org.strbio.mol.Polymer
Deprecated. use alignToInverseArray.
correctAlignSeq(int[]) - Method in class org.strbio.mol.Polymer
Deprecated. Use alignToArray instead.
correctFoldToSeq() - Method in class org.strbio.mol.AlignmentSet
Return a vector of which sequence is related to which fold monomer.
correctlyAlign() - Method in class org.strbio.mol.AlignmentSet
re-align both sequence and fold to conform to the correct alignment.
CorrectMatrix - Class in org.strbio.math
If your prediction is yes/no, or if you are only interested in stats on correctness and incorrectness, you can create a matrix which is 2xN, where N is the number of possible categories in reality, and data[0][i] indicates the number of wrong predictions of things belonging to catogory i (you predicted them as something other than i), while data[1][i] indicates the number of correct predictions of things belonging to category i.
CorrectMatrix() - Constructor for class org.strbio.math.CorrectMatrix
 
CorrectMatrix(int) - Constructor for class org.strbio.math.CorrectMatrix
 
CorrectMatrix(IMatrix) - Constructor for class org.strbio.math.CorrectMatrix
 
CorrectMatrix(int[][]) - Constructor for class org.strbio.math.CorrectMatrix
 
correctRMS() - Method in class org.strbio.mol.AlignmentSet
return correct RMS; assume molecules already superimposed.
correctSeqToFold() - Method in class org.strbio.mol.AlignmentSet
Return a vector of which fold monomer is related to which seq.
countJurors() - Method in class org.strbio.mol.lib.pred2ary.Jury
returns the number of jurors in the file networkSet.
countNodes() - Method in class org.strbio.util.DLinkedList
count how many nodes are really in the list, in case the user messed with it somehow.
covar() - Method in class org.strbio.math.Bin2D
Returns the covariance of values sampled.
covar(DMatrix) - Method in class org.strbio.math.DMatrix
Returns the covariance of values in this matrix with those in another matrix.
covar(DVector) - Method in class org.strbio.math.DVector
Returns the covariance of values in this array with those in another array.
covar(FMatrix) - Method in class org.strbio.math.FMatrix
Returns the covariance of values in this matrix with those in another matrix.
covar(FVector) - Method in class org.strbio.math.FVector
Returns the covariance of values in this array with those in another array.
cPhi - Variable in class org.strbio.mol.Residue
Pre-calculated phi angle at this residue.
cPsi - Variable in class org.strbio.mol.Residue
Pre-calculated psi angle at this residue.
create(boolean, int, String) - Method in class org.strbio.mol.lib.BackbonePotential
Create histograms by binning angles from a file.
createLegend() - Method in class org.strbio.util.graph.PointColorPlot
creates a new legend
createLegend() - Method in class org.strbio.util.graph.PointPlot
creates a new legend
creationAP - Variable in class org.strbio.mol.lib.FRParametersNode
Alignment parameters used to create the alignment.
cross(DVector) - Method in class org.strbio.math.DVector
Returns the cross product of multiplying this with another vector.
cross(DVector, DVector) - Static method in class org.strbio.math.DVector
Returns the cross product of multiplying two vectors.
cross(FVector) - Method in class org.strbio.math.FVector
Returns the cross product of multiplying this with another vector.
cross(FVector, FVector) - Static method in class org.strbio.math.FVector
Returns the cross product of multiplying two vectors.
cross(IVector) - Method in class org.strbio.math.IVector
Returns the cross product of multiplying this with another vector.
cross(IVector, IVector) - Static method in class org.strbio.math.IVector
Returns the cross product of multiplying two vectors.
CSM - Variable in class org.strbio.mol.lib.pred2ary.TPSet
 
CSM1 - Variable in class org.strbio.mol.lib.pred2ary.TPSet
 
cTau - Variable in class org.strbio.mol.Residue
Pre-calculated tau angle at this residue.
currentJury - Variable in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
customIs3Res(String) - Method in class org.strbio.raf.RAFResidue
Is your string a valid 3-letter code?
customThree2One(String) - Method in class org.strbio.raf.RAFResidue
Convert your 3-letter code into 1-letter code.
cutoff_2ary - Variable in class org.strbio.mol.lib.pred2ary.TPSet
 
cutoff_class - Variable in class org.strbio.mol.lib.pred2ary.TPSet
 
cutoff_lvl2 - Variable in class org.strbio.mol.lib.pred2ary.TPSet
 

D

data - Variable in class org.strbio.math.DMatrix
data contains the actual matrix itself; it's public so that it can be manipulated directly (for speed, such as that is in java) and so that you can do something like 'dm.data[0][0] = tmp' as well as 'tmp = dm.data[0][0]' without needing 2 different functions.
data - Variable in class org.strbio.math.DVector
data contains the actual array itself; it's public so that it can be manipulated directly (for speed, such as that is in java) and so that you can do something like 'dv.data[0] = tmp' as well as 'tmp = dv.data[0]' without needing 2 different functions.
data - Variable in class org.strbio.math.FMatrix
data contains the actual matrix itself; it's public so that it can be manipulated directly (for speed, such as that is in java) and so that you can do something like 'dm.data[0][0] = tmp' as well as 'tmp = dm.data[0][0]' without needing 2 different functions.
data - Variable in class org.strbio.math.FVector
data contains the actual array itself; it's public so that it can be manipulated directly (for speed, such as that is in java) and so that you can do something like 'dv.data[0] = tmp' as well as 'tmp = dv.data[0]' without needing 2 different functions.
data - Variable in class org.strbio.math.IMatrix
data contains the actual matrix itself; it's public so that it can be manipulated directly (for speed, such as that is in java) and so that you can do something like 'im.data[0][0] = tmp' as well as 'tmp = im.data[0][0]' without needing 2 different functions.
data - Variable in class org.strbio.math.IVector
data contains the actual array itself; it's public so that it can be manipulated directly (for speed, such as that is in java) and so that you can do something like 'iv.data[0] = tmp' as well as 'tmp = iv.data[0]' without needing 2 different functions.
data - Variable in class org.strbio.mol.Molecule
data that is known about this molecule.
Data - Class in org.strbio.util.db
This is a very simple database, containing a collection of Info elements.
Data() - Constructor for class org.strbio.util.db.Data
 
Data.InfoEnumeration - Class in org.strbio.util.db
An enumeration that strips out all info of a certain type.
Data.InfoEnumeration(Data, Class) - Constructor for class org.strbio.util.db.Data.InfoEnumeration
 
databases - Variable in class org.strbio.local.BlastP
databases to search in.
databases - Variable in class org.strbio.local.TBlastN
databases to search in.
databases2 - Variable in class org.strbio.local.PSIBlastP2
databases to search in.
DayhoffFreq() - Static method in class org.strbio.mol.lib.DayhoffMatrices
Dayhoff frequencies for each amino acid.
DayhoffMatrices - Class in org.strbio.mol.lib
Dayhoff matrices (various) Dayhoff, MO 1978 Atlas of Protein Sequence and Structure volume 5, #3 p. 353 - 358.
DayhoffMatrices() - Constructor for class org.strbio.mol.lib.DayhoffMatrices
 
DayhoffMdm78() - Static method in class org.strbio.mol.lib.DayhoffMatrices
Dayhoff mutation data matrix 78.
DayhoffPam250() - Static method in class org.strbio.mol.lib.DayhoffMatrices
Dayhoff, MO 1978 Atlas of Protein Sequence and Structure volume 5, #3 p. 353 - 358.
DayhoffRelatednessOdds() - Static method in class org.strbio.mol.lib.DayhoffMatrices
Dayhoff relatedness odds matrix.
dealWithEndPenalties(float[][], Polymer, Polymer) - Method in class org.strbio.mol.lib.GapModelAdapter
This fills in the matrix with impossible penalties, if we want to disallow gaps at the ends.
DEFAULT_PDB_PATH - Static variable in class org.strbio.local.PDB
The default PDB path for all users of this library.
defaultEAFileAA() - Method in class org.strbio.mol.lib.AlignmentParametersEA
get the default file name (in the classpath) for alignment accuracy parameters.
defaultEAFileAA() - Method in class org.strbio.mol.lib.OptimalAAParameters
Accuracy was parameterized on the TOM data set.
defaultEAFileFR() - Method in class org.strbio.mol.lib.AlignmentParametersEA
get the default file name (in the classpath) for fold recognition parameters.
defaultEAFileFR() - Method in class org.strbio.mol.lib.FRParameters
get the default file name (in the classpath) for fold recognition parameters.
defaultEAFileFR() - Method in class org.strbio.mol.lib.OptimalAAParametersFR
Accuracy was parameterized on the TOM data set.
defaultEAFileFR() - Method in class org.strbio.mol.lib.OptimalFRParameters
Accuracy was parameterized on the TOM data set.
defaultFile - Variable in class org.strbio.mol.lib.ScorePhiPsi
the default potential was parameterized using the 681 proteins from Chandonia & Karplus, 1999, with separate GPN residues.
defaultFile - Static variable in class org.strbio.mol.lib.ScoreSippl90
the default potential was parameterized using the 681 proteins from Chandonia & Karplus, 1999.
defaultFile - Variable in class org.strbio.mol.lib.ScoreUFSippl90
the default potential was parameterized using the 681 proteins from Chandonia & Karplus, 1999.
defaultTable - Variable in class org.strbio.mol.lib.ScoreDefay
the default table comes from Tom Defay's "easy table"
defaultTable - Variable in class org.strbio.mol.lib.ScoreJDB10
the default table comes from Tom Defay's "easy table"
delete2aryNet() - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
 
deleteBackbonePotential(boolean) - Method in class org.strbio.mol.ProfilePSI
delete the BackbonePotential scoring matrices for all residues.
deleteBackbonePotential(boolean) - Method in class org.strbio.mol.ProfResPSI
delete the BackbonePotential scoring matrices
deleteClassNet() - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
 
deleteLvl2Net() - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
 
deleteMonDistance() - Method in class org.strbio.mol.Polymer
get rid of the inter-monomer distance matrix and free up the memory it was using.
deletePSIBlastMatrix() - Method in class org.strbio.mol.ProfilePSI
Delete PSI-blast matrices at each position.
deleteSM() - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
Delete all stats matrices.
deleteSM() - Method in class org.strbio.mol.lib.pred2ary.TPSet
 
deleteTranslations() - Method in class org.strbio.raf.RAFResidue
delete custom translations
deltaE(char, char, int, double) - Method in class org.strbio.mol.lib.Sippl90
Returns the deltaE(a,b,k,d).
DensityPlot - Class in org.strbio.util
A component that displays a density plot (an overhead view of a matrix, with squares colored by value).
DensityPlot(DMatrix, ColorScale) - Constructor for class org.strbio.util.DensityPlot
A density plot needs a matrix and a color scale to draw it with.
describe(Printf) - Method in interface org.strbio.io.Description
This should print info about the object to an output file.
describe(Printf) - Method in class org.strbio.mol.lib.AlignmentParameters
Describe prints parameters of the components, if they support it
describe(Printf) - Method in class org.strbio.mol.lib.FoldLibrary
The default fold library description just prints the name of the class.
describe(Printf) - Method in class org.strbio.mol.lib.FRParameters
Describe prints parameters of the components, if they support it
describe(Printf) - Method in class org.strbio.mol.lib.FRParametersNode
Describe prints parameters of the components, if they support it
describe(Printf) - Method in class org.strbio.mol.lib.GapAffine
 
describe(Printf) - Method in class org.strbio.mol.lib.GapConstant
 
describe(Printf) - Method in class org.strbio.mol.lib.GapDistanceDependent
 
describe(Printf) - Method in class org.strbio.mol.lib.GapModelAdapter
the default function describes only ends.
describe(Printf) - Method in class org.strbio.mol.lib.ScoreAveragePSIBlast
 
describe(Printf) - Method in class org.strbio.mol.lib.ScoreAverageReversePSIBlast
 
describe(Printf) - Method in class org.strbio.mol.lib.ScoreList
Tell scoring functions to describe themselves, if possible.
describe(Printf) - Method in class org.strbio.mol.lib.ScorePhiPsi
 
describe(Printf) - Method in class org.strbio.mol.lib.ScorePSIBlast
 
describe(Printf) - Method in class org.strbio.mol.lib.ScoreReversePSIBlast
 
describe(Printf) - Method in class org.strbio.mol.lib.ScoreSippl90
 
describe(Printf) - Method in class org.strbio.mol.lib.ScoreUFSippl90
 
describe(Printf) - Method in class org.strbio.mol.lib.TOMFoldLibrary
 
describe(Printf) - Method in class org.strbio.mol.lib.UserFoldLibrary
The default fold library description just prints the name of the class.
describe(Printf) - Method in class org.strbio.raf.GapRAF
 
describeBriefly(Printf) - Method in class org.strbio.mol.lib.GapConstant
 
describeBriefly(Printf) - Method in class org.strbio.mol.lib.GapDistanceDependent
 
describeBriefly(Printf) - Method in class org.strbio.raf.GapRAF
 
describeEnds(Printf) - Method in class org.strbio.mol.lib.GapModelAdapter
describe how ends are treated.
Description - Interface in org.strbio.io
This interface is for objects that want to describe themselves to the user... i.e. serialize their important parameters in English.
design(String, double, int) - Static method in class org.strbio.mol.Primer
make a primer with melting temperature of at least N degrees, for a given sequence
design(String, String, double, int) - Static method in class org.strbio.mol.Primer
Design a primer that has a specified start pattern.
designPrimers(String, int, int, PrimerSet) - Method in class org.strbio.local.Primer3
Design primers to clone a region of dna between 2 coordinates.
designPrimers(String, int, int) - Method in class org.strbio.local.Primer3
Design primers to clone a region of dna between 2 coordinates
DHalfMatrix - Class in org.strbio.math
like an upper triangular DMatrix.
DHalfMatrix(int) - Constructor for class org.strbio.math.DHalfMatrix
This makes a new DHalfMatrix which is the upper triangular part of a square matrix.
DHalfMatrix() - Constructor for class org.strbio.math.DHalfMatrix
Makes a new DHalfMatrix with no data.
DHalfMatrix(DHalfMatrix) - Constructor for class org.strbio.math.DHalfMatrix
This makes a DHalfMatrix from another one, making a separate copy of the data.
diffuse() - Method in class org.strbio.math.DMatrix
This does a single round of 'diffusive smoothing' on the matrix.
diffuse() - Method in class org.strbio.math.FMatrix
This does a single round of 'diffusive smoothing' on the matrix.
dihedralAngle(Atom, Atom, Atom, Atom) - Static method in class org.strbio.mol.Atom
returns the dihedral angle in radians between four atoms, or Double.NaN if the coordinates of any are unknown.
dimension() - Method in class org.strbio.math.DVector
returns the dimension the encapsulated array.
dimension() - Method in class org.strbio.math.FVector
returns the dimension the encapsulated array.
dimension() - Method in class org.strbio.math.IVector
returns the dimension the encapsulated array.
disableActions() - Method in class org.strbio.app.JThread
disable all actions
disableActions() - Method in class org.strbio.util.ui.ProfileGUIApp
disable all actions
disableEverything() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
distance(DVector, DVector) - Static method in class org.strbio.math.DVector
Returns the distance between two points pointed to by DVectors a and b.
distance(DVector) - Method in class org.strbio.math.DVector
Returns the distance between this point and one pointed two by another DVector.
distance(FVector, FVector) - Static method in class org.strbio.math.FVector
Returns the distance between two points pointed to by FVectors a and b.
distance(FVector) - Method in class org.strbio.math.FVector
Returns the distance between this point and one pointed two by another FVector.
distance(Atom, Atom) - Static method in class org.strbio.mol.Atom
returns the distance between two atoms, or Double.NaN if the coordinates of either are unknown.
divide(double) - Method in class org.strbio.math.DMatrix
Divides this DMatrix by a specified double.
divide(DMatrix, int) - Static method in class org.strbio.math.DMatrix
Divides a DMatrix by a double, and returns a new DMatrix containing the result.
divide(double) - Method in class org.strbio.math.DVector
Divides this DVector by a specified double.
divide(DVector, double) - Static method in class org.strbio.math.DVector
Divides a DVector by a double, and returns a new DVector containing the result.
divide(float) - Method in class org.strbio.math.FMatrix
Divides this FMatrix by a specified float.
divide(FMatrix, int) - Static method in class org.strbio.math.FMatrix
Divides a FMatrix by a float, and returns a new FMatrix containing the result.
divide(float) - Method in class org.strbio.math.FVector
Divides this FVector by a specified float.
divide(FVector, float) - Static method in class org.strbio.math.FVector
Divides a FVector by a float, and returns a new FVector containing the result.
divideClassPred(double) - Method in class org.strbio.mol.lib.pred2ary.PCPSet
 
divideClassPred(double) - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
divide class pred by a number
dividePred(double) - Method in class org.strbio.mol.lib.pred2ary.PCPSet
divide pred by a double
dividePred(double) - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
divide h,e by a number
DLinkedList - Class in org.strbio.util
A double linked list of objects, with random access to the nth object in the list.
DLinkedList() - Constructor for class org.strbio.util.DLinkedList
Create a new list with no objects.
DLinkedList(DLinkedList) - Constructor for class org.strbio.util.DLinkedList
Copy another list (including the data)
DLinkedList.Node - Interface in org.strbio.util
This is the interface you have to implement if you want to put objects in this linked list.
DMatrix - Class in org.strbio.math
a class to encapsulate a 2-D matrix of doubles.
DMatrix(int, int) - Constructor for class org.strbio.math.DMatrix
makes an emptry DMatrix object with a specified number of columns and rows.
DMatrix() - Constructor for class org.strbio.math.DMatrix
makes a blank 0x0 matrix; you can assign a double[][] to the data directly, or load data in from a file
DMatrix(double[][]) - Constructor for class org.strbio.math.DMatrix
makes a new DMatrix object out of a double[][] array.
DMatrix(DMatrix) - Constructor for class org.strbio.math.DMatrix
copies another DMatrix.
DMatrix(int[][]) - Constructor for class org.strbio.math.DMatrix
makes a new DMatrix object out of an int[][] array, copying the data and casting to doubles.
DMatrix(IMatrix) - Constructor for class org.strbio.math.DMatrix
copies an IMatrix, making a copy of the data, and casting to doubles.
dna - Variable in class org.strbio.mol.Primer
the DNA sequence
domainCode - Variable in class org.strbio.util.db.CATHInfo
CATH code for the domain; i.e. 1abcA1
domainCode - Variable in class org.strbio.util.db.SCOPInfo
SCOP code for the domain; i.e. d3sdha_
done_2ary - Variable in class org.strbio.mol.lib.pred2ary.TrainingSet
 
done_class - Variable in class org.strbio.mol.lib.pred2ary.TrainingSet
 
done_lvl2 - Variable in class org.strbio.mol.lib.pred2ary.TrainingSet
 
doPrediction(PredictionSet) - Method in class org.strbio.mol.lib.pred2ary.Jury
predict 2ary structure.
dot(DVector) - Method in class org.strbio.math.DVector
Returns the dot product of multiplying this with another vector.
dot(DVector, DVector) - Static method in class org.strbio.math.DVector
Returns the dot product of multiplying two vectors.
dot(FVector) - Method in class org.strbio.math.FVector
Returns the dot product of multiplying this with another vector.
dot(FVector, FVector) - Static method in class org.strbio.math.FVector
Returns the dot product of multiplying two vectors.
dot(IVector) - Method in class org.strbio.math.IVector
Returns the dot product of multiplying this with another vector.
dot(IVector, IVector) - Static method in class org.strbio.math.IVector
Returns the dot product of multiplying two vectors.
DotPoint - Class in org.strbio.util.graph
A point type that paints dots.
DotPoint() - Constructor for class org.strbio.util.graph.DotPoint
 
doVarTom(Printf) - Method in class org.strbio.mol.Profile
Do var-tom on this profile.
draw2aryStructure(Graphics, int, int, int, int, int, Protein, int, int) - Static method in class org.strbio.util.ui.ProteinTools
This draws a line of letters showing the actual 2ary structure of a protein, from residue startRes (expressed in the protein's internal numbering scheme; 0 = first residue, etc).
drawAxes(Graphics, int, int, int, int) - Static method in class org.strbio.util.ui.ProteinTools
This draws a set of axes for a graph.
drawGraph(Graphics, int, int, int, int, double[], int, int) - Static method in class org.strbio.util.ui.ProteinTools
This graphs a set of generic data in the 0-1 range.
drawLineDashed(Graphics, int, int, int, int, int) - Static method in class org.strbio.util.JMC
draw a dashed line from point a to point b.
drawLineDashed(Graphics, int, int, int, int) - Static method in class org.strbio.util.JMC
draw a dashed line from point a to point b.
drawLineDotted(Graphics, int, int, int, int) - Static method in class org.strbio.util.JMC
draw a dotted line from point a to point b.
drawLineHalfway(Graphics, int, int, int, int) - Static method in class org.strbio.util.JMC
draw a line from point a halfway to point b.
drawMajorNumberTick(Graphics, int, int, int, int, boolean) - Static method in class org.strbio.util.ui.ProteinTools
Draw a major tick for sequence number above or below a given positon.
drawMajorTic(Graphics, Rectangle, double) - Method in class org.strbio.util.graph.XAxisScale
Draw a major tic at a given x position.
drawMajorTic(Graphics, Rectangle, double) - Method in class org.strbio.util.graph.YAxisScale
Draw a major tic at a given y position.
drawMinorNumberTick(Graphics, int, int, int, int, boolean) - Static method in class org.strbio.util.ui.ProteinTools
Draw a minor number tick for sequence number above or below a given positon.
drawMinorTic(Graphics, Rectangle, double) - Method in class org.strbio.util.graph.XAxisScale
Draw a minor tic at a given x position
drawMinorTic(Graphics, Rectangle, double) - Method in class org.strbio.util.graph.YAxisScale
Draw a minor tic at a given y position
drawNumber(Graphics, int, int, int, int) - Static method in class org.strbio.util.ui.ProteinTools
Draw sequence number at a given position.
drawNumberLine(Graphics, int, int, int, int, int, int, boolean, boolean[]) - Static method in class org.strbio.util.ui.ProteinTools
Draw a line of numbers labeling residue positions in a protein.
drawPred2aryGraph(Graphics, int, int, int, int, Protein, int, int) - Static method in class org.strbio.util.ui.ProteinTools
This draws a graph of the secondary structure probabilities.
drawPred2aryStructure(Graphics, int, int, int, int, int, Protein, int, int) - Static method in class org.strbio.util.ui.ProteinTools
This draws a line of letters showing the actual 2ary structure of a protein, from residue startRes to startRes+n (expressed in the protein's internal numbering scheme; 0 = first residue, etc).
drawTextGraph(Graphics, int, int, int, int, int, char[], double[], int, int) - Static method in class org.strbio.util.ui.ProteinTools
This draws a line of text, and colors the text according to a set of data in the 0-1 range.
DSSP - Class in org.strbio.local
Class to run DSSP on a protein.
DSSP() - Constructor for class org.strbio.local.DSSP
 
DVector - Class in org.strbio.math
a class to encapsulate a 1-D array of doubles.
DVector(int) - Constructor for class org.strbio.math.DVector
makes an emptry DVector object with a specified dimension All data should be zeroed out... this is not done explicitly, but relies on Java's default values.
DVector() - Constructor for class org.strbio.math.DVector
makes a blank vector of dimension 0; you can assign a int[] to the data directly, or load data in from a file
DVector(double[]) - Constructor for class org.strbio.math.DVector
makes a new DVector object out of a int[] array.
DVector(DVector) - Constructor for class org.strbio.math.DVector
copies another DVector.
DVector(int[]) - Constructor for class org.strbio.math.DVector
makes a new DVector object out of a int[] array.
DVector(IVector) - Constructor for class org.strbio.math.DVector
copies an IVector, copying the data and casting to doubles.
DVectorSet - Class in org.strbio.math
A class to encapsulate a set of points, where each point is represented as a DVector.
DVectorSet() - Constructor for class org.strbio.math.DVectorSet
Create an empty set of points, with no minimum dimension
DVectorSet(int) - Constructor for class org.strbio.math.DVectorSet
Create an empty set of points, with a particular minimum dimension.
DVectorSet(DVectorSet) - Constructor for class org.strbio.math.DVectorSet
Create a set by copying another set, but not the DVectors in it.
DVectorSet(DMatrix) - Constructor for class org.strbio.math.DVectorSet
Create a set from a DMatrix, creating a new point for each row in the matrix.

E

e - Variable in class org.strbio.local.BlastP
Expectation value (E) (default = 10.0)
Ecocyc - Class in org.strbio.net
Class to access Ecocyc Version 1.0, 12/13/04 - original version
Ecocyc() - Constructor for class org.strbio.net.Ecocyc
 
editor - Variable in class org.strbio.util.ui.HelpFrame
the editor pane that shows stuff.
eliminate(int) - Method in class org.strbio.math.IVector
Return a copy of the vector with one position removed.
enableActions() - Method in class org.strbio.app.JThread
enable options, depending on whether there are proteins.
enableActions() - Method in class org.strbio.util.ui.ProfileGUIApp
enable various actions, depending on conditions
enableWithoutProteins() - Method in class org.strbio.app.JThread
enable various actions when there are no proteins
enableWithoutProteins() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
enableWithProteins() - Method in class org.strbio.app.JThread
enable various actions when proteins are there.
enableWithProteins() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
endGapFoldOK - Variable in class org.strbio.mol.lib.GapConstant
Gaps at the end of the fold - ok?
endGapFoldOK - Variable in class org.strbio.raf.GapRAF
Gaps at the end of the fold - ok?
endGapSeqOK - Variable in class org.strbio.mol.lib.GapConstant
Gaps at the end of the sequence - ok?
endGapSeqOK - Variable in class org.strbio.raf.GapRAF
Gaps at the end of the sequence - ok?
endRes - Variable in class org.strbio.util.db.CATHInfo
ending residue in domain, or -1 for whole chain.
ensureNames() - Method in class org.strbio.mol.PolymerSet
name unnamed Polymers according to position in set (starting at 1)
ensureUniqueNames(int) - Method in class org.strbio.mol.Profile
This makes sure that every seqName is unique and non-null.
ensureUniqueNames() - Method in class org.strbio.mol.Profile
This makes sure that every seqName is unique and non-null.
Entrez - Class in org.strbio.net
Class to access Entrez over the web.
Entrez() - Constructor for class org.strbio.net.Entrez
 
env - Variable in class org.strbio.mol.Residue
Environment code.
EOF - Variable in class org.strbio.io.EOFStringReader
 
EOFStringReader - Class in org.strbio.io
StringReader that returns false for ready() when at the end of the string.
EOFStringReader(String) - Constructor for class org.strbio.io.EOFStringReader
 
EOL - Static variable in class org.strbio.io.PrintfStream
The end of line character(s) on this system.
EOL - Static variable in class org.strbio.util.StringUtil
The end of line character(s) on this system.
epsilon - Variable in class org.strbio.util.NeuralNet
user-dependent variables for SD BP method: step size
EQUAL - Static variable in class org.strbio.mol.lib.Score2ary
 
EQUAL - Static variable in class org.strbio.mol.lib.ScoreFischer
 
EQUAL - Static variable in class org.strbio.mol.lib.ScoreID
 
EQUAL - Static variable in class org.strbio.mol.lib.ScorePred2ary
 
EQUAL - Static variable in class org.strbio.mol.lib.ScorePredFreq
 
EQUAL - Static variable in class org.strbio.mol.lib.ScoreScaledID
 
equals(Object) - Method in class org.strbio.math.DMatrix
mathematical objects are equal if their contents are.
equals(Object) - Method in class org.strbio.math.DVector
mathematical objects are equal if their contents are.
equals(Object) - Method in class org.strbio.math.FMatrix
mathematical objects are equal if their contents are.
equals(Object) - Method in class org.strbio.math.FVector
mathematical objects are equal if their contents are.
equals(Object) - Method in class org.strbio.math.IMatrix
mathematical objects are equal if their contents are.
equals(Object) - Method in class org.strbio.math.IVector
mathematical objects are equal if their contents are.
error() - Method in class org.strbio.util.NeuralNet
get last error.
estAccy(IMatrix, IMatrix, IMatrix) - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
estimate accuracy on this protein
estAccy() - Method in class org.strbio.mol.lib.pred2ary.PredictionSet
 
estAccy(IMatrix, IMatrix, IMatrix) - Method in class org.strbio.mol.lib.pred2ary.TPSet
estimate accuracy, replacing h, e, predStructure, and the SM matrices
estAccy() - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
Estimate accuracy.
estAccyCount(IMatrix, IMatrix, IMatrix) - Method in class org.strbio.mol.lib.pred2ary.TPSet
make count matrices for est_accy
estASns1 - Variable in class org.strbio.mol.AlignmentStats
estimated asns1
estASns1(double) - Method in class org.strbio.mol.lib.AlignmentParametersEA
estimate the asns1, given an average score (with gap penalties counted).
estASns1SD - Variable in class org.strbio.mol.AlignmentStats
estimated SD in asns1
estASns1SD(double) - Method in class org.strbio.mol.lib.AlignmentParametersEA
get the SD for the asns1 estimation, given an average score (with gap penalties counted).
estFRAccy(double, double) - Method in class org.strbio.mol.lib.AlignmentParametersEA
Estimate the accuracy of a given prediction, given the average score and the z score of the total score.
estFRAccy(double) - Method in class org.strbio.mol.lib.FRParameters
Estimate the accuracy of a given prediction, given the composite score.
estPMatch - Variable in class org.strbio.mol.AlignmentStats
estimated probability of match
evaluationAP - Variable in class org.strbio.mol.lib.FRParametersNode
Alignment parameters used to evaluate the alignment.
exists() - Method in class org.strbio.local.Program
Can we run the program on this system?
exists() - Method in class org.strbio.mol.lib.pred2ary.AppletJury
All applet juries are assumed to exist.
exists() - Method in class org.strbio.mol.lib.pred2ary.Jury
see if the file exists on this system.
exists() - Method in class org.strbio.mol.lib.pred2ary.StandardJury
see if the file exists on this system.
expectedAccuracy() - Method in class org.strbio.mol.Protein
Expected accuracy of the secondary structure prediction that's been done on this protein.
expectedSize - Variable in class org.strbio.mol.lib.pred2ary.AppletJury
 
exposedArea - Variable in class org.strbio.mol.Residue
Area of the residue (in square angstroms) exposed to solvent, as calculated from Scott Presnell's access program.
extraLibrary - Variable in class org.strbio.mol.lib.JMCThreadMethod2
 

F

f - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
Font used for text labels.
fatal(String) - Static method in class org.strbio.util.JMC
Print a fatal error, attempt to flush System.out and System.err, and exit with status one.
FBin - Class in org.strbio.math
a class which does 1-D histogram-FBins.
FBin(int, float, float) - Constructor for class org.strbio.math.FBin
to set up the histogram-FBin, you need to know the number of FBins you want, the minimum possible value, and the maximum possible value of the data.
FBinsize - Variable in class org.strbio.math.FBin
 
fBold - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
 
fcut2ary(int, Printf) - Method in class org.strbio.mol.lib.pred2ary.PredictionSet
 
fcut2ary(NeuralNet, int, Printf) - Method in class org.strbio.mol.lib.pred2ary.TPSet
find best 2ary cutoff
fcut2ary(int, Printf) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
 
fcutClass(NeuralNet, NeuralNet[], Printf) - Method in class org.strbio.mol.lib.pred2ary.TPSet
find cutoff, and compute class stats
fcutClass(Printf) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
 
fcutLvl2(int, Printf) - Method in class org.strbio.mol.lib.pred2ary.PredictionSet
 
fcutLvl2(NeuralNet, int, Printf) - Method in class org.strbio.mol.lib.pred2ary.TPSet
find cutoff, and compute stats on a training set.
fcutLvl2(int, Printf) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
 
FHalfMatrix - Class in org.strbio.math
like an upper triangular DMatrix.
FHalfMatrix(int) - Constructor for class org.strbio.math.FHalfMatrix
This makes a new FHalfMatrix which is the upper triangular part of a square matrix.
FHalfMatrix() - Constructor for class org.strbio.math.FHalfMatrix
Makes a new FHalfMatrix with no data.
FHalfMatrix(FHalfMatrix) - Constructor for class org.strbio.math.FHalfMatrix
This makes a FHalfMatrix from another one, making a separate copy of the data.
fileName - Variable in class org.strbio.mol.lib.pred2ary.Jury
Name of file associated with the binary jury data.
filter - Variable in class org.strbio.local.BlastP
Filter out promiscuous input.
filterByDistance(double) - Method in class org.strbio.mol.Alignment
Check all aligned pairs of residues; remove any with CA-CA distance greater than CUTOFF.
filterByDistance() - Method in class org.strbio.mol.Alignment
This uses the default cutoff (LONGEST_DISTANCE_CUTOFF).
filterByLength(int) - Method in class org.strbio.mol.Alignment
Check all aligned pairs of residues; remove any stretches of alignment shorter than SHORTEST_ALIGNMENT_LENGTH.
filterByLength() - Method in class org.strbio.mol.Alignment
This uses the default cutoff (SHORTEST_ALIGNMENT_LENGTH).
filterPred() - Method in class org.strbio.mol.lib.pred2ary.TPSet
filter out short predictions
filterPred(boolean) - Method in class org.strbio.mol.Protein
filters predStructure predictions in a protein's residues according to DSSP rules: no helix shorter than 4, no strand shorter than 2.
filterPred() - Method in class org.strbio.mol.Protein
filters predStructure predictions in a protein's residues according to DSSP rules: no helix shorter than 4, no strand shorter than 2.
filterReal(boolean) - Method in class org.strbio.mol.Protein
filters DSSP structure in a protein's residues according to DSSP rules: no helix shorter than 4, no strand shorter than 2.
filterReal() - Method in class org.strbio.mol.Protein
filters DSSP structure in a protein's residues according to DSSP rules: no helix shorter than 4, no strand shorter than 2.
filterTrain(PredClassProfile) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
reduce training set based on predicted classes of a protein
find4(Atom, Atom, Atom, double, double, double) - Method in class org.strbio.mol.Atom
relocate this atom (D) , given three nearby atoms (A, B, and C) with known location, a bond length CD, bond angle BCD, and dihedral angle ABCD.
find4(Atom, Atom, Atom, Atom, double, double, double) - Static method in class org.strbio.mol.Atom
relocate an atom (D) , given three nearby atoms (A, B, and C) with known location, a bond length CD, bond angle BCD, and dihedral angle ABCD.
findAccess(Printf) - Method in class org.strbio.mol.Protein
find a protein in a PDB file which should be this one, based on the name.
findClass() - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
find actual kneller class, and AA percentages.
findClassStop(int[]) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
find optimum number of steps to stop after, based on a training set
findClosest(Polymer) - Method in class org.strbio.mol.PolymerSet
return the most similar Polymer (by sequence ID) in a set to a given Polymer.
findConsensus() - Method in class org.strbio.mol.Profile
Find the consensus residue for each residue in the profile.
findConservationWeights() - Method in class org.strbio.mol.Profile
Calculate conservation weight for each residue in the profile.
findDSSP(Printf) - Method in class org.strbio.mol.Protein
finds a protein in a PDB file which should be this one, based on the name.
findDSSP(String, Printf) - Static method in class org.strbio.mol.ProteinSet
find and load proteins from a DSSP file (do DSSP on PDB file)
findDSSPResult(ProteinSet, Printf) - Method in class org.strbio.mol.Protein
returns the appropriate protein from a set of DSSP results, aligned to this one.
findFrequencies() - Method in class org.strbio.mol.Profile
Calculate the frequencies for each residue in the profile, but leave the consensus residue as it is.
findFrequencies() - Method in class org.strbio.mol.ProfRes
Calculate the frequencies for this residue from the seq.
findInputs(double) - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
find network inputs for protein, after 2ary structure is predicted.
findInputs() - Method in class org.strbio.mol.lib.pred2ary.TPSet
find class inputs for all proteins in set
findNClosest(int, double) - Method in class org.strbio.math.DVector
What are the indices of the N closest values to a given double?
findNClosest(int, DVector) - Method in class org.strbio.math.DVectorSet
What are the indices of the N closest values to a DVector?
findNClosest(int, float) - Method in class org.strbio.math.FVector
What are the indices of the N closest values to a given float?
findNonZeroFrequencies() - Method in class org.strbio.mol.Profile
Find the non-zero frequencies for each residue in the profile.
findNonZeroFrequencies() - Method in class org.strbio.mol.ProfRes
Index which frequencies are non-zero.
findPDB(Printf) - Method in class org.strbio.mol.Protein
find a protein in a PDB file which should be this one, based on the name.
findPDB(String, Printf) - Static method in class org.strbio.mol.ProteinSet
find and load proteins from a PDB file.
findPDBName(String, Printf) - Static method in class org.strbio.local.PDB
Find PDB file corresponding to a given protein name.
FindProteins - Class in org.strbio.app
Finds proteins in a list.
FindProteins() - Constructor for class org.strbio.app.FindProteins
 
findSameSeqs() - Method in class org.strbio.mol.ThreadSet
Find seq-fold pairs with the same name.
findSeqByName(String) - Method in class org.strbio.mol.Profile
Find a sequence by name, if it exists.
finished(Polymer, Polymer) - Method in class org.strbio.mol.lib.AlignmentParameters
Tell objects that we're done doing an alignment on a given seq and fold.
finished(Polymer, Polymer) - Method in class org.strbio.mol.lib.GapDistanceDependent
Forget about distance matrix.
finished(Polymer, Polymer) - Method in interface org.strbio.mol.lib.GapModel
Do anything after align/comparison?
finished(Polymer, Polymer) - Method in class org.strbio.mol.lib.GapModelAdapter
Default is no finish.
finished(Polymer) - Method in class org.strbio.mol.lib.ScoreAlphaTau
 
finished(Polymer, Polymer) - Method in class org.strbio.mol.lib.ScoreAveragePSIBlast
 
finished(Polymer) - Method in class org.strbio.mol.lib.ScoreAveragePSIBlast
 
finished(Polymer) - Method in class org.strbio.mol.lib.ScoreAverageReversePSIBlast
 
finished(Polymer) - Method in class org.strbio.mol.lib.ScoreList
Tell scoring functions you're finished with a given protein, for all scoring functions that implement ScoreSetup.
finished(Polymer, Polymer) - Method in class org.strbio.mol.lib.ScoreList
Tell scoring functions you're finished with a given protein pair, for all scoring functions that implement ScoreSetup2.
finished(Polymer) - Method in class org.strbio.mol.lib.ScorePhiPsi
 
finished(Polymer) - Method in class org.strbio.mol.lib.ScorePSIBlast
 
finished(Polymer) - Method in class org.strbio.mol.lib.ScoreReversePSIBlast
 
finished(Polymer) - Method in interface org.strbio.mol.lib.ScoreSetup
This function is called when you are done using the function on a polymer.
finished(Polymer, Polymer) - Method in interface org.strbio.mol.lib.ScoreSetup2
This function is called when you are done using the function on a pair.
finished(Polymer, Polymer) - Method in class org.strbio.mol.lib.ScoreSippl90
 
finished(Polymer, Polymer) - Method in class org.strbio.mol.lib.ScoreUFSippl90
 
firstMon() - Method in class org.strbio.mol.Polymer
Return first monomer if there is one, else null.
firstNonGap(int) - Method in class org.strbio.mol.Profile
What's the position of the first non-gap residue in sequence N?
firstRes() - Method in class org.strbio.mol.Protein
Return first residue if there is one.
fixDistanceGaps() - Method in class org.strbio.mol.Protein
Filter out distance gaps (inter-CA > 4 A or < 3.6 A), returning a new set of proteins consisting of this protein broken into fragments everywhere there is a problem.
fixDistanceGaps() - Method in class org.strbio.mol.ProteinSet
Fix distance gaps in this set; replace all proteins with gaps with a set of chains that has been split up at the gap boundaries.
FLIP_X - Static variable in class org.strbio.util.DensityPlot
Flip the plot left-right (i.e. 0 on the right, going left)
FLIP_X - Static variable in class org.strbio.util.graph.Graph2D
Flip the plot left-right (i.e. 0 on the right, going left)
FLIP_Y - Static variable in class org.strbio.util.DensityPlot
Flip the plot up-down (i.e. 0 on the bottom, going up)
FLIP_Y - Static variable in class org.strbio.util.graph.Graph2D
Flip the plot up-down (i.e. 0 on the bottom, going up)
flipX - Variable in class org.strbio.util.DensityPlot
 
flipX - Variable in class org.strbio.util.graph.Graph2D
 
flipY - Variable in class org.strbio.util.DensityPlot
 
flipY - Variable in class org.strbio.util.graph.Graph2D
 
flush() - Method in class org.strbio.io.OldBufferedPrintfTextArea
Text is not actually appended until you call flush().
flush() - Method in class org.strbio.io.OldPrintfJLabel
 
flush() - Method in class org.strbio.io.OldPrintfJTextArea
 
flush() - Method in class org.strbio.io.OldPrintfTextArea
 
flush() - Method in interface org.strbio.io.Printf
Flushes the output if necessary.
flush() - Method in class org.strbio.io.PrintfJLabel
 
flush() - Method in class org.strbio.io.PrintfJTextArea
 
flush() - Method in class org.strbio.io.PrintfTee
 
flush() - Method in class org.strbio.io.PrintfTextArea
 
flush() - Method in class org.strbio.util.ui.ProfileGUIApp.LoadProgressDialog
 
FMatrix - Class in org.strbio.math
a class to encapsulate a 2-D matrix of floats.
FMatrix(int, int) - Constructor for class org.strbio.math.FMatrix
makes an emptry FMatrix object with a specified number of columns and rows.
FMatrix() - Constructor for class org.strbio.math.FMatrix
makes a blank 0x0 matrix; you can assign a float[][] to the data directly, or load data in from a file
FMatrix(float[][]) - Constructor for class org.strbio.math.FMatrix
makes a new FMatrix object out of a float[][] array.
FMatrix(FMatrix) - Constructor for class org.strbio.math.FMatrix
copies another FMatrix.
FMatrix(int[][]) - Constructor for class org.strbio.math.FMatrix
makes a new FMatrix object out of an int[][] array, copying the data and casting to floats.
FMatrix(IMatrix) - Constructor for class org.strbio.math.FMatrix
copies an IMatrix, making a copy of the data, and casting to floats.
fold - Variable in class org.strbio.mol.Alignment
the fold in the alignment.
fold - Variable in class org.strbio.mol.AlignmentSet
The fold being aligned.
FoldLibrary - Class in org.strbio.mol.lib
A standard fold library for threading; i.e. the TOM fold library, or the Fischer fold library.
FoldLibrary() - Constructor for class org.strbio.mol.lib.FoldLibrary
 
foldRank(int) - Method in class org.strbio.mol.lib.ThreadResults
Get protein number corresponding to rank N, (starting at 0), or null for 'no match'.
folds - Variable in class org.strbio.mol.ThreadSet
Folds being threaded.
foldToSeq(int) - Method in class org.strbio.mol.Alignment
Return a vector of which fold monomer is related to which sequence monomer.
foldToSeq() - Method in class org.strbio.mol.Alignment
Return a vector of which fold monomer is related to which sequence monomer.
fontHeight - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
 
fontSize - Variable in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
fontSize - Variable in class org.strbio.util.ui.GUIApp
 
fontWidth - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
 
frame - Variable in class org.strbio.mol.lib.pred2ary.Pred2aryApplet
 
frame - Variable in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
frame - Variable in class org.strbio.util.ui.HelpFrame
A pointer to this frame, for "quit" button to access.
frequencies2Consensus() - Method in class org.strbio.mol.ProfRes
Find the consensus residue for this residue from the frequencies.
frequency - Variable in class org.strbio.mol.ProfRes
0-100 frequency for each residue in the profile, in alphabetical order by 3-letter code, multiplied by 1000.
FRParameters - Class in org.strbio.mol.lib
Fold recognition parameters.
FRParameters() - Constructor for class org.strbio.mol.lib.FRParameters
Create an empty list.
FRParametersNode - Class in org.strbio.mol.lib
Fold recognition parameters.
FRParametersNode() - Constructor for class org.strbio.mol.lib.FRParametersNode
Create an empty node.
FruitFly - Class in org.strbio.net
Class to access fruitfly.org over the web.
FruitFly() - Constructor for class org.strbio.net.FruitFly
 
func - Variable in class org.strbio.mol.lib.ScoreList
This encapsulates an object that implements ScoreFunction.
FVector - Class in org.strbio.math
a class to encapsulate a 1-D array of floats.
FVector(int) - Constructor for class org.strbio.math.FVector
makes an emptry FVector object with a specified dimension All data should be zeroed out... this is not done explicitly, but relies on Java's default values.
FVector() - Constructor for class org.strbio.math.FVector
makes a blank vector of dimension 0; you can assign a int[] to the data directly, or load data in from a file
FVector(float[]) - Constructor for class org.strbio.math.FVector
makes a new FVector object out of a int[] array.
FVector(FVector) - Constructor for class org.strbio.math.FVector
copies another FVector.
FVector(int[]) - Constructor for class org.strbio.math.FVector
makes a new FVector object out of a int[] array.
FVector(IVector) - Constructor for class org.strbio.math.FVector
copies an IVector, copying the data and casting to floats.
fwd - Variable in class org.strbio.mol.PrimerSet
forward primer

G

GapAffine - Class in org.strbio.mol.lib
Affine gap penalties.
GapAffine(double, double) - Constructor for class org.strbio.mol.lib.GapAffine
Set the penalties.
GapAffine(double, double, boolean, boolean) - Constructor for class org.strbio.mol.lib.GapAffine
Set the penalties.
GapConstant - Class in org.strbio.mol.lib
Constant gap penalties.
GapConstant(double) - Constructor for class org.strbio.mol.lib.GapConstant
Set the penalty.
GapConstant(double, boolean, boolean) - Constructor for class org.strbio.mol.lib.GapConstant
Set the penalty.
gapCostDeletion(Polymer, Polymer, int, int, int, int) - Method in class org.strbio.mol.lib.GapAffine
 
gapCostDeletion(Polymer, Polymer, int, int, int, int) - Method in class org.strbio.mol.lib.GapConstant
 
gapCostDeletion(Polymer, Polymer, int, int, int, int) - Method in class org.strbio.mol.lib.GapDistanceDependent
 
gapCostDeletion(Polymer, Polymer, int, int, int, int) - Method in interface org.strbio.mol.lib.GapModel
This function should return the gap cost for aligning residues seqi and foldi, then seqj and foldj.
gapCostDeletion(Polymer, Polymer, int, int, int, int) - Method in class org.strbio.raf.GapRAF
 
gapCostInsertion(Polymer, Polymer, int, int, int, int) - Method in class org.strbio.mol.lib.GapAffine
 
gapCostInsertion(Polymer, Polymer, int, int, int, int) - Method in class org.strbio.mol.lib.GapConstant
 
gapCostInsertion(Polymer, Polymer, int, int, int, int) - Method in class org.strbio.mol.lib.GapDistanceDependent
 
gapCostInsertion(Polymer, Polymer, int, int, int, int) - Method in interface org.strbio.mol.lib.GapModel
This function should return the gap cost for aligning residues seqi and foldi, then seqj and foldj.
gapCostInsertion(Polymer, Polymer, int, int, int, int) - Method in class org.strbio.raf.GapRAF
 
gapD - Variable in class org.strbio.mol.lib.GapDistanceDependent
Distance penalty.
GapDistanceDependent - Class in org.strbio.mol.lib
Distance dependent gap penalties.
GapDistanceDependent(double, double, double) - Constructor for class org.strbio.mol.lib.GapDistanceDependent
Set the penalties.
GapDistanceDependent(double, double, double, boolean, boolean) - Constructor for class org.strbio.mol.lib.GapDistanceDependent
Set the penalties.
gapE - Variable in class org.strbio.mol.lib.GapAffine
Gap extention penalty.
gapI - Variable in class org.strbio.mol.lib.GapConstant
Gap opening penalty.
gapModel - Variable in class org.strbio.mol.lib.AlignmentParameters
The gap model used.
GapModel - Interface in org.strbio.mol.lib
Interface for gap penalties for alignment.
GapModelAdapter - Class in org.strbio.mol.lib
Default implementation of GapModel.
GapModelAdapter() - Constructor for class org.strbio.mol.lib.GapModelAdapter
 
GapRAF - Class in org.strbio.raf
Gap penalties for RAF.
GapRAF() - Constructor for class org.strbio.raf.GapRAF
Set the penalties.
getA() - Method in class org.strbio.util.db.CATHInfo
return the architecture number
getAlignment(int) - Method in class org.strbio.mol.lib.ThreadResults
get an alignment, or null if it hasn't been done.
getAlignmentRank(int) - Method in class org.strbio.mol.lib.ThreadResults
get an alignment for a given rank, or null if it hasn't been done.
getAllInfo() - Method in class org.strbio.util.db.Data
Return an enumeration of all the info.
getAnnot(String, Printf) - Static method in class org.strbio.net.ProtParam
gets annot for a protein... returns null error processing or reading sequence.
getAnnot(Protein, Printf) - Static method in class org.strbio.net.ProtParam
gets annot for a protein... returns null error processing or reading sequence.
getArm(String) - Static method in class org.strbio.net.FruitFly
Return the arm from a search, or null if not there.
getBaseURL() - Method in class org.strbio.net.BlastWeb
Returns the current base url.
getBinaryData() - Method in class org.strbio.mol.lib.pred2ary.AppletJury
Open jury for processing.
getBinaryData() - Method in class org.strbio.mol.lib.pred2ary.Jury
Open jury for processing.
getBinaryData() - Method in class org.strbio.mol.lib.pred2ary.StandardJury
Open jury for processing.
getBody(String) - Static method in class org.strbio.net.ProtParam
strip header and footer from raw output...
getC() - Method in class org.strbio.util.db.CATHInfo
return the class number.
getC() - Method in class org.strbio.util.db.SCOPInfo
return the class number.
getCG(String) - Static method in class org.strbio.net.FruitFly
returns cg from query, if found, or -1 if not found.
getCGOptions(String) - Static method in class org.strbio.net.FruitFly
returns multiple CG options from query.
GetChainSeqs - Class in org.strbio.app
get sequences/numbering from pdb for chains
GetChainSeqs() - Constructor for class org.strbio.app.GetChainSeqs
 
getChanges(String) - Static method in class org.strbio.net.TargetDB
 
getCheckedAnnot(String, Printf) - Static method in class org.strbio.net.ProtParam
gets raw annot for a protein... returns null error processing or reading sequence
getCheckedAnnot(Protein, Printf) - Static method in class org.strbio.net.ProtParam
gets raw annot for a protein... returns null error processing or reading sequence
getClass(String) - Static method in class org.strbio.util.db.Info
Convenience class returning the class for a given org.strbio.util.db Info type, if available.
getClassName(String) - Static method in class org.strbio.net.SCOP
returns name of class from query, if found, or null if not found.
getColorScale() - Method in class org.strbio.util.BarLegend
Return the color scale being used.
getColorScale() - Method in class org.strbio.util.DensityPlot
Return the color scale being used.
getColorScale() - Method in class org.strbio.util.graph.ColorScaleLegend
Return the color scale being used.
getColorScale() - Method in class org.strbio.util.graph.PointColorPlot
Return the color scale being used.
getCytogenetic(String) - Static method in class org.strbio.net.FruitFly
Return the cytogenetic position from a search, or null if not there.
getDescription() - Method in class org.strbio.mol.lib.ProteinFilter
 
getDG(String) - Method in class org.strbio.local.Mfold
get dG from raw output, or Double.NaN if not found
getDimension(int) - Method in class org.strbio.math.DVectorSet
get a DVector of returning the d'th coordinate for each point.
getDimensions() - Method in class org.strbio.util.NeuralNet
Get dimensions of a loaded network.
getDimensions(BufferedReader) - Static method in class org.strbio.util.NeuralNet
Get dimensions of a network in a file, then reset to the point before anything (except comments) was read in.
getDimensions(DataInputStream) - Static method in class org.strbio.util.NeuralNet
Get dimensions of a network in a binary file, then reset to the point before anything was read in.
getDimensions(String) - Static method in class org.strbio.util.NeuralNet
Get dimensions of a network in a file with a given name.
getDSSPResults(Printf) - Method in class org.strbio.mol.Protein
runs DSSP on a protein, returning a ProteinSet containing results from DSSP.
getEstPMatch(int) - Method in class org.strbio.mol.ThreadSet
Get a DVector of estimated probabilities for one of the proteins in the seqs set, or null if this has not been calculated.
getFamily() - Method in class org.strbio.util.db.SCOPInfo
return the family number
getFamilyName(String) - Static method in class org.strbio.net.SCOP
returns name of family from query, if found, or null if not found.
getFBan(String) - Static method in class org.strbio.net.FruitFly
Return the FBan (annotation number) from a search, or -1 if not there.
getFBgn(String) - Static method in class org.strbio.net.FruitFly
Return the FBgn (gene number) from a search, or -1 if not there.
getFileName() - Method in class org.strbio.mol.lib.FoldLibrary
Every local fold library must have a name that it can be loaded from; other ways of getting a fold library still need to be implemented.
getFileName() - Method in class org.strbio.mol.lib.TOMFoldLibrary
Every local fold library must have a name that it can be loaded from; other ways of getting a fold library still need to be implemented.
getFirstInfo(Class) - Method in class org.strbio.util.db.Data
Get first info of a certain type, or null if there is none.
getFold() - Method in class org.strbio.util.db.SCOPInfo
return the fold number.
getFoldName(String) - Static method in class org.strbio.net.SCOP
returns name of fold from query, if found, or null if not found.
getGlobalAlignment(Polymer, AlignmentParameters, Alignment) - Method in class org.strbio.mol.Polymer
This does the above, but without actually storing the alignment as gaps in the polymers.
getH() - Method in class org.strbio.util.db.CATHInfo
return the homologous superfamily number
getHeight() - Method in class org.strbio.util.graph.CirclePoint
Get the height that the point wants to take up.
getHeight() - Method in class org.strbio.util.graph.ColorScaleLegend
 
getHeight() - Method in class org.strbio.util.graph.DotPoint
Get the height that the point wants to take up.
getHeight() - Method in interface org.strbio.util.graph.Legend
Get the height that the legend wants to draw in.
getHeight() - Method in class org.strbio.util.graph.PointLegend
 
getHeight() - Method in interface org.strbio.util.graph.PointType
Get the height that the point wants to take up.
getHeight() - Method in class org.strbio.util.graph.UnfilledCirclePoint
Get the height that the point wants to take up.
getHistogram(char, int) - Method in class org.strbio.mol.lib.BackbonePotential
Get a raw histogram for a given residue type. 0 = all, 1 = helix, 2 = sheet, 3 = coil.
getHScrollbar() - Method in class org.strbio.util.JMCScrollPane
returns the horizontal scroll bar.
getImageIcon(String, int) - Method in class org.strbio.util.ui.GUIApp
Try to load an image icon out of the appDataPath.
getInfo(String, Printf) - Static method in class org.strbio.local.PDB
Gets info on a PDB file for a given PDB code.
getInfo(Printf, boolean, boolean, boolean, boolean, boolean, boolean, boolean) - Method in class org.strbio.mol.Protein
Get info for a protein out of local databases.
getInfo(String, Printf) - Static method in class org.strbio.net.CATH
Gets all CATH entries for a given PDB code.
getInfo(String) - Static method in class org.strbio.net.SCOP
returns numbers and domain name from query, if found, or null if not found.
getInfo(Class) - Method in class org.strbio.util.db.Data
Return an enumeration of all info of a certain type.
getInfoLinks(String) - Static method in class org.strbio.net.SCOP
returns numbers in links from query, if found, or null if not found
getLegend() - Method in class org.strbio.util.graph.BarPlot
 
getLegend() - Method in class org.strbio.util.graph.ClickablePointPlot
there is no legend for this type of graph.
getLegend() - Method in interface org.strbio.util.graph.Graphable2D
gets the legend, or none if n/a
getLegend() - Method in class org.strbio.util.graph.PointPlot
get legend
getLevel(int) - Method in class org.strbio.util.db.CATHInfo
Get the part of the number corresponding to the classification at level N (starting at 0 to mean the leftmost, or Class).
getLevel(int) - Method in class org.strbio.util.db.SCOPInfo
Get the part of the number corresponding to the classification at level N (starting at 0 to mean the leftmost, or Class).
getMask() - Method in class org.strbio.util.DensityPlot
Returns the current mask matrix.
getMatrix() - Method in class org.strbio.util.DensityPlot
Returns a copy of the matrix being drawn.
getMax() - Method in class org.strbio.util.DensityPlot
Returns the maximum value currently being plotted.
getMaxDistance(int) - Method in class org.strbio.mol.lib.Sippl90
get the maximum distance for toplogical level k
getMaxX() - Method in class org.strbio.util.graph.Graph2D
Returns the maximum x value currently being plotted.
getMaxY() - Method in class org.strbio.util.graph.Graph2D
Returns the maximum y value currently being plotted.
getMin() - Method in class org.strbio.util.DensityPlot
Returns the minimum value currently being plotted.
getMinDistance(int) - Method in class org.strbio.mol.lib.Sippl90
get the minimum distance for toplogical level k
getMinimumSize() - Method in class org.strbio.app.NSPred2ary.AboutMessage
 
getMinimumSize() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.AboutMessage
 
getMinimumSize() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.ProteinPane
 
getMinimumSize() - Method in class org.strbio.util.BarLegend
 
getMinimumSize() - Method in class org.strbio.util.DensityPlot
 
getMinimumSize() - Method in class org.strbio.util.graph.Graph2D
 
getMinX() - Method in class org.strbio.util.graph.Graph2D
Returns the minimum x value currently being plotted.
getMinY() - Method in class org.strbio.util.graph.Graph2D
Returns the minimum y value currently being plotted.
getMolecularWeight(String) - Static method in class org.strbio.net.ProtParam
get molecular weight from raw output, or Double.NaN if not found
getMonomers() - Method in class org.strbio.mol.Polymer
get an array of the monomers.
getName() - Method in class org.strbio.mol.lib.pred2ary.Jury
Get the filename associated with the jury.
getNames() - Method in class org.strbio.mol.PolymerSet
get names of Polymers in this set.
getNetworkStats(int, int[]) - Method in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
This sets various network variable from a vector of network sizes.
getNetworkStats(int, BufferedReader) - Method in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
this automatically figures out network topology from a vector of layer sizes.
getNetworkStats(int, NeuralNet) - Method in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
This automatically figures out network topology from a loaded network. 0 = first level 2ary 1 = lvl 2 2ary 2 = class
getNetworkStats(int, String) - Method in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
this automatically figures out network topology from weight file.
getNonGapMonomers() - Method in class org.strbio.mol.Polymer
get an array of the valid non-gap monomers.
getOptimizableParameters() - Method in class org.strbio.mol.lib.GapAffine
get all the optimizable (double) parameters as a vector.
getOptimizableParameters() - Method in class org.strbio.mol.lib.GapConstant
get all the optimizable (double) parameters as a vector.
getOptimizableParameters() - Method in class org.strbio.mol.lib.GapDistanceDependent
get all the optimizable (double) parameters as a vector.
getOptimizableParameters() - Method in interface org.strbio.mol.lib.GapModel
get all the optimizable (double) parameters as a vector.
getOptimizableParameters() - Method in class org.strbio.mol.lib.GapModelAdapter
by default, nothing is optimizable.
getOutput(String) - Method in class org.strbio.local.Mfold
get output for sequence, or null if it doesn't run
getOwner(String) - Static method in class org.strbio.local.Ls
get file's owner on a unix system, if available
getParallelSpace() - Method in interface org.strbio.util.graph.AxisScale
How much space parallel to the axis is required to draw the scale, outside the graph box?
getParallelSpace() - Method in class org.strbio.util.graph.XAxisScale
How much space parallel to the axis is required to draw the scale, outside the graph box?
getParallelSpace() - Method in class org.strbio.util.graph.YAxisScale
How much space parallel to the axis is required to draw the scale, outside the graph box?
getPDBDomains(String) - Static method in class org.strbio.net.SCOP
returns pdb entry domains if not found
getPerpendicularSpace() - Method in interface org.strbio.util.graph.AxisScale
How much space is required perpendicular to the axis, outside the graph box?
getPerpendicularSpace() - Method in class org.strbio.util.graph.XAxisScale
How much space is required perpendicular to the axis, outside the graph box?
getPerpendicularSpace() - Method in class org.strbio.util.graph.YAxisScale
How much space is required perpendicular to the axis, outside the graph box?
getPI(String) - Static method in class org.strbio.net.ProtParam
get pI from raw output, or Double.NaN if not found
getPoints() - Method in class org.strbio.util.graph.ClickablePointPlot
Returns a pointer to the points being drawn.
getPoints() - Method in class org.strbio.util.graph.PointPlot
Returns a pointer to the points being drawn.
getPotential() - Method in class org.strbio.mol.lib.ScorePhiPsi
Return the current potential.
getPreferredSize() - Method in class org.strbio.app.NSPred2ary.AboutMessage
 
getPreferredSize() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.AboutMessage
 
getPreferredSize() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.ProteinPane
 
getPreferredSize() - Method in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
This gets the preferred size of the component; the parent container should probably just return this.
getPreferredSize() - Method in class org.strbio.util.BarLegend
 
getPreferredSize() - Method in class org.strbio.util.DensityPlot
 
getPreferredSize() - Method in class org.strbio.util.graph.Graph2D
 
getProfile(String) - Method in class org.strbio.local.ClustalW
return the profile stored in the raw clustal output
getProperty(int) - Method in class org.strbio.mol.Polymer
looks up one property.
getPropertyAll(int) - Method in class org.strbio.mol.PolymerSet
looks up one property; returns true only if all polymers in the set have the property.
getPropertyOne(int) - Method in class org.strbio.mol.PolymerSet
looks up a property; returns true if at least one polymer in the set has the property.
getProtein(String, Printf) - Static method in class org.strbio.net.Entrez
Searches on a given protein identifier.
getProtein() - Method in class org.strbio.util.db.SCOPInfo
return the protein number
getProteinName(String) - Static method in class org.strbio.net.SCOP
returns name of protein from query, if found, or null if not found.
getPSIBlastMatrices() - Method in class org.strbio.local.PSIBlastP
Get scoring matrix.
getPSIBlastMatrices() - Method in interface org.strbio.mol.lib.PSIBlast
Should get the matrices used in the last query, or null if there's some problem.
getPSIBlastMatrices() - Method in class org.strbio.net.PSIBlastWeb
Get scoring matrix.
getPSIBlastMatrix() - Method in class org.strbio.mol.ProfilePSI
Get the psi-blast matrix back from this profile.
getRaw(char, char, int) - Method in class org.strbio.mol.lib.Sippl90
Returns a vector of raw N(a,b,k)
getRawAnnot(String, Printf) - Static method in class org.strbio.net.Alces
Query the server for annotation data
getRawAnnot(String, Printf) - Static method in class org.strbio.net.Ecocyc
Query the server for annotation data
getRawAnnot(int, String, Printf) - Static method in class org.strbio.net.FruitFly
Query the server for annotation data
getRawAnnot(String, Printf) - Static method in class org.strbio.net.FruitFly
Query the server for annotation data
getRawAnnot(String, Printf) - Static method in class org.strbio.net.ProtParam
Query the server for annotation data
getRawAnnot(String, Printf) - Static method in class org.strbio.net.SCOP
Query the server for annotation data
getRawAnnotNumeric(SCOPInfo, Printf) - Static method in class org.strbio.net.SCOP
Query the server for annotation data, using numeric entries in SCOPInfo.
getRawAnnotPDB(String, Printf) - Static method in class org.strbio.net.SCOP
Query the server for annotation data for a given pdb string
getRawAnnotSlow(int, String, Printf) - Static method in class org.strbio.net.FruitFly
Query the server for annotation data
getRawData(String, Printf) - Static method in class org.strbio.net.TargetDB
Query the server for data on a given target
getSeqName(int) - Method in class org.strbio.mol.Profile
get the name of sequence i
GetSEQRES - Class in org.strbio.raf
Class to read a pdb file and make a fasta file of its SEQRES entries.
GetSEQRES() - Constructor for class org.strbio.raf.GetSEQRES
 
getSequence(String) - Static method in class org.strbio.net.ProtParam
get sequence given in raw output, or null if not found
getServerData(String) - Method in class org.strbio.mol.lib.pred2ary.Pred2aryApplet
Read a file on the server.
getSortedScores(int) - Method in class org.strbio.mol.ThreadSet
Get an IVector of sorted probabilities for one of the proteins in the seqs set, from most to least likely, or null if this has not been calculated.
getSpeciesName(String) - Static method in class org.strbio.net.SCOP
returns name of species from query, if found, or null if not found.
getStrMatch(int) - Method in class org.strbio.mol.ThreadSet
Return a given structural match, or null if out of range.
getStrMatch(Polymer, Polymer) - Method in class org.strbio.mol.ThreadSet
Get first structural match, if one exists, with a given seq and fold, or null if one doesn't exist.
getSuperfamily() - Method in class org.strbio.util.db.SCOPInfo
return the superfamily number.
getSuperfamilyName(String) - Static method in class org.strbio.net.SCOP
returns name of superfamily from query, if found, or null if not found.
getT() - Method in class org.strbio.util.db.CATHInfo
return the topology number
getTabulated(char, char, int) - Method in class org.strbio.mol.lib.Sippl90
Returns a vector of deltaE(a,b,k).
getTm(String) - Method in class org.strbio.local.Mfold
get tm from raw output, or Double.NaN if not found
getURLData(URL, String, String, Printf) - Static method in class org.strbio.IO
Get raw data from a web server, as a string.
getValidNonGapMonomers() - Method in class org.strbio.mol.Polymer
get an array of the valid non-gap monomers.
getVars() - Method in interface org.strbio.util.CGOptimizer.Optimizable
This should return an array of variables you want optimized.
getVars() - Method in interface org.strbio.util.Hooke.Optimizable
This should return an array of variables you want optimized.
getViewRect() - Method in class org.strbio.util.JMCScrollPane
Gets the viewport rectangle
getVScrollbar() - Method in class org.strbio.util.JMCScrollPane
returns the vertical scroll bar.
getWidth() - Method in class org.strbio.util.graph.CirclePoint
Get the width that the point wants to take up.
getWidth() - Method in class org.strbio.util.graph.ColorScaleLegend
 
getWidth() - Method in class org.strbio.util.graph.DotPoint
Get the width that the point wants to take up.
getWidth() - Method in interface org.strbio.util.graph.Legend
Get the width that the legend wants to draw in.
getWidth() - Method in class org.strbio.util.graph.PointLegend
 
getWidth() - Method in interface org.strbio.util.graph.PointType
Get the width that the point wants to take up.
getWidth() - Method in class org.strbio.util.graph.UnfilledCirclePoint
Get the width that the point wants to take up.
getXAxisScale() - Method in class org.strbio.util.graph.Graph2D
gets the x axis scale
getYAxisScale() - Method in class org.strbio.util.graph.Graph2D
gets y axis scale
globalAlign(AlignmentParameters, Alignment) - Method in class org.strbio.mol.Alignment
Do the global alignment, returning the score (which is also stored in lastScore)
globalAlign(AlignmentParameters) - Method in class org.strbio.mol.Alignment
Do the global alignment, returning the score (which is also stored in lastScore)
globalAlign(AlignmentParameters) - Method in class org.strbio.mol.AlignmentSet
Do the global alignment, store in 'calculated', return comparison score.
globalAlign(Polymer, AlignmentParameters, Alignment) - Method in class org.strbio.mol.Polymer
a mostly generic global alignment function.
globalAlign(Polymer, GapModel, ScoreList, int[]) - Method in class org.strbio.mol.Polymer
Deprecated. use AlignmentParameters
globalCompare(AlignmentParameters) - Method in class org.strbio.mol.AlignmentSet
Find the global comparison score.
globalCompare(Polymer, GapModel, ScoreList) - Method in class org.strbio.mol.Polymer
Deprecated. use AlignmentParameters
globalCompare(Polymer, AlignmentParameters) - Method in class org.strbio.mol.Polymer
a mostly generic global comparison function.
globalCompare(Printf, boolean, boolean) - Method in class org.strbio.mol.ThreadSet
do global comparison of all sequences, showing scores and z-scores.
glScore - Variable in class org.strbio.local.MaxSub.Results
 
Graph2D - Class in org.strbio.util.graph
A component that displays a 2D graph, similar to gnuplot.
Graph2D() - Constructor for class org.strbio.util.graph.Graph2D
Start with nothing.
Graph2D.ClickListener - Interface in org.strbio.util.graph
This is an interface for things that are interested in knowing when the graph is clicked.
Graphable2D - Interface in org.strbio.util.graph
Something that can be graphed in the middle of a Graph2D component.
Graphable3D - Interface in org.strbio.util.graph
Something that can be graphed in the middle of a Graph3D component.
graphPrediction - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
 
greenScale - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
 
GribskovBurgess() - Static method in class org.strbio.mol.lib.DayhoffMatrices
g_b matrix used in: mclachlan, eisenberg - PNAS 84:4355 - 4358 Gribskov & Burgess 1986 Nucleic Acid Research vol 14 p 6745 - 6763 this is mdm78, adjusted to have mean of 0, and sd of 1.
GUIApp - Class in org.strbio.util.ui
A generic set of functions for GUI apps to use, which should provide something of a common L&F.
GUIApp() - Constructor for class org.strbio.util.ui.GUIApp
 

H

handleEvent(Event) - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.AboutDialog
 
handleEvent(Event) - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
handleEvent(Event) - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.LoadWindow
 
handleEvent(Event) - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.ProgressDialog
 
handleEvent(Event) - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.SaveWindow
 
handleEvent(Event) - Method in class org.strbio.util.JMCScrollPane
 
hasGaps() - Method in class org.strbio.mol.Protein
Are any residues missing?
hasHairpin(String) - Method in class org.strbio.local.Mfold
"hairpin" defined as any secondary structure with Tm of at least 55 degrees.
hasInfo(Class) - Method in class org.strbio.util.db.Data
Does the data include any info of a certain type?
hasMoreElements() - Method in class org.strbio.mol.PolymerSet.PolymerEnumeration
Are there any more polymers in the file?
hasMoreElements() - Method in class org.strbio.util.db.Data.InfoEnumeration
 
head() - Method in class org.strbio.util.DLinkedList
returns the head of the list.
helpFrame - Variable in class org.strbio.util.ui.GUIApp
 
HelpFrame - Class in org.strbio.util.ui
Implements a help dialog, loosely modeled on OS/2's.
HelpFrame(URL) - Constructor for class org.strbio.util.ui.HelpFrame
Create a help frame with the given index url.
HelpFrame(URL, URL) - Constructor for class org.strbio.util.ui.HelpFrame
Create a help frame with the given index url, initially showing another url (if non-null)
HelpFrame(URL, URL, Point, Dimension) - Constructor for class org.strbio.util.ui.HelpFrame
Create a help frame with the given index url, initially showing another url (if non-null)
helpFrameLoc - Variable in class org.strbio.util.ui.GUIApp
 
helpFrameSize - Variable in class org.strbio.util.ui.GUIApp
 
history - Variable in class org.strbio.util.ui.HelpFrame
history list of things clicked on.
hls - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
hls_2 - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
Hooke - Class in org.strbio.util
Class for numerical nonlinear optimzation, using the method of Hooke and Jeeves.
Hooke() - Constructor for class org.strbio.util.Hooke
 
Hooke.Optimizable - Interface in org.strbio.util
This is the interface you have to implement if you want to optimize using Hooke.
HSSPnum2Num(int) - Static method in class org.strbio.mol.ProfRes
Translate the ordering used in the HSSP code to my numbering.
HTML - Class in org.strbio.util
Useful functions for manipulating HTML Version 1.0, 5/18/07
HTML() - Constructor for class org.strbio.util.HTML
 

I

IMatrix - Class in org.strbio.math
a class to encapsulate a 2-D matrix of integers Can do a bunch of math functions, and save/load from a file.
IMatrix(int, int) - Constructor for class org.strbio.math.IMatrix
makes an emptry IMatrix object with a specified number of columns and rows.
IMatrix() - Constructor for class org.strbio.math.IMatrix
makes a blank 0x0 matrix; you can assign a int[][] to the data directly, or load data in from a file
IMatrix(int[][]) - Constructor for class org.strbio.math.IMatrix
makes a new IMatrix object out of a int[][] array.
IMatrix(IMatrix) - Constructor for class org.strbio.math.IMatrix
copies another IMatrix.
includeFile - Static variable in class org.strbio.mol.Polymer
 
includeOriginal - Variable in class org.strbio.mol.lib.JMCThreadMethod2
 
includeThreshold - Variable in class org.strbio.local.PSIBlastP
Expectation value (E) threshold for including values in the score matrix model.
includingFile - Static variable in class org.strbio.mol.Polymer
 
index - Variable in class org.strbio.mol.Primer
index of primer within larger DNA sequence (e.g., chromosome)
index - Variable in class org.strbio.util.ui.HelpFrame
This is the index url.
Info - Class in org.strbio.util.db
A piece of info that can be put in a database.
Info() - Constructor for class org.strbio.util.db.Info
 
init() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryApplet
 
inPath(String) - Static method in class org.strbio.IO
Check to see if a program is in your path.
input(int) - Method in class org.strbio.util.NeuralNet
return a network input
insertNode(DLinkedList.Node, DLinkedList.Node) - Method in class org.strbio.util.DLinkedList
Inserts another object in the linked list after a certain node.
insertNode(DLinkedList.Node, int) - Method in class org.strbio.util.DLinkedList
Inserts another object in the linked list after the n'th one.
insertNodeBefore(DLinkedList.Node, DLinkedList.Node) - Method in class org.strbio.util.DLinkedList
Inserts another object in the linked list before a certain one.
insertNodeBefore(DLinkedList.Node, int) - Method in class org.strbio.util.DLinkedList
Inserts another object in the linked list before the n'th one.
insertNodeFirst(DLinkedList.Node) - Method in class org.strbio.util.DLinkedList
Inserts another object at the beginning of the list.
insertNodeLast(DLinkedList.Node) - Method in class org.strbio.util.DLinkedList
Inserts another object at the end of the list.
insertNodeQuickly(AtomNode) - Method in class org.strbio.mol.AtomNode
Inserts another AtomNode in the linked list after this atom, without going through the DLinkedList routines.
inverse() - Method in class org.strbio.math.DMatrix
Returns the inverse of this matrix.
inverse() - Method in class org.strbio.math.FMatrix
Returns the inverse of this matrix.
inverse() - Method in class org.strbio.mol.Alignment
invert alignment, returning fold->seq alignment
IO - Class in org.strbio
A class containing some useful IO functions which don't really merit their own classes.
IO() - Constructor for class org.strbio.IO
 
is3Res(String) - Static method in class org.strbio.mol.Residue
Is your string a valid 3-letter code?
is3Res(String) - Static method in class org.strbio.raf.RAFResidue
Is your string a valid 3-letter code?
isArmUnknown(String) - Static method in class org.strbio.net.FruitFly
Is there an annotation of unknown Arm?
isCATHMatch(Protein) - Method in class org.strbio.mol.Protein
Does this protein match another at the H level or below, according to CATH codes?
isEmpty() - Method in class org.strbio.math.DMatrix
Does the matrix contain all zeroes?
isEmpty() - Method in class org.strbio.math.FMatrix
Does the matrix contain all zeroes?
isEmpty() - Method in class org.strbio.math.IMatrix
Does the matrix contain all zeroes?
isEndGapFoldOK() - Method in class org.strbio.mol.lib.GapConstant
 
isEndGapFoldOK() - Method in interface org.strbio.mol.lib.GapModel
See if aligning the end of the fold vs a gap is OK (not penalized)
isEndGapFoldOK() - Method in class org.strbio.raf.GapRAF
 
isEndGapSeqOK() - Method in class org.strbio.mol.lib.GapConstant
 
isEndGapSeqOK() - Method in interface org.strbio.mol.lib.GapModel
See if aligning the end of the sequence vs a gap is OK (not penalized)
isEndGapSeqOK() - Method in class org.strbio.raf.GapRAF
 
isEqual(PolymerSet) - Method in class org.strbio.mol.PolymerSet
do 2 sets of Polymers contain the same Polymers?
isGap() - Method in class org.strbio.mol.Monomer
does this monomer represent a gap?
isGap(char) - Static method in class org.strbio.mol.Nucleotide
Is a character a gap code?
isGap() - Method in class org.strbio.mol.Nucleotide
is the character used to represent a gap?
isGap(char) - Static method in class org.strbio.mol.Residue
Is a character a gap code?
isGap() - Method in class org.strbio.mol.Residue
is the character used to represent a gap?
isInitialized() - Method in class org.strbio.mol.lib.PSIBlastMatrices
Has the matrix been properly loaded/initialized?
isLittleEndian() - Static method in class org.strbio.util.JMC
This guesses whether the current machine is little-endian, and would therefore need to use the reverseEndian calls when reading/writing DataStreams for use with C programs.
isMatch(int, int) - Method in class org.strbio.mol.ThreadSet
is sequence N a known structural match for fold M?
isNuc(char) - Static method in class org.strbio.mol.Nucleotide
Is your character a valid 1-letter code?
isRes(char) - Static method in class org.strbio.mol.Residue
Is your character a valid 1-letter code?
isSame(int, int) - Method in class org.strbio.mol.ThreadSet
is sequence N the same as fold M?
isValidNonGap() - Method in class org.strbio.mol.Monomer
Is this monomer something which is valid, but not a gap?
isValidType() - Method in class org.strbio.mol.Monomer
is the character in 'type' valid for this monomer?
isValidType() - Method in class org.strbio.mol.Nucleotide
is the character in 'type' valid for this residue?
isValidType() - Method in class org.strbio.mol.Residue
is the character in 'type' valid for this residue?
iterations - Variable in class org.strbio.net.PSIBlastWeb
How many iterations to do this for?
IVector - Class in org.strbio.math
a class to encapsulate a 1-D matrix of integers.
IVector(int) - Constructor for class org.strbio.math.IVector
makes an emptry IVector object with a specified dimension All data should be zeroed out... this is not done explicitly, but relies on Java's default values.
IVector() - Constructor for class org.strbio.math.IVector
makes a blank vector of dimension 0; you can assign a int[] to the data directly, or load data in from a file
IVector(int[]) - Constructor for class org.strbio.math.IVector
makes a new IVector object out of a int[] array.
IVector(IVector) - Constructor for class org.strbio.math.IVector
copies another IVector.

J

jackknife - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
jackknife(int, Printf) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
split up a set using jackknife procedure
jackknife_2 - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
JMC - Class in org.strbio.util
A class containing a bunch of useful functions
JMC2ary - Class in org.strbio.app
Train and test secondary structure/class networks, using profiles.
JMC2ary() - Constructor for class org.strbio.app.JMC2ary
 
JMCAlphaTau - Variable in class org.strbio.mol.ProfResPSI
JMC's alpha/tau potential matrix.
JMCPhiPsi - Variable in class org.strbio.mol.ProfResPSI
JMC's phi/psi potential matrix for this postion.
JMCScrollPane - Class in org.strbio.util
This is basically a lame re-implementation of ScrollPane, but it works with AWT 1.0 applets... can therefore use for Netscape 4.0, which supports Java 1.1 with AWT 1.0.
JMCScrollPane(Component) - Constructor for class org.strbio.util.JMCScrollPane
Create a ScrollPane containing an AWT component; this component shouldn't be added anywhere else.
JMCThreadMethod - Class in org.strbio.mol.lib
JMC's global threading method.
JMCThreadMethod() - Constructor for class org.strbio.mol.lib.JMCThreadMethod
Use the default fold library.
JMCThreadMethod(FoldLibrary) - Constructor for class org.strbio.mol.lib.JMCThreadMethod
Use a user-specified fold library.
JMCThreadMethod(PSIBlast) - Constructor for class org.strbio.mol.lib.JMCThreadMethod
Use a user-specified psiblast method
JMCThreadMethod(FoldLibrary, PSIBlast) - Constructor for class org.strbio.mol.lib.JMCThreadMethod
Use a user-specified library and psiblast method
JMCThreadMethod2 - Class in org.strbio.mol.lib
JMC's global threading method, based on a combination of methods.
JMCThreadMethod2() - Constructor for class org.strbio.mol.lib.JMCThreadMethod2
Use the default fold library.
JMCThreadMethod2(FoldLibrary) - Constructor for class org.strbio.mol.lib.JMCThreadMethod2
Use a user-specified fold library.
JMCThreadMethod2(PSIBlast) - Constructor for class org.strbio.mol.lib.JMCThreadMethod2
Use a user-specified psiblast method
JMCThreadMethod2(FoldLibrary, PSIBlast) - Constructor for class org.strbio.mol.lib.JMCThreadMethod2
Use a user-specified library and psiblast method
JMCThreadMethod2(FoldLibrary, FoldLibrary, PSIBlast) - Constructor for class org.strbio.mol.lib.JMCThreadMethod2
Use a user-specified base library, extra library and psiblast method.
JThread - Class in org.strbio.app
Thread one or more proteins.
JThread() - Constructor for class org.strbio.app.JThread
 
JThread(String[]) - Constructor for class org.strbio.app.JThread
 
JThreadServer - Class in org.strbio.app
Thread one or more proteins.
JThreadServer(String[]) - Constructor for class org.strbio.app.JThreadServer
 
JThreadText - Class in org.strbio.app
Thread one or more proteins.
JThreadText(String[]) - Constructor for class org.strbio.app.JThreadText
 
Jury - Class in org.strbio.mol.lib.pred2ary
Class that implements a jury of secondary structure prediction networks.
jury - Variable in class org.strbio.mol.lib.Pred2ary
 
Jury(String) - Constructor for class org.strbio.mol.lib.pred2ary.Jury
Create a new jury, given the name of the binary input file.
Jury.ProgressIndicator - Interface in org.strbio.mol.lib.pred2ary
Indicator to update with verbose output, after every juror finishes.

K

keepAllResults - Variable in class org.strbio.local.PSIBlastP2
Keep the results from the first search as well as the second?
keepMonomers(int, int) - Method in class org.strbio.mol.Polymer
Keep the monomers not between n1 and n2 (inclusive); strip away the rest.
keepOnlyChainID(char) - Method in class org.strbio.mol.PolymerSet
Removes all polymers in the set not having a particular chain ID.
keepOnlyNames(String[]) - Method in class org.strbio.mol.PolymerSet
Like searchByName, but for a whole set of names.
keepOnlyNamesFuzzy(String[]) - Method in class org.strbio.mol.PolymerSet
Like searchByNameFuzzy, but for a whole set of names.
kHigh - Variable in class org.strbio.mol.lib.ScoreSippl90
Highest k value to restrict scoring to, or 0 for no restrictions.
kHigh - Variable in class org.strbio.mol.lib.ScoreUFSippl90
Highest k value to restrict scoring to, or 0 for no restrictions.
kLow - Variable in class org.strbio.mol.lib.ScoreSippl90
Lowest k value to restrict scoring to, or 0 for no restrictions.
kLow - Variable in class org.strbio.mol.lib.ScoreUFSippl90
Lowest k value to restrict scoring to, or 0 for no restrictions.
kludgeChainID() - Method in class org.strbio.mol.Polymer
Kludge chain ID from the name, assuming the name is PDB-style 1abcD (D=chain id), or ASTRAL-style d1abcD_/e1abc.1D _ gives no chain id.
KNOWN_2ARY - Static variable in class org.strbio.mol.PolymerProperties
Protein property: is there known secondary structure?
KNOWN_ATOMS - Static variable in class org.strbio.mol.PolymerProperties
Polymer property: is there information on atomic coordinates?
KNOWN_ENV - Static variable in class org.strbio.mol.PolymerProperties
Protein property: is there information on environmental class?

L

LargeJury - Class in org.strbio.mol.lib.pred2ary
The 'large' network set. 120 jurors (level 1 and 2 networks, 15 of which use reduced training) trained on all training sets (0 through 14), 7 unreduced and 1 reduced juror per set.
LargeJury() - Constructor for class org.strbio.mol.lib.pred2ary.LargeJury
Create a new jury.
lastMon() - Method in class org.strbio.mol.Polymer
Return last monomer if there is one, else null.
lastNonGap(int) - Method in class org.strbio.mol.Profile
What's the position of the first non-gap residue in sequence N?
lastScore - Variable in class org.strbio.mol.Alignment
last total score for when this alignment was made.
layers() - Method in class org.strbio.util.NeuralNet
return number of layers.
layerSize(int) - Method in class org.strbio.util.NeuralNet
return size of a given layer.
Legend - Interface in org.strbio.util.graph
A legend for a Graphable2D (or Graphable3D) piece of data.
legend - Variable in class org.strbio.util.graph.PointPlot
legend, if there
length() - Method in class org.strbio.math.DVector
returns the dimension the encapsulated array.
length() - Method in class org.strbio.math.FVector
returns the dimension the encapsulated array.
length() - Method in class org.strbio.math.IVector
returns the dimension the encapsulated array.
length() - Method in class org.strbio.mol.Polymer
Length is synonym for nMonomers.
library - Variable in class org.strbio.mol.lib.JMCThreadMethod
 
library - Variable in class org.strbio.mol.lib.JMCThreadMethod2
 
library - Variable in class org.strbio.mol.lib.ThreadResults
The library the threading was done on.
linearFit() - Method in class org.strbio.math.Bin2D
This will return the best linear fit of the sampled points.
linearFit(DVector) - Method in class org.strbio.math.DVector
This will return the best linear fit to a bunch of points, assuming that this DVector contains x's, and DVectory y contains y's.
linearFit(FVector) - Method in class org.strbio.math.FVector
This will return the best linear fit to a bunch of points, assuming that this FVector contains x's, and FVectory y contains y's.
link(TrainingSet) - Method in class org.strbio.mol.lib.pred2ary.PredictionSet
 
link(PredictionSet) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
 
load(BufferedReader) - Method in class org.strbio.math.DHalfMatrix
Loads from an open BufferedReader.
load(BufferedReader) - Method in class org.strbio.math.DMatrix
Load Ascii from an open BufferedReader.
load(DataInputStream) - Method in class org.strbio.math.DMatrix
Load binary matrix from an open DataInputStream.
load(String) - Method in class org.strbio.math.DMatrix
Loads matrix from a file; file type (text/binary) is autodetected.
load(BufferedReader) - Method in class org.strbio.math.DVector
Load from an open BufferedReader.
load(String) - Method in class org.strbio.math.DVector
Loads from a text file.
load(BufferedReader) - Method in class org.strbio.math.FHalfMatrix
Loads from an open BufferedReader.
load(BufferedReader) - Method in class org.strbio.math.FMatrix
Load Ascii from an open BufferedReader.
load(DataInputStream) - Method in class org.strbio.math.FMatrix
Load binary matrix from an open DataInputStream.
load(String) - Method in class org.strbio.math.FMatrix
Loads matrix from a file; file type (text/binary) is autodetected.
load(BufferedReader) - Method in class org.strbio.math.FVector
Load from an open BufferedReader.
load(String) - Method in class org.strbio.math.FVector
Loads from a text file.
load(BufferedReader) - Method in class org.strbio.math.IMatrix
Load text matrix from an open BufferedReader.
load(DataInputStream) - Method in class org.strbio.math.IMatrix
Load binary matrix from an open DataInputStream.
load(String) - Method in class org.strbio.math.IMatrix
Loads matrix from a file; file type (text/binary) is autodetected.
load(BufferedReader) - Method in class org.strbio.math.IVector
Load from an open BufferedReader.
load(String) - Method in class org.strbio.math.IVector
Loads from a text file.
load(BufferedReader, PolymerSet, PolymerSet) - Method in class org.strbio.mol.AlignmentSet
Load alignment out of new format file.
load(BufferedReader) - Method in class org.strbio.mol.AlignmentSet
 
load(String, PolymerSet, PolymerSet) - Method in class org.strbio.mol.AlignmentSet
Load alignment out of new format file.
load(String) - Method in class org.strbio.mol.AlignmentSet
Load alignment out of new format file.
load(String) - Method in class org.strbio.mol.AlignmentStats
load results from a line in a saved file.
load(BufferedReader) - Method in class org.strbio.mol.lib.BackbonePotential
load histograms from an open Reader... format should be all_raw, all_h, all_e, all_c, gly_raw, gly_h...
load(String) - Method in class org.strbio.mol.lib.BackbonePotential
load histograms from a file... format should be all_raw, all_h, all_e, all_c, gly_raw, gly_h...
load(boolean) - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.LoadWindow
 
load(String) - Method in class org.strbio.mol.lib.PSIBlastMatrices
Load scoring matrix from a file.
load(BufferedReader) - Method in class org.strbio.mol.lib.PSIBlastMatrices
Load scoring matrix from a BufferedReader.
load(BufferedReader) - Method in class org.strbio.mol.lib.Sippl90
Load tabulated values from an open BufferedReader.
load(String) - Method in class org.strbio.mol.lib.Sippl90
Loads tabulated values from a text file.
load(String, Printf) - Method in class org.strbio.mol.PolymerSet
Default load automatically figures out file type.
load(BufferedReader) - Method in class org.strbio.util.NeuralNet
load from an open text file; check network dimensions.
load(DataInputStream) - Method in class org.strbio.util.NeuralNet
load from an open binary file; check network dimensions.
load(String) - Method in class org.strbio.util.NeuralNet
load from a text file; check network dimensions.
load3DPSSM(String) - Method in class org.strbio.mol.ThreadSet
loads seqs, folds, and str matches from 3DPSSM output (mailbox of messages from server).
loadCheckpoint - Variable in class org.strbio.local.PSIBlastP
load checkpoint?
loadCheckpoint(DataInputStream) - Method in class org.strbio.mol.lib.PSIBlastMatrices
Load everything out of a file, created by 'blastpgp -C filename'.
loadCheckpoint(String) - Method in class org.strbio.mol.lib.PSIBlastMatrices
Load everything out of a file with a given name.
loadCheckpointName - Variable in class org.strbio.local.PSIBlastP
 
loadClassPred(double[]) - Method in class org.strbio.mol.lib.pred2ary.PCPSet
 
loadClassPred(double[], int) - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
take class pred from array
loadCorrect(String) - Method in class org.strbio.mol.AlignmentSet
load correct alignment from file.
loadDir - Variable in class org.strbio.util.ui.ProfileGUIApp
 
loadEstAAStats(BufferedReader) - Method in class org.strbio.mol.lib.AlignmentParametersEA
Get the accuracy stats out of a file.
loadEstAAStats(String) - Method in class org.strbio.mol.lib.AlignmentParametersEA
Get the accuracy stats out of a file.
loadEstAAStats() - Method in class org.strbio.mol.lib.AlignmentParametersEA
Load the default accuracy stats from a file in the classpath.
loadEstAAStatsRaw(BufferedReader) - Method in class org.strbio.mol.lib.AlignmentParametersEA
Get raw accuracy stats out of a file.
loadEstAAStatsRaw(String) - Method in class org.strbio.mol.lib.AlignmentParametersEA
Get the raw accuracy stats out of a file.
loadEstFRStats(BufferedReader) - Method in class org.strbio.mol.lib.AlignmentParametersEA
Get the FR accuracy stats out of a file.
loadEstFRStats(String) - Method in class org.strbio.mol.lib.AlignmentParametersEA
Get the FR accuracy stats out of a file.
loadEstFRStats() - Method in class org.strbio.mol.lib.AlignmentParametersEA
Load the default accuracy stats from a file in the classpath.
loadEstFRStats(BufferedReader) - Method in class org.strbio.mol.lib.FRParameters
Get the FR accuracy stats out of a file.
loadEstFRStats(String) - Method in class org.strbio.mol.lib.FRParameters
Get the FR accuracy stats out of a file.
loadEstFRStats() - Method in class org.strbio.mol.lib.FRParameters
Load the default accuracy stats from a file in the classpath.
loadEstFRStatsRaw(BufferedReader) - Method in class org.strbio.mol.lib.AlignmentParametersEA
Get the raw FR accuracy stats out of a file.
loadEstFRStatsRaw(String) - Method in class org.strbio.mol.lib.AlignmentParametersEA
Get the raw FR accuracy stats out of a file.
loadEstFRStatsRaw(BufferedReader) - Method in class org.strbio.mol.lib.FRParameters
Get the raw FR accuracy stats out of a file.
loadEstFRStatsRaw(String) - Method in class org.strbio.mol.lib.FRParameters
Get the raw FR accuracy stats out of a file.
loadFile - Variable in class org.strbio.util.ui.ProfileGUIApp
 
loadFreqs(DataInputStream) - Method in class org.strbio.mol.lib.PSIBlastMatrices
Load frequencies from checkpoint file.
loadFromClassPath() - Method in class org.strbio.mol.lib.FoldLibrary
Load in the fold library, silently, from the CLASSPATH.
loadNail(String) - Method in class org.strbio.mol.AlignmentSet
load 'nail' alignment from file.
loadOld(String, int, int) - Method in class org.strbio.mol.Alignment
load an Alignment out of a simple format file; contains pairs of numbers indicating which res in the sequence aligns to which res in the fold.
loadPD - Variable in class org.strbio.util.ui.ProfileGUIApp
 
loadPred(double[]) - Method in class org.strbio.mol.lib.pred2ary.PCPSet
 
loadPred(double[], int) - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
take h, e from array
loadProteins() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
open up a new load window.
loadProteins - Variable in class org.strbio.util.ui.ProfileGUIApp
 
loadProteinsB - Variable in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
loadProteinsMI - Variable in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
loadRaw(BufferedReader) - Method in class org.strbio.mol.lib.Sippl90
Load tabulated values from an open BufferedReader.
loadRaw(String) - Method in class org.strbio.mol.lib.Sippl90
Loads raw values from a text file.
loadStrMatches(String) - Method in class org.strbio.mol.ThreadSet
get structural matches from a file, with or without correct and naildown alignments.
loadThread - Variable in class org.strbio.util.ui.ProfileGUIApp
 
loadWindow - Variable in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
logText - Variable in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
logText - Variable in class org.strbio.util.ui.ProfileGUIApp
 
LONGEST_DISTANCE_CUTOFF - Static variable in class org.strbio.mol.Alignment
The longest distance 2 aligned CA atoms can be apart in the makeFromSuperposition* algorithms: currently 6 A.
low_error - Variable in class org.strbio.util.NeuralNet
stopping parameter for scg and sd.
lowerror - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
lowerror_2 - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
Ls - Class in org.strbio.local
Class to run ls Version 1.0, 10/3/02
Ls() - Constructor for class org.strbio.local.Ls
 

M

main(String[]) - Static method in class org.strbio.app.Align
 
main(String[]) - Static method in class org.strbio.app.BlastProtein
 
main(String[]) - Static method in class org.strbio.app.CompareFolds
 
main(String[]) - Static method in class org.strbio.app.CompileJuryScript
 
main(String[]) - Static method in class org.strbio.app.ConvertProtein
 
main(String[]) - Static method in class org.strbio.app.FindProteins
 
main(String[]) - Static method in class org.strbio.app.GetChainSeqs
 
main(String[]) - Static method in class org.strbio.app.JMC2ary
 
main(String[]) - Static method in class org.strbio.app.JThread
 
main(String[]) - Static method in class org.strbio.app.JThreadServer
 
main(String[]) - Static method in class org.strbio.app.JThreadText
 
main(String[]) - Static method in class org.strbio.app.MakeModeller
 
main(String[]) - Static method in class org.strbio.app.MinareaAlign
 
main(String[]) - Static method in class org.strbio.app.Model
 
main(String[]) - Static method in class org.strbio.app.Modify2ary
 
main(String[]) - Static method in class org.strbio.app.NSPred2ary
 
main(String[]) - Static method in class org.strbio.app.Pred2ary
 
main(String[]) - Static method in class org.strbio.app.Pred2aryText
 
main(String[]) - Static method in class org.strbio.app.SplitProteins
 
main(String[]) - Static method in class org.strbio.local.Ls
 
main(String[]) - Static method in class org.strbio.local.MaxSub
 
main(String[]) - Static method in class org.strbio.local.Melting
Looks up sequences on cmd line
main(String[]) - Static method in class org.strbio.mol.lib.BackbonePotential
Does what the C++ program 'anglehist' used to do, except slower... also does the smoothing in advance as the histograms are created.
main(String[]) - Static method in class org.strbio.mol.lib.FRParameters
main processes the old raw EA files and re-saves them in the new format.
main(String[]) - Static method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
main(String[]) - Static method in class org.strbio.mol.lib.ScoreSippl90
 
main(String[]) - Static method in class org.strbio.mol.lib.Sippl90
Use proteins in a file to parameterize the function.
main(String[]) - Static method in class org.strbio.net.Alces
Looks up sequences on cmd line
main(String[]) - Static method in class org.strbio.net.Ecocyc
Looks up sequences in file
main(String[]) - Static method in class org.strbio.net.Entrez
Looks up something in entrez.
main(String[]) - Static method in class org.strbio.net.FruitFly
Looks up something in entrez.
main(String[]) - Static method in class org.strbio.net.ProtParam
Looks up sequences in file
main(String[]) - Static method in class org.strbio.net.PubMed
Looks up something in pubmed
main(String[]) - Static method in class org.strbio.net.TargetDB
Looks up sequences on cmd line
main(String[]) - Static method in class org.strbio.net.ThreeDPSSM
Looks up sequences on cmd line
main(String[]) - Static method in class org.strbio.raf.GetSEQRES
 
main(String[]) - Static method in class org.strbio.raf.MakeRAF
 
mainFrame - Variable in class org.strbio.util.ui.GUIApp
 
mainFrameLoc - Variable in class org.strbio.util.ui.GUIApp
 
mainFrameSize - Variable in class org.strbio.util.ui.GUIApp
 
mainLabel - Variable in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
makeAlignment(Printf, AlignmentParameters, int) - Method in class org.strbio.mol.lib.ThreadResults
make one alignment to a given fold.
makeAlignments(Printf, AlignmentParameters, double) - Method in class org.strbio.mol.lib.ThreadResults
make alignments for all folds >= a certain pMatch value.
makeAllStrMatches() - Method in class org.strbio.mol.ThreadSet
add all possible structural matches to the set.
makeCalculatedFromCurrent() - Method in class org.strbio.mol.AlignmentSet
Sets up 'calculated' array based on current alignment.
makeCATHStrMatches() - Method in class org.strbio.mol.ThreadSet
make a set of StrMatches using CATH data.
makeCurrentFromCalculated() - Method in class org.strbio.mol.AlignmentSet
Sets up gaps in both Polymers as in 'calculated' array.
makeEnergyHist(char, double, double, double, double) - Method in class org.strbio.mol.lib.BackbonePotential
returns energy histogram for a residue with helix probability pH, and strand probability pE.
makeEnergyHist(char, double, double) - Method in class org.strbio.mol.lib.BackbonePotential
returns energy histogram for a residue with helix probability pH, and strand probability pE.
makeFromSuperposition(Protein, Protein) - Static method in class org.strbio.mol.Alignment
Make from 2 superimposed proteins, using JDB's method. 1) Make table of everything in (fold) which is <= CUTOFF angstroms from each residue in (seq). 2) Get longest consecutive stretch, and set them as aligned; remove these residues from future consideration. 3) Repeat until nothing is left that has any matches.
makeFromSuperpositionDP(Protein, Protein) - Static method in class org.strbio.mol.Alignment
Make from a superposition, using dynamic programming.
makeInverseTransform(double, double, double, double, double, double) - Static method in class org.strbio.math.DMatrix
Return an inverse transformation matrix given 3 transformation coordinates and 3 Euler rotation angles.
makeInverseTransform(float, float, float, float, float, float) - Static method in class org.strbio.math.FMatrix
Return an inverse transformation matrix given 3 transformation coordinates and 3 Euler rotation angles.
makeInverseTransform() - Method in class org.strbio.mol.lib.MinareaResults
Matrix to transform one protein on top of the other, based on the numbers from minarea.
MakeModeller - Class in org.strbio.app
Takes a set of single chains; runs clustalw and outputs a bunch of modeller input files and the clustalw alignment
MakeModeller() - Constructor for class org.strbio.app.MakeModeller
 
makeMonDistance() - Method in class org.strbio.mol.Polymer
calculate inter-monomer distance matrix for use in threading functions.
makeMonDistance() - Method in class org.strbio.mol.Protein
calculate inter-residue distance matrix (CA-CA distances) for use in threading functions.
makeMonDistanceAllAtomMin() - Method in class org.strbio.mol.Polymer
calculate inter-monomer distance matrix for use in threading functions.
makeMonDistanceCB() - Method in class org.strbio.mol.Protein
calculate inter-residue distance matrix (CB-CB distances, or CA for Gly residues) for use in threading functions.
MakeRAF - Class in org.strbio.raf
Class to read a PDB file and make a raf file.
MakeRAF() - Constructor for class org.strbio.raf.MakeRAF
 
makeSameLength() - Method in class org.strbio.mol.Alignment
pad both seqs to same length
makeSameLength() - Method in class org.strbio.mol.AlignmentSet
Pad both sequences to same length.
makeScoreMatrix() - Method in class org.strbio.mol.lib.PSIBlastMatrices
Convert pseudo-count frequencies to a score matrix.
makeTransform(double, double, double, double, double, double) - Static method in class org.strbio.math.DMatrix
Return a transformation matrix given 3 transformation coordinates and 3 Euler rotation angles.
makeTransform(float, float, float, float, float, float) - Static method in class org.strbio.math.FMatrix
Return a transformation matrix given 3 transformation coordinates and 3 Euler rotation angles.
makeTransform() - Method in class org.strbio.mol.lib.MinareaResults
Matrix to transform one protein on top of the other, based on the numbers from minarea.
makeVirtualCB() - Method in class org.strbio.mol.Protein
Add a virtual CB atom for residues that don't have one.
makeVirtualCB() - Method in class org.strbio.mol.Residue
Construct a virtual CB atom.
makeXAxisScale() - Method in class org.strbio.util.graph.Graph2D
make new x axis scale.
makeYAxisScale() - Method in class org.strbio.util.graph.Graph2D
make new y axis scale.
makeZScores() - Method in class org.strbio.math.DVector
returns a vector containing the Z scores for all data in the array.
makeZScores() - Method in class org.strbio.math.FVector
returns a vector containing the Z scores for all data in the array.
Malfe - Class in org.strbio.local
Class to run new minarea front end malfe.
Malfe() - Constructor for class org.strbio.local.Malfe
 
mask - Variable in class org.strbio.util.DensityPlot
A 2-d array of booleans showing which positions to draw and which not to.
matchesLevel(CATHInfo) - Method in class org.strbio.util.db.CATHInfo
What is the highest level this matches another record at?
matchesLevel(SCOPInfo) - Method in class org.strbio.util.db.SCOPInfo
What is the highest level this matches another record at?
matchesUpTo(CATHInfo, int) - Method in class org.strbio.util.db.CATHInfo
Does this match another CATH record up to level N?
matchesUpTo(SCOPInfo, int) - Method in class org.strbio.util.db.SCOPInfo
Does this match another SCOP record up to level N?
matthews(int) - Method in class org.strbio.math.CorrectMatrix
Return the Matthews correlation coefficient for property A.
matthews(int) - Method in class org.strbio.math.SimMatrix
Return the Matthews correlation coefficient for category A.
matthews(int) - Method in class org.strbio.math.StatsMatrix
Return the Matthews correlation coefficient for category A.
max() - Method in class org.strbio.math.DMatrix
What's the maximum value in the matrix?
max() - Method in class org.strbio.math.DVector
What's the maximum value in the array?
max(int) - Method in class org.strbio.math.DVectorSet
Get maximum value in dimension d (i.e. 0 = x, 1 = y)
max() - Method in class org.strbio.math.FMatrix
What's the maximum value in the matrix?
max() - Method in class org.strbio.math.FVector
What's the maximum value in the array?
max() - Method in class org.strbio.math.IMatrix
What's the maximum value in the matrix?
max() - Method in class org.strbio.math.IVector
What's the maximum value in the array?
max_error - Variable in class org.strbio.util.NeuralNet
stopping parameter for scg and sd.
MAX_NAME_LENGTH - Static variable in class org.strbio.mol.Molecule
maximum name length, currently 4096 chars.
MAX_NAME_PRINTED - Static variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
maximum length of a name to print (beyond gets truncated)
maxerror - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
maxerror_2 - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
maxLength - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
largest protein length in set
maxN - Variable in class org.strbio.local.BlastP
Number of sequences returned (default = 250)
maxNameLength - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
largest name length in set
maxSampled(int) - Method in class org.strbio.math.Bin2D
Max value sampled in a particular bin.
maxSampled() - Method in class org.strbio.math.Sampler
what's the maximum value we sampled?
maxSeqNameLength - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
largest name of a sequence
MaxSub - Class in org.strbio.local
Class to run MaxSub Version 1.0, 10/9/02 - original version
MaxSub() - Constructor for class org.strbio.local.MaxSub
 
MaxSub.Results - Class in org.strbio.local
 
MaxSub.Results() - Constructor for class org.strbio.local.MaxSub.Results
 
maxX - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
Preferred width of component.
maxX() - Method in class org.strbio.util.graph.BarPlot
 
maxX() - Method in class org.strbio.util.graph.ClickablePointPlot
 
maxX - Variable in class org.strbio.util.graph.Graph2D
 
maxX() - Method in interface org.strbio.util.graph.Graphable2D
maximum x value that will be graphed.
maxX() - Method in class org.strbio.util.graph.PointPlot
 
maxY - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
Preferred height of component.
maxY() - Method in class org.strbio.util.graph.BarPlot
 
maxY() - Method in class org.strbio.util.graph.ClickablePointPlot
 
maxY - Variable in class org.strbio.util.graph.Graph2D
 
maxY() - Method in interface org.strbio.util.graph.Graphable2D
maximum y value that will be graphed.
maxY() - Method in class org.strbio.util.graph.PointPlot
 
maxZ() - Method in interface org.strbio.util.graph.Graphable3D
maximum z value that will be graphed.
maxZ() - Method in class org.strbio.util.graph.PointColorPlot
Returns the maximum z value currently being plotted.
Mclachlan() - Static method in class org.strbio.mol.lib.DayhoffMatrices
mclachlan matrix described in: McLachlan Andrew D.
mean() - Method in class org.strbio.math.DMatrix
Returns the mean value in the matrix.
mean() - Method in class org.strbio.math.FMatrix
Returns the mean value in the matrix.
median() - Method in class org.strbio.math.DVector
Returns the median value in the array.
median() - Method in class org.strbio.math.FVector
Returns the median value in the array.
medianRank() - Method in class org.strbio.mol.ThreadSet
median rank of structural matches
medianZ() - Method in class org.strbio.mol.ThreadSet
median z score of structural matches
MediumAppletJury - Class in org.strbio.mol.lib.pred2ary
The 'medium' network set. 8 jurors (level 1 and 2 networks, one of which uses reduced training) trained on training sets 0 through 7 only.
MediumAppletJury(Pred2aryApplet) - Constructor for class org.strbio.mol.lib.pred2ary.MediumAppletJury
Create a new jury.
MediumJury - Class in org.strbio.mol.lib.pred2ary
The 'medium' network set. 8 jurors (level 1 and 2 networks, one of which uses reduced training) trained on training sets 0 through 7 only.
MediumJury() - Constructor for class org.strbio.mol.lib.pred2ary.MediumJury
Create a new jury.
Melting - Class in org.strbio.local
Class to run melting Version 1.0, 9/10/01 - original version
Melting() - Constructor for class org.strbio.local.Melting
 
method - Static variable in class org.strbio.app.JThreadServer
 
method(int) - Method in class org.strbio.mol.lib.FRParameters
Get the ith method
methods - Variable in class org.strbio.mol.lib.FRParameters
vector of methods and their weights.
Mfold - Class in org.strbio.local
Class to run Mfold Version 1.0, 6/22/06, based on Primer3
Mfold() - Constructor for class org.strbio.local.Mfold
 
min() - Method in class org.strbio.math.DMatrix
What's the minimum value in the matrix?
min() - Method in class org.strbio.math.DVector
What's the minimum value in the array?
min(int) - Method in class org.strbio.math.DVectorSet
Get minimum value in dimension d (i.e. 0 = x, 1 = y)
min() - Method in class org.strbio.math.FMatrix
What's the minimum value in the matrix?
min() - Method in class org.strbio.math.FVector
What's the minimum value in the array?
min() - Method in class org.strbio.math.IMatrix
What's the minimum value in the matrix?
min() - Method in class org.strbio.math.IVector
What's the minimum value in the array?
min_v - Variable in class org.strbio.math.Bin
 
min_v - Variable in class org.strbio.math.FBin
 
Minarea - Class in org.strbio.local
Class to run minarea.
Minarea() - Constructor for class org.strbio.local.Minarea
 
MinareaAlign - Class in org.strbio.app
This does automatic minarea alignment and superposition on 2 sets of proteins.
MinareaAlign() - Constructor for class org.strbio.app.MinareaAlign
 
minareaAlign() - Method in class org.strbio.mol.AlignmentSet
get 'correct' alignment of sequence and fold using minarea.
minareaInfo(Printf) - Method in class org.strbio.mol.AlignmentSet
Shows some info from minarea: ratio score, RMS, and pct_id The minarea command is 'nw_minarea -A -g 0.1'.
minareaInfo(Printf) - Method in class org.strbio.mol.ThreadSet
Show info on all structural matches.
minareaInfoAll(Printf) - Method in class org.strbio.mol.ThreadSet
Show info on all seq/fold pairs.
minareaResults - Variable in class org.strbio.mol.AlignmentSet
minarea superposition results; assume fold rotated onto sequence.
MinareaResults - Class in org.strbio.mol.lib
Class containing results of minarea.
MinareaResults(String) - Constructor for class org.strbio.mol.lib.MinareaResults
parses results from a buffer.
MinareaResults() - Constructor for class org.strbio.mol.lib.MinareaResults
sets everything to 0.0, alignment to null.
minareaSuperimpose() - Method in class org.strbio.mol.AlignmentSet
Superimpose seq and fold.
minareaSuperimpose(Polymer, Polymer) - Static method in class org.strbio.mol.Polymer
Superimpose two polymers using minarea.
minareaUnSuperimpose() - Method in class org.strbio.mol.AlignmentSet
Undo minareaSuperimpose()
minimumFoldLength() - Method in class org.strbio.mol.Alignment
Return the last monomer in the fold which is aligned to something in the sequence.
minimumSize() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.AboutMessage
 
minimumSize() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.ProteinPane
 
minSampled(int) - Method in class org.strbio.math.Bin2D
Min value sampled in a particular bin.
minSampled() - Method in class org.strbio.math.Sampler
what's the minimum value we sampled?
minX() - Method in class org.strbio.util.graph.BarPlot
 
minX() - Method in class org.strbio.util.graph.ClickablePointPlot
 
minX - Variable in class org.strbio.util.graph.Graph2D
 
minX() - Method in interface org.strbio.util.graph.Graphable2D
minimum x value that will be graphed.
minX() - Method in class org.strbio.util.graph.PointPlot
 
minY() - Method in class org.strbio.util.graph.BarPlot
 
minY() - Method in class org.strbio.util.graph.ClickablePointPlot
 
minY - Variable in class org.strbio.util.graph.Graph2D
 
minY() - Method in interface org.strbio.util.graph.Graphable2D
minimum y value that will be graphed.
minY() - Method in class org.strbio.util.graph.PointPlot
 
minZ() - Method in interface org.strbio.util.graph.Graphable3D
minimum z value that will be graphed.
minZ() - Method in class org.strbio.util.graph.PointColorPlot
Returns the minimum z value currently being plotted.
Model - Class in org.strbio.app
Models a set of proteins based on saved alignments.
Model() - Constructor for class org.strbio.app.Model
 
model(Alignment) - Method in class org.strbio.local.Modeller
Make a model for a given alignment
Modeller - Class in org.strbio.local
Class to run Modeller Version 1.0, 10/3/02 - original version
Modeller() - Constructor for class org.strbio.local.Modeller
 
Modify2ary - Class in org.strbio.app
Modify 2ary structure prediction Version 1.0, 11/22/00 - original version
Modify2ary() - Constructor for class org.strbio.app.Modify2ary
 
molecularWeight() - Method in class org.strbio.mol.Monomer
molecular weight; default zero.
molecularWeight() - Method in class org.strbio.mol.Polymer
Calculate molecular weight
molecularWeight() - Method in class org.strbio.mol.Protein
Calculate molecular weight; add back the last water
molecularWeight() - Method in class org.strbio.mol.Residue
molecular weight for residue of a residue, minus 18 for the water missing in the peptide bond
Molecule - Class in org.strbio.mol
Class to represent a molecule.
Molecule() - Constructor for class org.strbio.mol.Molecule
Constructor makes everything null.
Molecule(Molecule) - Constructor for class org.strbio.mol.Molecule
copy another molecule, including the atoms.
monDistance - Variable in class org.strbio.mol.Polymer
Distance between every pair of different monomers.
Monomer - Class in org.strbio.mol
Class to represent a single monomer in a linear polymer.
Monomer() - Constructor for class org.strbio.mol.Monomer
Constructor makes everything null.
Monomer(char) - Constructor for class org.strbio.mol.Monomer
Construct from a character with the monomer type.
Monomer(String) - Constructor for class org.strbio.mol.Monomer
Construct from a string with the monomer type.
Monomer(Monomer) - Constructor for class org.strbio.mol.Monomer
copy another monomer, including the atoms.
monomer(int) - Method in class org.strbio.mol.Polymer
returns the N'th monomer in the sequence.
monomers - Variable in class org.strbio.mol.Polymer
Polymers are made out of a set of monomers.
mouseDown(Event, int, int) - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.ProteinPane
 
mouseDown(Event, int, int) - Method in class org.strbio.util.JMCScrollPane
mouse events are passed through to the child
mouseUp(Event, int, int) - Method in class org.strbio.util.JMCScrollPane
mouse events are passed through to the child
MULTI_CHAIN - Static variable in class org.strbio.mol.PolymerProperties
Polymer property: Are there multiple chains?
multiply(double) - Method in class org.strbio.math.DMatrix
Multiplies all values in this DMatrix by a specified double.
multiply(DMatrix, double) - Static method in class org.strbio.math.DMatrix
Multiplies a DMatrix by a double and returns a new DMatrix containing the result.
multiply(double, DMatrix) - Static method in class org.strbio.math.DMatrix
Multiplies a DMatrix by a double and returns a new DMatrix containing the result.
multiply(DMatrix) - Method in class org.strbio.math.DMatrix
Multiples this DMatrix by another DMatrix, and returns another DMatrix containing the result.
multiply(DMatrix, DMatrix) - Static method in class org.strbio.math.DMatrix
Multiplies two DMatrix's, and returns another DMatrix containing the result.
multiply(double) - Method in class org.strbio.math.DVector
Multiplies all values in this DVector by a specified int.
multiply(DVector, double) - Static method in class org.strbio.math.DVector
Multiplies a DVector by an int and returns a new DVector containing the result.
multiply(double, DVector) - Static method in class org.strbio.math.DVector
Multiplies a DVector by an int and returns a new DVector containing the result.
multiply(DMatrix) - Method in class org.strbio.math.DVector
Multplies this DVector by a DMatrix.
multiply(DVector, DMatrix) - Static method in class org.strbio.math.DVector
Multplies a DVector by a DMatrix, and returns a new DVector with the result.
multiply(DMatrix, DVector) - Static method in class org.strbio.math.DVector
Multplies a DVector by a DMatrix, and returns a new DVector with the result.
multiply(float) - Method in class org.strbio.math.FMatrix
Multiplies all values in this FMatrix by a specified float.
multiply(FMatrix, float) - Static method in class org.strbio.math.FMatrix
Multiplies a FMatrix by a float and returns a new FMatrix containing the result.
multiply(float, FMatrix) - Static method in class org.strbio.math.FMatrix
Multiplies a FMatrix by a float and returns a new FMatrix containing the result.
multiply(FMatrix) - Method in class org.strbio.math.FMatrix
Multiples this FMatrix by another FMatrix, and returns another FMatrix containing the result.
multiply(FMatrix, FMatrix) - Static method in class org.strbio.math.FMatrix
Multiplies two FMatrix's, and returns another FMatrix containing the result.
multiply(float) - Method in class org.strbio.math.FVector
Multiplies all values in this FVector by a specified int.
multiply(FVector, float) - Static method in class org.strbio.math.FVector
Multiplies a FVector by an int and returns a new FVector containing the result.
multiply(float, FVector) - Static method in class org.strbio.math.FVector
Multiplies a FVector by an int and returns a new FVector containing the result.
multiply(FMatrix) - Method in class org.strbio.math.FVector
Multplies this FVector by a FMatrix.
multiply(FVector, FMatrix) - Static method in class org.strbio.math.FVector
Multplies a FVector by a FMatrix, and returns a new FVector with the result.
multiply(FMatrix, FVector) - Static method in class org.strbio.math.FVector
Multplies a FVector by a FMatrix, and returns a new FVector with the result.
multiply(int) - Method in class org.strbio.math.IMatrix
Multiplies all values in this IMatrix by a specified int.
multiply(IMatrix, int) - Static method in class org.strbio.math.IMatrix
Multiplies a IMatrix by an int and returns a new IMatrix containing the result.
multiply(int, IMatrix) - Static method in class org.strbio.math.IMatrix
Multiplies a IMatrix by an int and returns a new IMatrix containing the result.
multiply(int) - Method in class org.strbio.math.IVector
Multiplies all values in this IVector by a specified int.
multiply(IVector, int) - Static method in class org.strbio.math.IVector
Multiplies a IVector by an int and returns a new IVector containing the result.
multiply(int, IVector) - Static method in class org.strbio.math.IVector
Multiplies a IVector by an int and returns a new IVector containing the result.
Muscle - Class in org.strbio.local
Class to run Muscle Verions 1.1, 3/30/07 - added ability to pass other options to muscle Version 1.0, 11/27/06 - original version, based on ClustalW
Muscle() - Constructor for class org.strbio.local.Muscle
 

N

n() - Method in class org.strbio.math.DVectorSet
How many DVectors are in the set?
n - Variable in class org.strbio.mol.Atom
Atom serial number.
n() - Method in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea.ClickedArea
How many areas of interest are there?
n - Variable in class org.strbio.mol.Monomer
sequence number, which is the number in the file for files (like PDB) that contain this info; otherwise numbering starts at 0.
n() - Method in class org.strbio.mol.PolymerSet
How many polymers are in the set?
n() - Method in class org.strbio.util.db.Data
How many elements of data are there?
nAbove(double) - Method in class org.strbio.mol.lib.ThreadResults
How many folds are there above or equal to a given probability (including 'no match')
nail - Variable in class org.strbio.mol.AlignmentSet
A vector of 'nailed down' seq-fold monomer pairs.
nAligned() - Method in class org.strbio.mol.Alignment
Returns the number of aligned positions.
name - Variable in class org.strbio.mol.Atom
Name of the atom (as used in the PDB)... i.e.
name - Variable in class org.strbio.mol.Molecule
Name of this molecule.
name2ary(int) - Method in class org.strbio.mol.lib.pred2ary.TPSet
return name of various types of 2ary str
nAtoms() - Method in class org.strbio.mol.Monomer
How many atoms are there?
nAtomsWithCoord() - Method in class org.strbio.mol.Monomer
How many atoms are there with known coordinates?
nCA - Variable in class org.strbio.local.MaxSub.Results
 
net - Variable in class org.strbio.mol.lib.pred2ary.TrainingSet
 
net_2 - Variable in class org.strbio.mol.lib.pred2ary.TrainingSet
 
networkLabel - Variable in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
NeuralNet - Class in org.strbio.util
Class encapsulating a neural network.
NeuralNet(int[], Random) - Constructor for class org.strbio.util.NeuralNet
Initialize a new network with a given topology and a given random number generator.
NeuralNet(int[]) - Constructor for class org.strbio.util.NeuralNet
Initialize a new network with a given topology and a new random seed
NeuralNet(BufferedReader) - Constructor for class org.strbio.util.NeuralNet
Initialize a network by reading it out of an open BufferedReader.
NeuralNet(DataInputStream) - Constructor for class org.strbio.util.NeuralNet
Initialize a network by reading it out of an open DataInputStream.
NeuralNet(String) - Constructor for class org.strbio.util.NeuralNet
Initialize a network by reading it out of a file with a given name.
NeuralNet() - Constructor for class org.strbio.util.NeuralNet
Make an 'empty' neural network.. must be loaded out of file to be useful.
NeuralNet.Trainable - Interface in org.strbio.util
This is the interface you have to implement for objects that are to be used used in training neural nets.
new_cutoff - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
newLine() - Method in class org.strbio.io.PrintfStream
Print a newline to the output, in a system-independent manner.
newMonomer() - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
 
newMonomer(char) - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
 
newMonomer(String) - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
 
newMonomer() - Method in class org.strbio.mol.Polymer
This should return a new monomer of whatever type this polymer is made of (i.e.
newMonomer(char) - Method in class org.strbio.mol.Polymer
This should return a new monomer of whatever type this polymer is made of (i.e.
newMonomer(String) - Method in class org.strbio.mol.Polymer
This should return a new monomer of whatever type this polymer is made of (i.e.
newMonomer() - Method in class org.strbio.mol.Profile
Profiles are made of ProfRes-type monomers.
newMonomer(char) - Method in class org.strbio.mol.Profile
 
newMonomer(String) - Method in class org.strbio.mol.Profile
 
newMonomer() - Method in class org.strbio.mol.ProfilePSI
This returns a new ProfResPSI.
newMonomer(char) - Method in class org.strbio.mol.ProfilePSI
This returns a new ProfResPSI.
newMonomer(String) - Method in class org.strbio.mol.ProfilePSI
This returns a new ProfResPSI.
newMonomer() - Method in class org.strbio.mol.Protein
This should return a new monomer of whatever type this polymer is made of (i.e.
newMonomer(char) - Method in class org.strbio.mol.Protein
This should return a new monomer of whatever type this polymer is made of (i.e.
newMonomer(String) - Method in class org.strbio.mol.Protein
This should return a new monomer of whatever type this polymer is made of (i.e.
newPolymer() - Method in class org.strbio.mol.lib.pred2ary.PCPSet
 
newPolymer(ProteinSet) - Method in class org.strbio.mol.lib.pred2ary.PCPSet
 
newPolymer() - Method in class org.strbio.mol.PolymerSet
Create a new polymer to add to the set... this may be replaced by subclasses which encapsulate specific polymers.
newPolymer() - Method in class org.strbio.mol.ProfilePSISet
 
newPolymer() - Method in class org.strbio.mol.ProfileSet
Everything in this set should be a Profile (or subclass of it).
newPolymer(ProteinSet) - Method in class org.strbio.mol.ProfileSet
 
newPolymer() - Method in class org.strbio.mol.ProteinSet
Make sure this set contains only Proteins.
newProfileSet() - Method in class org.strbio.app.JThread
 
newProfileSet() - Method in class org.strbio.app.JThreadText
 
newProfileSet() - Method in class org.strbio.util.ui.ProfileGUIApp
Return a new profile set of whatever subclass is wanted.
newSM(int) - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
Make n stats matrices, keeping existing ones also.
newSM(int) - Method in class org.strbio.mol.lib.pred2ary.TPSet
make/delete stats for all proteins in a set
newSM(int) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
make/delete stats for all proteins in a set, and related sets
next - Variable in class org.strbio.mol.AtomNode
the next atom in the list
next() - Method in class org.strbio.mol.AtomNode
return the next AtomNode
next - Variable in class org.strbio.mol.lib.ScoreList
The next in the list, or null if there are no more scoring functions.
next() - Method in class org.strbio.mol.Monomer
return the next monomer in the polymer.
next() - Method in interface org.strbio.util.DLinkedList.Node
This should return the next node in the list, or null if there is none.
nextElement() - Method in class org.strbio.mol.PolymerSet.PolymerEnumeration
Get the next polymer.
nextElement - Variable in class org.strbio.util.db.Data.InfoEnumeration
 
nextElement() - Method in class org.strbio.util.db.Data.InfoEnumeration
 
nID() - Method in class org.strbio.mol.Alignment
Returns the number of identical residues in the alignment.
nJurors - Variable in class org.strbio.mol.lib.pred2ary.Jury
How many jurors there are in the jury.
nJurors() - Method in class org.strbio.mol.lib.pred2ary.Jury
See how many jurors are in the jury.
nMatches() - Method in class org.strbio.mol.ThreadSet
How many structural matches do we know about?
nMethods() - Method in class org.strbio.mol.lib.FRParameters
how many methods are there?
nMonomers() - Method in class org.strbio.mol.Polymer
How many monomers do we have?
nMonomers(char) - Method in class org.strbio.mol.Polymer
How many monomers do we have of type c?
nMonomers() - Method in class org.strbio.mol.PolymerSet
total # of monomers in the set
node(int) - Method in class org.strbio.util.DLinkedList
returns the N'th node in the list, starting at zero.
nodes() - Method in class org.strbio.util.DLinkedList
how many nodes do we think are in the list?
nonGapMonomers() - Method in class org.strbio.mol.Polymer
How many non-gap monomers do we have?
nonZeroFrequency - Variable in class org.strbio.mol.ProfRes
Index of non-zero frequencies, if calculated.
norm() - Method in class org.strbio.math.DVector
What's the norm of this array?
norm() - Method in class org.strbio.math.FVector
What's the norm of this array?
normalize() - Method in class org.strbio.math.DMatrix
Rescale matrix so the average is one.
normalize() - Method in class org.strbio.math.DVector
Rescale array so the norm is one.
normalize() - Method in class org.strbio.math.FMatrix
Rescale matrix so the average is one.
normalize() - Method in class org.strbio.math.FVector
Rescale array so the norm is one.
normalizeWeights() - Method in class org.strbio.mol.lib.AlignmentParameters
make the relative absolute weights for the scoring functions add up to one.
normalizeWeights() - Method in class org.strbio.mol.lib.ScoreList
make the absolute value of all the weights in this list (starting at this) add up to one.
noSpaceNames() - Method in class org.strbio.mol.PolymerSet
strip names after the first space
NOTEQUAL - Static variable in class org.strbio.mol.lib.Score2ary
 
NOTEQUAL - Static variable in class org.strbio.mol.lib.ScoreFischer
 
NOTEQUAL - Static variable in class org.strbio.mol.lib.ScoreID
 
NOTEQUAL - Static variable in class org.strbio.mol.lib.ScorePred2ary
 
NOTEQUAL - Static variable in class org.strbio.mol.lib.ScorePredFreq
 
NOTEQUAL - Static variable in class org.strbio.mol.lib.ScoreScaledID
 
notifyOfChange() - Method in class org.strbio.util.DLinkedList
Tell the list you have made some changes to it, but not necessarily changed the number of objects.
nPolymersInFile(BufferedReader) - Method in class org.strbio.mol.PolymerSet
Count the number of polymers in a file.
nSame() - Method in class org.strbio.mol.ThreadSet
How many seq-fold pairs are the same?
nsamples - Variable in class org.strbio.math.Bin
 
nsamples - Variable in class org.strbio.math.FBin
 
NSPred2ary - Class in org.strbio.app
Predict secondary structure/class, using profiles.
NSPred2ary() - Constructor for class org.strbio.app.NSPred2ary
This handles the interactive, GUI version of the program.
NSPred2ary(String[]) - Constructor for class org.strbio.app.NSPred2ary
This constructor handles the non-interactive text version of the program.
NSPred2ary.AboutMessage - Class in org.strbio.app
 
NSPred2ary.AboutMessage() - Constructor for class org.strbio.app.NSPred2ary.AboutMessage
 
nstats - Variable in class org.strbio.mol.lib.pred2ary.TPSet
 
nSuperimposed - Variable in class org.strbio.local.MaxSub.Results
 
Nucleotide - Class in org.strbio.mol
Class to represent a single nucleotide Version 1.0, 8/17/01 - original version, based on org.strbio.mol.Residue
Nucleotide() - Constructor for class org.strbio.mol.Nucleotide
 
Nucleotide(char) - Constructor for class org.strbio.mol.Nucleotide
Make a new nucleotide of a given type.
Nucleotide(Nucleotide) - Constructor for class org.strbio.mol.Nucleotide
copy another residue, including the atoms.
num2Res(int) - Static method in class org.strbio.mol.Residue
Convert a number to amino acid one letter code (0-20), in the order shown in Residue.oneLetter.
num2ResBLAST(int) - Static method in class org.strbio.mol.lib.BlastConstants
Convert a number to amino acid one letter code (0-25), in the order shown in oneLetterBlast
num2ResDefay(int) - Static method in class org.strbio.mol.Residue
Convert a number to amino acid one letter code (0-20), in the order shown in Residue.oneLetterDefay.
number - Variable in class org.strbio.util.db.CATHInfo
CATH number; i.e. 2.20.200.10...
number - Variable in class org.strbio.util.db.SCOPInfo
SCOP number; i.e. 1.1.1.1.1
numberFound(int) - Method in class org.strbio.mol.ThreadSet
number of structural matches in top N scores (cutoff)
numBuffer - Variable in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
numsmooth - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
numsmooth_2 - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 

O

objectiveFunction() - Method in interface org.strbio.util.CGOptimizer.Optimizable
The variables will be optimized in such a way as to minimize the value returned by calls to objectiveFunction().
objectiveFunction() - Method in interface org.strbio.util.Hooke.Optimizable
The variables will be optimized in such a way as to minimize the value returned by calls to objectiveFunction().
objectiveGradient(double[]) - Method in interface org.strbio.util.CGOptimizer.Optimizable
The gradient function must return the gradient at the current point with respect to each variable in the vector.
occupancy - Variable in class org.strbio.mol.Atom
Occupancy in a structure.
oldAlignStrMatchesMinarea() - Method in class org.strbio.mol.ThreadSet
Deprecated.  
OldBufferedPrintfTextArea - Class in org.strbio.io
A TextArea that you can do printf() on, like a civilized (C) programmer.
OldBufferedPrintfTextArea() - Constructor for class org.strbio.io.OldBufferedPrintfTextArea
 
OldBufferedPrintfTextArea(String) - Constructor for class org.strbio.io.OldBufferedPrintfTextArea
 
OldBufferedPrintfTextArea(int, int) - Constructor for class org.strbio.io.OldBufferedPrintfTextArea
 
OldBufferedPrintfTextArea(String, int, int) - Constructor for class org.strbio.io.OldBufferedPrintfTextArea
 
oldCenterFrame(Frame) - Static method in class org.strbio.util.JMC
Center a frame on the screen.
OldPrintfJLabel - Class in org.strbio.io
A JLabel that you can do printf() on, like a civilized (C) programmer.
OldPrintfJLabel() - Constructor for class org.strbio.io.OldPrintfJLabel
 
OldPrintfJLabel(String) - Constructor for class org.strbio.io.OldPrintfJLabel
 
OldPrintfJTextArea - Class in org.strbio.io
A JTextArea that you can do printf() on, like a civilized (C) programmer.
OldPrintfJTextArea() - Constructor for class org.strbio.io.OldPrintfJTextArea
 
OldPrintfJTextArea(String) - Constructor for class org.strbio.io.OldPrintfJTextArea
 
OldPrintfJTextArea(int, int) - Constructor for class org.strbio.io.OldPrintfJTextArea
 
OldPrintfJTextArea(String, int, int) - Constructor for class org.strbio.io.OldPrintfJTextArea
 
OldPrintfTextArea - Class in org.strbio.io
A TextArea that you can do printf() on, like a civilized (C) programmer.
OldPrintfTextArea() - Constructor for class org.strbio.io.OldPrintfTextArea
 
OldPrintfTextArea(String) - Constructor for class org.strbio.io.OldPrintfTextArea
 
OldPrintfTextArea(int, int) - Constructor for class org.strbio.io.OldPrintfTextArea
 
OldPrintfTextArea(String, int, int) - Constructor for class org.strbio.io.OldPrintfTextArea
 
oldRandomlyLocateFrame(Frame) - Static method in class org.strbio.util.JMC
Randomly locate a frame somewhere on the screen where it fits.
one2Three(char) - Static method in class org.strbio.mol.Residue
Convert your 1-letter code into 3-letter code.
oneLetter - Static variable in class org.strbio.mol.Nucleotide
unlike Residue, don't make - a valid type
oneLetter - Static variable in class org.strbio.mol.Residue
one letter code, in alphabetical order by 3-letter code.
oneLetter - Static variable in class org.strbio.raf.RAFResidue
one letter code, in same order as 3-letter code.
oneLetterBLAST - Static variable in class org.strbio.mol.lib.BlastConstants
one letter code used by BLAST.
oneLetterBLAST - Static variable in class org.strbio.mol.Residue
one letter code used by BLAST.
oneLetterDefay - Static variable in class org.strbio.mol.Residue
one letter code, in alphabetical order by 1-letter code.
oneLetterHSSP - Static variable in class org.strbio.mol.ProfRes
one letter code, in the order used in the HSSP.
openReader(String) - Static method in class org.strbio.IO
Open a file with transparent gunzipping.
openReaderResource(String, Object) - Static method in class org.strbio.IO
Open a file stored somewhere in the CLASSPATH (a resource, in Java terms).
openStream(String) - Static method in class org.strbio.IO
Open a file with transparent gunzipping.
openStreamResource(String, Object) - Static method in class org.strbio.IO
Open a file stored somewhere in the CLASSPATH (a resource, in Java terms).
OptimalAAParameters - Class in org.strbio.mol.lib
The optimal alignment parameters for maximizing alignment accuracy.
OptimalAAParameters() - Constructor for class org.strbio.mol.lib.OptimalAAParameters
Optimal parameters are: 70% backbone phi/psi potential, 30% psiblast, affine gap penalty of 3.955210, 0.124641 (with overhanging ends penalized).
OptimalAAParametersFR - Class in org.strbio.mol.lib
The optimal fold recognition parameters.
OptimalAAParametersFR() - Constructor for class org.strbio.mol.lib.OptimalAAParametersFR
THESE ARE CURRENTLY THE AA PARAMETERS.
OptimalFRParameters - Class in org.strbio.mol.lib
The optimal fold recognition parameters.
OptimalFRParameters() - Constructor for class org.strbio.mol.lib.OptimalFRParameters
optimal fr parameters, by top5
optimize() - Method in interface org.strbio.util.CGOptimizer
optimizes your function, returning the number of steps.
optimize(Hooke.Optimizable, double, double, int) - Static method in class org.strbio.util.Hooke
Optimize an optimizable object.
optimizeAlignment(Printf) - Method in class org.strbio.mol.ThreadSet
optimize the gap penalties for highest alignment accuracy.
optimizeASns(Printf) - Method in class org.strbio.mol.ThreadSet
optimize the gap penalties for highest asns(1).
optimizeMedianRank(Printf) - Method in class org.strbio.mol.ThreadSet
optimize the gap penalties for best median rank of known structural matches.
optimizeRank(Printf) - Method in class org.strbio.mol.ThreadSet
optimize the gap penalties for best average rank of known structural matches.
optimizeRankRW(Printf) - Method in class org.strbio.mol.ThreadSet
optimize the gap penalties for best reciprocal weighted average rank of known structural matches.
optimizeTopN(int, Printf) - Method in class org.strbio.mol.ThreadSet
optimize the gap penalties for most correct structural matches in the top N.
optimizeZScore(Printf) - Method in class org.strbio.mol.ThreadSet
optimize the gap penalties for highest average Z score among structural matches.
org.strbio - package org.strbio
The StrBio library is a set of Java classes useful for development of software for computational structural biology research.
org.strbio.app - package org.strbio.app
These classes are stand-alone applications.
org.strbio.io - package org.strbio.io
These classes perform I/O functions, especially related to stream I/O or string formatting using C-like "Printf" calls.
org.strbio.local - package org.strbio.local
These classes are for running or exchanging data with local programs (other programs installed on your computer).
org.strbio.math - package org.strbio.math
These classes perform functions related to mathematics and statistics.
org.strbio.mol - package org.strbio.mol
These classes represent objects or concepts useful to structural biologists.
org.strbio.mol.lib - package org.strbio.mol.lib
These classes represent conceptual objects used in structural biology algorithms.
org.strbio.mol.lib.pred2ary - package org.strbio.mol.lib.pred2ary
These classes represent conceptual objects used in the Pred2ary program, which are probably not very useful for other purposes.
org.strbio.net - package org.strbio.net
These classes are for running or exchanging data with non-local programs (i.e., programs that you run by submitting data to a web page).
org.strbio.raf - package org.strbio.raf
These classes are related to the RAF file format used by the ASTRAL database.
org.strbio.sql - package org.strbio.sql
These classes perform generally useful functions related to SQL.
org.strbio.util - package org.strbio.util
These classes perform general purpose utility functions.
org.strbio.util.db - package org.strbio.util.db
These classes are a primitive interface to store and manipulate protein structure information from various commonly used databases.
org.strbio.util.graph - package org.strbio.util.graph
These classes perform utility functions related to 2D and 3D graphics.
org.strbio.util.ui - package org.strbio.util.ui
These classes are general purpose utility functions related to a program's user interface.
outfile - Variable in class org.strbio.mol.lib.pred2ary.Jury
File to print output to.
output(int) - Method in class org.strbio.util.NeuralNet
return a network output

P

p - Variable in class org.strbio.app.JThreadText
 
p(int) - Method in class org.strbio.math.DVectorSet
short for point(i)
p - Variable in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
p - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
Profiles to display.
p(int) - Method in class org.strbio.mol.PolymerSet
short for polymer(i)
p - Variable in class org.strbio.util.ui.ProfileGUIApp
 
p_set - Variable in class org.strbio.mol.lib.pred2ary.TrainingSet
 
pad(int) - Method in class org.strbio.mol.Polymer
pads a sequence out (at the end) to a specified number of nmon using '.' as a filler residue
padX - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
Padding constant for X dimension.
padY - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
Padding constant for Y dimension.
paint(Graphics) - Method in class org.strbio.app.NSPred2ary.AboutMessage
 
paint(Graphics) - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.AboutMessage
 
paint(Graphics) - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.ProteinPane
 
paint(Graphics, Rectangle) - Method in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
Paint the area within a viewport; the parent component should provide the dimensions.
paint(Graphics) - Method in class org.strbio.util.JMCScrollPane
 
paintArea(Graphics, int, int) - Method in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
Paint graphics from y=yLo to y=yHi.
paintAxisScale(Graphics, Rectangle) - Method in interface org.strbio.util.graph.AxisScale
Draw the axis scale, relative to a given rectangle containing the graph.
paintAxisScale(Graphics, Rectangle) - Method in class org.strbio.util.graph.XAxisScale
Draw the axis scale, relative to a given rectangle containing the graph.
paintAxisScale(Graphics, Rectangle) - Method in class org.strbio.util.graph.YAxisScale
Draw the axis scale, relative to a given rectangle containing the graph.
paintComponent(Graphics) - Method in class org.strbio.util.BarLegend
 
paintComponent(Graphics) - Method in class org.strbio.util.DensityPlot
 
paintComponent(Graphics) - Method in class org.strbio.util.graph.Graph2D
display on screen.
paintGraph(Graphics, Rectangle, Graph2D) - Method in class org.strbio.util.graph.BarPlot
 
paintGraph(Graphics, Rectangle, Graph2D) - Method in class org.strbio.util.graph.ClickablePointPlot
 
paintGraph(Graphics, int, int) - Method in class org.strbio.util.graph.Graph2D
Displays everything on a given sized area (printer page, or screen).
paintGraph(Graphics, Rectangle, Graph2D) - Method in interface org.strbio.util.graph.Graphable2D
draw the graph, in a given rectangle.
paintGraph(Graphics, Rectangle, Graph2D) - Method in class org.strbio.util.graph.PointPlot
 
paintLegend(Graphics, int, int) - Method in class org.strbio.util.graph.ColorScaleLegend
 
paintLegend(Graphics, int, int) - Method in interface org.strbio.util.graph.Legend
draw the legend, at a given top, left position.
paintLegend(Graphics, int, int) - Method in class org.strbio.util.graph.PointLegend
 
paintPointAt(int, int, Graphics) - Method in class org.strbio.util.graph.CirclePoint
draw the point, at a given center position.
paintPointAt(int, int, Graphics) - Method in class org.strbio.util.graph.DotPoint
draw the point, at a given center position.
paintPointAt(int, int, Graphics) - Method in interface org.strbio.util.graph.PointType
draw the point, at a given center position.
paintPointAt(int, int, Graphics) - Method in class org.strbio.util.graph.UnfilledCirclePoint
draw the point, at a given center position.
paintVectorAt(int, int, DVector, Graphics) - Method in class org.strbio.util.graph.PointColorPlot
This is a function to put a dot wherever a point should be plotted.
paintVectorAt(int, int, DVector, Graphics) - Method in class org.strbio.util.graph.PointPlot
Draw one of the points somewhere.
parent - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
This is the component this is displayed in.
parent - Variable in class org.strbio.util.ui.AboutDialog
Parent app for this dialog.
parse(String) - Method in class org.strbio.mol.lib.MinareaResults
This should parse the results, except alignment, out of the saved line.
pbm - Variable in class org.strbio.local.PSIBlastP
 
pcp(int) - Method in class org.strbio.mol.lib.pred2ary.PCPSet
Return the i'th protein in the set.
PCPRes - Class in org.strbio.mol.lib.pred2ary
ProfRes with a couple extras useful for 2ary structure prediction.
PCPRes() - Constructor for class org.strbio.mol.lib.pred2ary.PCPRes
Most constructors just call the superclass one.
PCPRes(char) - Constructor for class org.strbio.mol.lib.pred2ary.PCPRes
 
PCPRes(String) - Constructor for class org.strbio.mol.lib.pred2ary.PCPRes
 
PCPRes(PCPRes) - Constructor for class org.strbio.mol.lib.pred2ary.PCPRes
Copy another PCPRes.
PCPSet - Class in org.strbio.mol.lib.pred2ary
Class to represent a set of profiles with information for 2ary structure prediction.
PCPSet() - Constructor for class org.strbio.mol.lib.pred2ary.PCPSet
 
PCPSet(PCPSet) - Constructor for class org.strbio.mol.lib.pred2ary.PCPSet
 
pctAligned() - Method in class org.strbio.mol.Alignment
Returns the percent aligned residues in the alignment.
pctAligned - Variable in class org.strbio.mol.AlignmentStats
pct aligned, correct.
pctAlignedLong - Variable in class org.strbio.mol.AlignmentStats
pct aligned, correct, vs longest seq
pctAlignedLongest() - Method in class org.strbio.mol.Alignment
Returns the percent aligned residues in the alignment, relative to the longer of the two sequences.
pctExposed - Variable in class org.strbio.mol.Residue
Percentage of surface-exposed area, from 0 - 100.0.
pctID() - Method in class org.strbio.mol.Alignment
Returns the percent identical residues in the alignment.
pctID - Variable in class org.strbio.mol.AlignmentStats
pct ID, correct.
pctRight() - Method in class org.strbio.math.CorrectMatrix
return percent right, from 0 to 100.
pctRight() - Method in class org.strbio.math.SimMatrix
return percent right, from 0 to 100.
pctRight() - Method in class org.strbio.math.StatsMatrix
return percent right, from 0 to 100.
pctRight(int) - Method in class org.strbio.mol.AlignmentSet
evaluates accuracy the calculated alignment.
pctRight(int) - Method in class org.strbio.mol.ThreadSet
Returns pctRight for the structural matches.
pctRight1 - Variable in class org.strbio.mol.AlignmentStats
percent correct, tolerance 1.
pctRightActually(int) - Method in class org.strbio.math.CorrectMatrix
Return the percent right only for predictions of items which actually belonged to category A.
pctRightActually(int) - Method in class org.strbio.math.SimMatrix
Return the percent right only for predictions of items which actually belonged to category A.
pctRightActually(int) - Method in class org.strbio.math.StatsMatrix
Return the percent right only for predictions of items which actually belonged to category A.
pctRightPred(int) - Method in class org.strbio.math.SimMatrix
Return the percent right only for predictions of items which were predicted to be in category A.
pd - Variable in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.ProteinPane
 
pda - Variable in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
PDB - Class in org.strbio.local
Class to access a local copy of the PDB.
PDB() - Constructor for class org.strbio.local.PDB
 
PDBInfo - Class in org.strbio.util.db
This is a class containing info that is found in PDB files, and links to related info.
PDBInfo() - Constructor for class org.strbio.util.db.PDBInfo
 
pearson() - Method in class org.strbio.math.Bin2D
Returns the Pearson correlation coefficient R of values sampled.
pearson(DMatrix) - Method in class org.strbio.math.DMatrix
Returns the Pearson correlation coefficient R of values in this matrix with values in another matrix.
pearson(DVector) - Method in class org.strbio.math.DVector
Returns the Pearson correlation coefficient R of values in this array with values in another array.
pearson(FMatrix) - Method in class org.strbio.math.FMatrix
Returns the Pearson correlation coefficient R of values in this matrix with values in another matrix.
pearson(FVector) - Method in class org.strbio.math.FVector
Returns the Pearson correlation coefficient R of values in this array with values in another array.
phi - Variable in class org.strbio.mol.lib.MinareaResults
 
phi() - Method in class org.strbio.mol.Residue
Phi is the bond angle between C(n-1), N(n), CA(n), C(n).
pMatch - Variable in class org.strbio.mol.lib.ThreadResults
A vector of the probabilities that each protein in the library is a match.
pNoMatch() - Method in class org.strbio.mol.lib.ThreadResults
Calculate the probability that no match is in the library.
point(int) - Method in class org.strbio.math.DVectorSet
Return the i'th point in the set.
PointColorPlot - Class in org.strbio.util.graph
A graph that displays a point plot (a 2D graph of a bunch of points), with the 3rd axis in color.
PointColorPlot(DVectorSet, ColorScale) - Constructor for class org.strbio.util.graph.PointColorPlot
Start with just a set of points to plot.
PointLegend - Class in org.strbio.util.graph
A legend for points, showing a the point next to a label.
PointLegend(PointType, Font, FontMetrics, String) - Constructor for class org.strbio.util.graph.PointLegend
Initialize new legend.
PointPlot - Class in org.strbio.util.graph
A component that displays a point plot (a 2D graph of a bunch of points).
PointPlot(DVectorSet) - Constructor for class org.strbio.util.graph.PointPlot
initialize with a set of points.
points - Variable in class org.strbio.util.graph.ClickablePointPlot
This is a vector of points to plot.
points - Variable in class org.strbio.util.graph.PointPlot
This is a vector of points to plot.
PointType - Interface in org.strbio.util.graph
A point plotted on a PointPlot, for example.
Polymer - Class in org.strbio.mol
Class to represent a linear, unbranched polymer.
Polymer() - Constructor for class org.strbio.mol.Polymer
Create a new polymer with no information known about it.
Polymer(Polymer) - Constructor for class org.strbio.mol.Polymer
Copy another Polymer, making copies of all data fields.
Polymer(String) - Constructor for class org.strbio.mol.Polymer
Make a new polymer from a string representing the monomer sequence.
polymer(int) - Method in class org.strbio.mol.PolymerSet
Return the i'th polymer in the set.
PolymerProperties - Class in org.strbio.mol
Class containing all possible Polymer properties, in one place, rather than spreading them out among many files.
PolymerProperties() - Constructor for class org.strbio.mol.PolymerProperties
 
polymers() - Method in class org.strbio.mol.PolymerSet
Return an enumeration of polymers in the set.
PolymerSet - Class in org.strbio.mol
Class to represent a set of polymers to be acted on in a group.
PolymerSet() - Constructor for class org.strbio.mol.PolymerSet
Create an empty set of polymers.
PolymerSet(PolymerSet) - Constructor for class org.strbio.mol.PolymerSet
Create a set by copying another set, but not the polymers in it.
PolymerSet.PolymerEnumeration - Class in org.strbio.mol
An enumeration of Polymers, that gets them one by one out of a file.
PolymerSet.PolymerEnumeration(BufferedReader, Printf, PolymerSet) - Constructor for class org.strbio.mol.PolymerSet.PolymerEnumeration
create an enumeration on a given file, with a given polymer set.
polymersInFile(BufferedReader) - Method in class org.strbio.mol.PolymerSet
Return an enumeration of polymers in a file.
polymersInFile(BufferedReader, Printf) - Method in class org.strbio.mol.PolymerSet
Return an enumeration of polymers in a file.
polymersInFile(String, Printf) - Method in class org.strbio.mol.PolymerSet
Return an enumeration of polymers in a file.
polymersInFile(String) - Method in class org.strbio.mol.PolymerSet
Return an enumeration of polymers in a file.
polymersToArray() - Method in class org.strbio.mol.Alignment
Sets up array based on alignment in Polymers.
posFreqs - Variable in class org.strbio.mol.lib.PSIBlastMatrices
N x 20 matrix of frequencies at each position.
positionSpecificScore(char) - Method in class org.strbio.mol.ProfResPSI
Return the position specific score for aligning this position to a certain type of residue.
positionSpecificScore(int) - Method in class org.strbio.mol.ProfResPSI
Return the position specific score for aligning this position to a certain type (1-20) of residue.
posMatrix - Variable in class org.strbio.mol.lib.PSIBlastMatrices
Position-specific scoring matrix, N x 20.
posScore - Variable in class org.strbio.mol.ProfResPSI
Position dependent alignment score, as in PSI-BLAST.
posToFreqs() - Method in class org.strbio.mol.lib.PSIBlastMatrices
Convert pseudo-count frequencies to a score matrix.
PR(int) - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
 
pRank(int) - Method in class org.strbio.mol.lib.ThreadResults
Get probability for rank N (starting at 0)... this includes 'no match'.
PRECALC_ALPHATAU - Static variable in class org.strbio.mol.PolymerProperties
Protein property: is there precalculated information on backbone alpha/tau dihedral angles?
PRECALC_CW - Static variable in class org.strbio.mol.PolymerProperties
Profile property: are R&S Conservation weights calculated?
PRECALC_FREQ - Static variable in class org.strbio.mol.PolymerProperties
Profile property: precalculated frequencies
PRECALC_PHIPSI - Static variable in class org.strbio.mol.PolymerProperties
Protein property: is there precalculated information on backbone phi/psi dihedral angles?
preCalculateAlphaTau() - Method in class org.strbio.mol.Protein
pre-calculates cAlpha and cTau for all residues.
preCalculateAngles() - Method in class org.strbio.mol.Protein
pre-calculates cPhi, cPsi, cAlpha, and cTau for all residues.
preCalculatePhiPsi() - Method in class org.strbio.mol.Protein
pre-calculates cPhi and cPsi for all residues.
Pred2ary - Class in org.strbio.app
Predict secondary structure/class, using profiles.
Pred2ary() - Constructor for class org.strbio.app.Pred2ary
This handles the interactive, GUI version of the program.
Pred2ary(String[]) - Constructor for class org.strbio.app.Pred2ary
This constructor handles the non-interactive text version of the program.
Pred2ary - Class in org.strbio.mol.lib
Predicts secondary structure using JMC's Pred2ary program.
Pred2ary() - Constructor for class org.strbio.mol.lib.Pred2ary
Initialize using the large jury.
Pred2ary(Jury) - Constructor for class org.strbio.mol.lib.Pred2ary
Initialize with a given jury set.
Pred2aryApplet - Class in org.strbio.mol.lib.pred2ary
Predict secondary structure/class, using profiles.
Pred2aryApplet() - Constructor for class org.strbio.mol.lib.pred2ary.Pred2aryApplet
 
Pred2aryAppletFrame - Class in org.strbio.mol.lib.pred2ary
Predict secondary structure/class, using profiles.
Pred2aryAppletFrame(Pred2aryApplet) - Constructor for class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
This handles the interactive, GUI version of the program.
Pred2aryAppletFrame.AboutDialog - Class in org.strbio.mol.lib.pred2ary
This gets displayed if user wants to know about the program.
Pred2aryAppletFrame.AboutDialog() - Constructor for class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.AboutDialog
 
Pred2aryAppletFrame.AboutMessage - Class in org.strbio.mol.lib.pred2ary
 
Pred2aryAppletFrame.AboutMessage() - Constructor for class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.AboutMessage
 
Pred2aryAppletFrame.LoadWindow - Class in org.strbio.mol.lib.pred2ary
 
Pred2aryAppletFrame.LoadWindow() - Constructor for class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.LoadWindow
 
Pred2aryAppletFrame.ProgressDialog - Class in org.strbio.mol.lib.pred2ary
 
Pred2aryAppletFrame.ProgressDialog() - Constructor for class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.ProgressDialog
 
Pred2aryAppletFrame.ProteinPane - Class in org.strbio.mol.lib.pred2ary
 
Pred2aryAppletFrame.ProteinPane() - Constructor for class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.ProteinPane
 
Pred2aryAppletFrame.SaveWindow - Class in org.strbio.mol.lib.pred2ary
 
Pred2aryAppletFrame.SaveWindow() - Constructor for class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.SaveWindow
 
Pred2aryText - Class in org.strbio.app
Predict secondary structure/class, using profiles.
Pred2aryText(String[]) - Constructor for class org.strbio.app.Pred2aryText
This constructor handles the non-interactive text version of the program.
PRED_2ARY - Static variable in class org.strbio.mol.PolymerProperties
Protein property: is there a secondary structure prediction?
PredClassProfile - Class in org.strbio.mol.lib.pred2ary
Class to represent a single protein, with class routines and lots of stats.
PredClassProfile() - Constructor for class org.strbio.mol.lib.pred2ary.PredClassProfile
 
PredClassProfile(ProteinSet) - Constructor for class org.strbio.mol.lib.pred2ary.PredClassProfile
 
PredClassProfile(Protein) - Constructor for class org.strbio.mol.lib.pred2ary.PredClassProfile
 
PredClassProfile(Profile) - Constructor for class org.strbio.mol.lib.pred2ary.PredClassProfile
 
predDiffs(PCPSet) - Method in class org.strbio.mol.lib.pred2ary.PCPSet
differnces between predictions from another set returns -1 if sets different
predDiffs(PredClassProfile) - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
shows number of diff predictions between 2 proteins; should be another copy of same proteins.
predE - Variable in class org.strbio.mol.Residue
Predicted strand probability.
predH - Variable in class org.strbio.mol.Residue
Predicted helix probability.
predict(Protein, Printf) - Method in class org.strbio.mol.lib.Pred2ary
Predicts on a given protein.
predict(ProteinSet, Printf) - Method in class org.strbio.mol.lib.Pred2ary
Predicts on a given set of proteins.
predict(Protein, Printf) - Method in interface org.strbio.mol.lib.SSPredictor
Predicts on a given protein.
predict(ProteinSet, Printf) - Method in interface org.strbio.mol.lib.SSPredictor
Predicts on a given set of proteins.
predict2ary(int, Printf) - Method in class org.strbio.mol.lib.pred2ary.PredictionSet
do 2ary prediction; train and find cutoff if necessary.
predict2ary(NeuralNet, int, Printf) - Method in class org.strbio.mol.lib.pred2ary.TPSet
do a 2ary prediction
predict2aryHE() - Method in class org.strbio.mol.lib.pred2ary.PredictionSet
 
predict2aryHE(NeuralNet) - Method in class org.strbio.mol.lib.pred2ary.TPSet
Predict level 1 H and E using network.
predict2aryHE() - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
 
predictClass(Printf) - Method in class org.strbio.mol.lib.pred2ary.PredictionSet
cutoff = 0.0 -> find correct cutoff.
predictClass(NeuralNet, NeuralNet[], Printf) - Method in class org.strbio.mol.lib.pred2ary.TPSet
do class prediction
predictClassDirectly() - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
predict class directly from 2ary prediction.
predictClassDirectly(Printf) - Method in class org.strbio.mol.lib.pred2ary.TPSet
do class prediction directly from 2ary prediction
predictClassRaw() - Method in class org.strbio.mol.lib.pred2ary.PredictionSet
 
predictClassRaw(NeuralNet, NeuralNet[]) - Method in class org.strbio.mol.lib.pred2ary.TPSet
predict class using both 4-output and 1-output networks.
predictClassRaw() - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
 
PredictionSet - Class in org.strbio.mol.lib.pred2ary
Class to represent a set of profiles being used in 2ary structure prediction as a prediction set.
PredictionSet() - Constructor for class org.strbio.mol.lib.pred2ary.PredictionSet
 
predictLvl1(int, Printf) - Method in class org.strbio.mol.lib.pred2ary.PredictionSet
cutoff = 0.0 -> find correct cutoff.
predictLvl2(int, Printf) - Method in class org.strbio.mol.lib.pred2ary.PredictionSet
cutoff = 0.0 -> find correct cutoff.
predictLvl2(NeuralNet, int, Printf) - Method in class org.strbio.mol.lib.pred2ary.TPSet
do a prediction
predictLvl2HE() - Method in class org.strbio.mol.lib.pred2ary.PredictionSet
 
predictLvl2HE(NeuralNet) - Method in class org.strbio.mol.lib.pred2ary.TPSet
do level 2 prediction
predictLvl2HE() - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
 
predictProteins() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
predictProteinsB - Variable in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
predictSS(Printf, SSPredictor) - Method in class org.strbio.mol.Protein
Predict the secondary structure of this protein, using a specified prediction method.
predictSS(Printf) - Method in class org.strbio.mol.Protein
Predict the secondary structure of this protein, using the default method (Pred2ary, with large jury).
predictSS(Printf, SSPredictor) - Method in class org.strbio.mol.ProteinSet
Predict the secondary structure of these proteins, using a specified prediction method.
predictSS(Printf) - Method in class org.strbio.mol.ProteinSet
Predict the secondary structure of these proteins, using the default method (Pred2ary, with large jury).
predStructure - Variable in class org.strbio.mol.Residue
Predicted secondary structure.
preferredSize() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.AboutMessage
 
preferredSize() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.ProteinPane
 
presentPatterns(NeuralNet) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet.Present2ary
 
presentPatterns(NeuralNet) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet.PresentClass1
 
presentPatterns(NeuralNet) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet.PresentClass4
 
presentPatterns(NeuralNet) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet.PresentLvl2
 
presentPatterns(NeuralNet) - Method in interface org.strbio.util.NeuralNet.Trainable
This method should not modify any weights itself; just present all the patterns and call prop() and backprop() for each.
prev - Variable in class org.strbio.mol.AtomNode
the previous atom in the list
prev() - Method in class org.strbio.mol.AtomNode
return the previous AtomNode
prev() - Method in class org.strbio.mol.Monomer
return the previous monomer in the polymer.
prev() - Method in interface org.strbio.util.DLinkedList.Node
This should return the previous node in the list, or null if there is none.
Primer - Class in org.strbio.mol
Class to represent a single primer.
Primer() - Constructor for class org.strbio.mol.Primer
new primer with no info
Primer(Primer) - Constructor for class org.strbio.mol.Primer
copy another primer
Primer3 - Class in org.strbio.local
Class to run Primer3 Version 1.0, 6/13/06, based on Modeller
Primer3() - Constructor for class org.strbio.local.Primer3
 
PrimerSet - Class in org.strbio.mol
Class to represent a set of primers used to clone one gene
PrimerSet() - Constructor for class org.strbio.mol.PrimerSet
new PrimerSet with no info
PrimerSet(PrimerSet) - Constructor for class org.strbio.mol.PrimerSet
copy another primer set
print(Printf) - Method in class org.strbio.math.Bin
print out bins to an open Printf.
print(String) - Method in class org.strbio.math.Bin
print out bins to a new file.
print(Printf) - Method in class org.strbio.math.Bin2D
print out bins to an open Printf.
print(PrintfStream) - Method in class org.strbio.math.DHalfMatrix
Print nicely formatted data to a PrintfStream.
print(Printf) - Method in class org.strbio.math.DMatrix
prints in ascii to an open Printf, with a nicer format than 'save'.
print(String) - Method in class org.strbio.math.DMatrix
prints in ascii to a new file, with a nicer format than 'save'.
print(Printf) - Method in class org.strbio.math.DVector
prints in ascii to an open Printf, with a nicer format than 'save'.
print(Printf) - Method in class org.strbio.math.FBin
print out FBins to an open Printf.
print(String) - Method in class org.strbio.math.FBin
print out FBins to a new file.
print(PrintfStream) - Method in class org.strbio.math.FHalfMatrix
Print nicely formatted data to a PrintfStream.
print(Printf) - Method in class org.strbio.math.FMatrix
prints in ascii to an open Printf, with a nicer format than 'save'.
print(String) - Method in class org.strbio.math.FMatrix
prints in ascii to a new file, with a nicer format than 'save'.
print(Printf) - Method in class org.strbio.math.FVector
prints in ascii to an open Printf, with a nicer format than 'save'.
print(Printf) - Method in class org.strbio.math.IMatrix
prints in ascii to an open Printf, with a nicer format than 'save'.
print(Printf) - Method in class org.strbio.math.IVector
prints in ascii to an open Printf, with a nicer format than 'save'.
print(Printf, boolean) - Method in class org.strbio.mol.Alignment
prints out both sequences with alternating seq and fold lines.
print(Frame) - Method in class org.strbio.util.graph.Graph2D
Print the graph to a printer.
print2ary(Printf, int) - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
print info on 2ary prediction.
print2ary(Printf, int) - Method in class org.strbio.mol.lib.pred2ary.TPSet
 
print2aryByClass(Printf) - Method in class org.strbio.mol.lib.pred2ary.TPSet
 
print2aryStats(Printf) - Method in class org.strbio.mol.lib.pred2ary.TPSet
 
print2aryUnreduced(Printf) - Method in class org.strbio.mol.lib.pred2ary.TPSet
 
print_e - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
printAlignment(Printf, AlignmentParametersEA, int) - Method in class org.strbio.mol.lib.ThreadResults
print one alignment in a standard format.
printAlignments(Printf, AlignmentParametersEA, double) - Method in class org.strbio.mol.lib.ThreadResults
print alignments in a standard format.
printArgs(String[], Printf) - Static method in class org.strbio.util.JMC
Print out the arguments used to call the program to a given Printf.
printArgs(String[]) - Static method in class org.strbio.util.JMC
Print out the arguments used to call the program to the standard output stream.
printCalculated(Printf, boolean) - Method in class org.strbio.mol.AlignmentSet
prints out both sequences in calculated alignment with alternating seq and fold lines.
printCalculatedOnCorrect(Printf) - Method in class org.strbio.mol.AlignmentSet
prints out both sequences with alternating seq and fold lines, secondary structure information, relative shift info.
printClass(Printf) - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
print class prediction info
printClass(Printf) - Method in class org.strbio.mol.lib.pred2ary.TPSet
 
printClassStats(Printf) - Method in class org.strbio.mol.lib.pred2ary.TPSet
 
printCorrect(Printf, boolean) - Method in class org.strbio.mol.AlignmentSet
prints out both sequences in correct alignment with alternating seq and fold lines.
printDirectClassPrediction(Printf) - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
show the class prediction from the 4-output network.
printDirectClassPrediction(Printf) - Method in class org.strbio.mol.lib.pred2ary.TPSet
 
printDirectClassStats(Printf) - Method in class org.strbio.mol.lib.pred2ary.TPSet
 
printf(String) - Method in class org.strbio.io.OldBufferedPrintfTextArea
Prints a string to the output, without any formatting or parameter substitution (because there are no parameters)
printf(String, double) - Method in class org.strbio.io.OldBufferedPrintfTextArea
Prints a double to the output with some formatting.
printf(String, float) - Method in class org.strbio.io.OldBufferedPrintfTextArea
Prints a float to the output with some formatting.
printf(String, long) - Method in class org.strbio.io.OldBufferedPrintfTextArea
Prints a long to the output with some formatting.
printf(String, int) - Method in class org.strbio.io.OldBufferedPrintfTextArea
Prints an integer to the output with some formatting.
printf(String, char) - Method in class org.strbio.io.OldBufferedPrintfTextArea
Prints an integer to the output with some formatting.
printf(String, String) - Method in class org.strbio.io.OldBufferedPrintfTextArea
Prints a String to the output with some formatting.
printf(String) - Method in class org.strbio.io.OldPrintfJLabel
Prints a string to the output, without any formatting or parameter substitution (because there are no parameters)
printf(String, double) - Method in class org.strbio.io.OldPrintfJLabel
Prints a double to the output with some formatting.
printf(String, float) - Method in class org.strbio.io.OldPrintfJLabel
Prints a float to the output with some formatting.
printf(String, long) - Method in class org.strbio.io.OldPrintfJLabel
Prints a long to the output with some formatting.
printf(String, int) - Method in class org.strbio.io.OldPrintfJLabel
Prints an integer to the output with some formatting.
printf(String, char) - Method in class org.strbio.io.OldPrintfJLabel
Prints an integer to the output with some formatting.
printf(String, String) - Method in class org.strbio.io.OldPrintfJLabel
Prints a String to the output with some formatting.
printf(String) - Method in class org.strbio.io.OldPrintfJTextArea
Prints a string to the output, without any formatting or parameter substitution (because there are no parameters)
printf(String, double) - Method in class org.strbio.io.OldPrintfJTextArea
Prints a double to the output with some formatting.
printf(String, float) - Method in class org.strbio.io.OldPrintfJTextArea
Prints a float to the output with some formatting.
printf(String, long) - Method in class org.strbio.io.OldPrintfJTextArea
Prints a long to the output with some formatting.
printf(String, int) - Method in class org.strbio.io.OldPrintfJTextArea
Prints an integer to the output with some formatting.
printf(String, char) - Method in class org.strbio.io.OldPrintfJTextArea
Prints an integer to the output with some formatting.
printf(String, String) - Method in class org.strbio.io.OldPrintfJTextArea
Prints a String to the output with some formatting.
printf(String) - Method in class org.strbio.io.OldPrintfTextArea
Prints a string to the output, without any formatting or parameter substitution (because there are no parameters)
printf(String, double) - Method in class org.strbio.io.OldPrintfTextArea
Prints a double to the output with some formatting.
printf(String, float) - Method in class org.strbio.io.OldPrintfTextArea
Prints a float to the output with some formatting.
printf(String, long) - Method in class org.strbio.io.OldPrintfTextArea
Prints a long to the output with some formatting.
printf(String, int) - Method in class org.strbio.io.OldPrintfTextArea
Prints an integer to the output with some formatting.
printf(String, char) - Method in class org.strbio.io.OldPrintfTextArea
Prints an integer to the output with some formatting.
printf(String, String) - Method in class org.strbio.io.OldPrintfTextArea
Prints a String to the output with some formatting.
Printf - Interface in org.strbio.io
An interface for routines that support a form of printf().
printf(String) - Method in interface org.strbio.io.Printf
Prints a string to the output, without any formatting or parameter substitution (because there are no parameters)
printf(String, double) - Method in interface org.strbio.io.Printf
Prints a double to the output with some formatting.
printf(String, float) - Method in interface org.strbio.io.Printf
Prints a float to the output with some formatting.
printf(String, long) - Method in interface org.strbio.io.Printf
Prints a long to the output with some formatting.
printf(String, int) - Method in interface org.strbio.io.Printf
Prints an integer to the output with some formatting.
printf(String, char) - Method in interface org.strbio.io.Printf
Prints an integer to the output with some formatting.
printf(String, String) - Method in interface org.strbio.io.Printf
Prints a String to the output with some formatting.
printf(String) - Method in class org.strbio.io.PrintfJLabel
Prints a string to the output, without any formatting or parameter substitution (because there are no parameters)
printf(String, double) - Method in class org.strbio.io.PrintfJLabel
Prints a double to the output with some formatting.
printf(String, float) - Method in class org.strbio.io.PrintfJLabel
Prints a float to the output with some formatting.
printf(String, long) - Method in class org.strbio.io.PrintfJLabel
Prints a long to the output with some formatting.
printf(String, int) - Method in class org.strbio.io.PrintfJLabel
Prints an integer to the output with some formatting.
printf(String, char) - Method in class org.strbio.io.PrintfJLabel
Prints an integer to the output with some formatting.
printf(String, String) - Method in class org.strbio.io.PrintfJLabel
Prints a String to the output with some formatting.
printf(String) - Method in class org.strbio.io.PrintfJTextArea
Prints a string to the output, without any formatting or parameter substitution (because there are no parameters)
printf(String, double) - Method in class org.strbio.io.PrintfJTextArea
Prints a double to the output with some formatting.
printf(String, float) - Method in class org.strbio.io.PrintfJTextArea
Prints a float to the output with some formatting.
printf(String, long) - Method in class org.strbio.io.PrintfJTextArea
Prints a long to the output with some formatting.
printf(String, int) - Method in class org.strbio.io.PrintfJTextArea
Prints an integer to the output with some formatting.
printf(String, char) - Method in class org.strbio.io.PrintfJTextArea
Prints an integer to the output with some formatting.
printf(String, String) - Method in class org.strbio.io.PrintfJTextArea
Prints a String to the output with some formatting.
printf(String) - Method in class org.strbio.io.PrintfStream
Prints a string to the output, without any parameter substitution, but with formatting (i.e.
printf(String, int) - Method in class org.strbio.io.PrintfStream
Prints a int to the output, with formatting.
printf(String, long) - Method in class org.strbio.io.PrintfStream
Prints a long to the output, with formatting.
printf(String, char) - Method in class org.strbio.io.PrintfStream
Prints a char to the output, with formatting.
printf(String, String) - Method in class org.strbio.io.PrintfStream
Prints a String to the output, with formatting.
printf(String, double) - Method in class org.strbio.io.PrintfStream
Prints a double to the output, with formatting.
printf(String, float) - Method in class org.strbio.io.PrintfStream
Prints a float to the output, with formatting.
printf(String) - Method in class org.strbio.io.PrintfTee
 
printf(String, double) - Method in class org.strbio.io.PrintfTee
 
printf(String, float) - Method in class org.strbio.io.PrintfTee
 
printf(String, long) - Method in class org.strbio.io.PrintfTee
 
printf(String, int) - Method in class org.strbio.io.PrintfTee
 
printf(String, char) - Method in class org.strbio.io.PrintfTee
 
printf(String, String) - Method in class org.strbio.io.PrintfTee
 
printf(String) - Method in class org.strbio.io.PrintfTextArea
Prints a string to the output, without any formatting or parameter substitution (because there are no parameters)
printf(String, double) - Method in class org.strbio.io.PrintfTextArea
Prints a double to the output with some formatting.
printf(String, float) - Method in class org.strbio.io.PrintfTextArea
Prints a float to the output with some formatting.
printf(String, long) - Method in class org.strbio.io.PrintfTextArea
Prints a long to the output with some formatting.
printf(String, int) - Method in class org.strbio.io.PrintfTextArea
Prints an integer to the output with some formatting.
printf(String, char) - Method in class org.strbio.io.PrintfTextArea
Prints an integer to the output with some formatting.
printf(String, String) - Method in class org.strbio.io.PrintfTextArea
Prints a String to the output with some formatting.
printf(String) - Method in class org.strbio.io.PrintfWriter
Prints a string to the output, without any formatting or parameter substitution (because there are no parameters)
printf(String, double) - Method in class org.strbio.io.PrintfWriter
Prints a double to the output with some formatting.
printf(String, float) - Method in class org.strbio.io.PrintfWriter
Prints a float to the output with some formatting.
printf(String, long) - Method in class org.strbio.io.PrintfWriter
Prints a long to the output with some formatting.
printf(String, int) - Method in class org.strbio.io.PrintfWriter
Prints an integer to the output with some formatting.
printf(String, char) - Method in class org.strbio.io.PrintfWriter
Prints an integer to the output with some formatting.
printf(String, String) - Method in class org.strbio.io.PrintfWriter
Prints a String to the output with some formatting.
printf(String) - Method in class org.strbio.util.ui.ProfileGUIApp.LoadProgressDialog
 
printf(String, double) - Method in class org.strbio.util.ui.ProfileGUIApp.LoadProgressDialog
 
printf(String, float) - Method in class org.strbio.util.ui.ProfileGUIApp.LoadProgressDialog
 
printf(String, long) - Method in class org.strbio.util.ui.ProfileGUIApp.LoadProgressDialog
 
printf(String, int) - Method in class org.strbio.util.ui.ProfileGUIApp.LoadProgressDialog
 
printf(String, char) - Method in class org.strbio.util.ui.ProfileGUIApp.LoadProgressDialog
 
printf(String, String) - Method in class org.strbio.util.ui.ProfileGUIApp.LoadProgressDialog
 
PrintfJLabel - Class in org.strbio.io
A JLabel that you can do printf() on, like a civilized (C) programmer.
PrintfJLabel() - Constructor for class org.strbio.io.PrintfJLabel
 
PrintfJLabel(String) - Constructor for class org.strbio.io.PrintfJLabel
 
PrintfJTextArea - Class in org.strbio.io
A JTextArea that you can do printf() on, like a civilized (C) programmer.
PrintfJTextArea() - Constructor for class org.strbio.io.PrintfJTextArea
 
PrintfJTextArea(String) - Constructor for class org.strbio.io.PrintfJTextArea
 
PrintfJTextArea(int, int) - Constructor for class org.strbio.io.PrintfJTextArea
 
PrintfJTextArea(String, int, int) - Constructor for class org.strbio.io.PrintfJTextArea
 
printFreqs(Printf) - Method in class org.strbio.mol.lib.PSIBlastMatrices
Print frequencies for debugging.
PrintfStream - Class in org.strbio.io
A BufferedOutputStream that you can do printf() on, like a civilized (C) programmer.
PrintfStream(String) - Constructor for class org.strbio.io.PrintfStream
Open up a new file with a given name.
PrintfStream(String, boolean) - Constructor for class org.strbio.io.PrintfStream
Open up a file with a given name.
PrintfStream(OutputStream) - Constructor for class org.strbio.io.PrintfStream
Attaches to an OutputStream, such as System.out or System.err
PrintfTee - Class in org.strbio.io
A printf object that forwards output to 2 Printf's.
PrintfTee(Printf, Printf) - Constructor for class org.strbio.io.PrintfTee
 
PrintfTextArea - Class in org.strbio.io
A TextArea that you can do printf() on, like a civilized (C) programmer.
PrintfTextArea() - Constructor for class org.strbio.io.PrintfTextArea
 
PrintfTextArea(String) - Constructor for class org.strbio.io.PrintfTextArea
 
PrintfTextArea(int, int) - Constructor for class org.strbio.io.PrintfTextArea
 
PrintfTextArea(String, int, int) - Constructor for class org.strbio.io.PrintfTextArea
 
PrintfTextArea(String, int, int, int) - Constructor for class org.strbio.io.PrintfTextArea
 
PrintfWriter - Class in org.strbio.io
A Writer that you can do printf() on, like a civilized (C) programmer.
PrintfWriter(String) - Constructor for class org.strbio.io.PrintfWriter
Open up a new file with a given name.
PrintfWriter(String, boolean) - Constructor for class org.strbio.io.PrintfWriter
Open up a file with a given name.
PrintfWriter(File) - Constructor for class org.strbio.io.PrintfWriter
Attaches to an open file?
PrintfWriter(FileWriter) - Constructor for class org.strbio.io.PrintfWriter
Attaches to an already open FileWriter.
PrintfWriter(FileDescriptor) - Constructor for class org.strbio.io.PrintfWriter
This is inherited from FileWriter.
PrintfWriter(OutputStream) - Constructor for class org.strbio.io.PrintfWriter
Attaches to an OutputStream, such as System.out or System.err
PrintfWriter(Writer) - Constructor for class org.strbio.io.PrintfWriter
Attaches to another Writer
printMatches(Printf, boolean) - Method in class org.strbio.mol.lib.ThreadResults
print fold rankings in a standard format.
printModeller(Printf) - Method in class org.strbio.mol.Alignment
prints both sequences in a format Modeller likes.
printModeller(Printf) - Method in class org.strbio.mol.AlignmentSet
prints both sequences in a format Modeller likes.
printNames(int, Printf) - Method in class org.strbio.mol.PolymerSet
print names of Polymers in this set.
printParameters(Printf) - Method in class org.strbio.mol.lib.GapAffine
 
printParameters(Printf) - Method in interface org.strbio.mol.lib.GapModel
Briefly print the gap parameters, for inclusion in a line of output.
printParameters(Printf) - Method in class org.strbio.mol.lib.GapModelAdapter
default printParameters function does nothing.
printProfile(Printf, int) - Method in class org.strbio.mol.Profile
Print profile to output in a pretty format.
printProfile(Printf) - Method in class org.strbio.mol.Profile
Print profile to output in a pretty format.
printRaw(String, Printf) - Static method in class org.strbio.net.Ecocyc
prints raw result of a search
printRaw(String, Printf) - Static method in class org.strbio.net.Entrez
prints raw query of an entrez search
printRaw(String, Printf) - Static method in class org.strbio.net.FruitFly
prints raw result of a flybase search
printRaw(String, Printf) - Static method in class org.strbio.net.ProtParam
prints raw result of a search
printRaw(String, int, Printf) - Static method in class org.strbio.net.PubMed
prints raw query of an pubmed search
printRaw2(int, Printf) - Static method in class org.strbio.net.PubMed
prints raw query of an pubmed id search
printRelative(Alignment, Printf) - Method in class org.strbio.mol.Alignment
prints out both sequences with alternating seq and fold lines, and also shows relation relative to another alignment (i.e. the correct alignment)
printScores(Printf) - Method in class org.strbio.mol.lib.PSIBlastMatrices
Print scores for debugging.
printSequence(Printf) - Method in class org.strbio.mol.Polymer
print out the sequence in a nice 1-letter code format
printStatus(String) - Method in class org.strbio.util.ui.GUIApp
give user a short message, on the staus line.
printTime(float, Printf) - Static method in class org.strbio.util.JMC
Given a time in seconds, prints it in hours:minutes:seconds format.
printTime(float) - Static method in class org.strbio.util.JMC
Given a time in seconds, prints it in hours:minutes:seconds format to standard output.
probabilityOfFindingMatch() - Method in class org.strbio.mol.ThreadSet
Calculates confidence vector... this is a DVector of the length of the number of folds.
processAA() - Method in class org.strbio.mol.lib.AlignmentParametersEA
process the AA stats, for speed in estimation.
processError - Variable in class org.strbio.local.Program
Stream for program to write error to; default System.err.
processFR() - Method in class org.strbio.mol.lib.AlignmentParametersEA
process the FR stats, for speed in estimation.
processFR() - Method in class org.strbio.mol.lib.FRParameters
process the FR stats, for speed in estimation.
processGlobalMatrix(float[][], int[][], int[][], Polymer, Polymer) - Method in class org.strbio.mol.lib.GapAffine
This function is optimized for affine gap penalties.
processGlobalMatrix(float[][], int[][], int[][], Polymer, Polymer) - Method in class org.strbio.mol.lib.GapConstant
This function is optimized for constant gap penalties.
processGlobalMatrix(float[][], int[][], int[][], Polymer, Polymer) - Method in class org.strbio.mol.lib.GapDistanceDependent
This function is optimized for gap penalties which are affine in only 1 direction, and have to be fully looked at in the other direction.
processGlobalMatrix(float[][], int[][], int[][], Polymer, Polymer) - Method in interface org.strbio.mol.lib.GapModel
This function is given a sequence and fold being aligned in a global alignment, and a S+1 x F+1 matrix containing the scores for aligning each monomer in the sequence to each monomer in the fold.
processGlobalMatrix(float[][], int[][], int[][], Polymer, Polymer) - Method in class org.strbio.mol.lib.GapModelAdapter
This function will handle any gap model, but very slowly.
processGlobalMatrix(float[][], int[][], int[][], Polymer, Polymer) - Method in class org.strbio.raf.GapRAF
This function is optimized for gap penalties which are affine in only 1 direction, and have to be fully looked at in the other direction.
processInput - Variable in class org.strbio.local.Program
Stream for program to take input from; default none.
processOutput - Variable in class org.strbio.local.Program
Stream for program to write output to; default System.out.
processYAPF(String) - Method in class org.strbio.mol.Polymer
Process a line from a YAPF file... this should ignore the line if it doesn't know what it is.
processYAPF(String) - Method in class org.strbio.mol.Profile
Process a line from a YAPF file... this should ignore the line if it doesn't know what it is.
processYAPF(String) - Method in class org.strbio.mol.ProfilePSI
Process a line from a YAPF file... this should ignore the line if it doesn't know what it is.
processYAPF(String) - Method in class org.strbio.mol.Protein
Process a line from a YAPF file... this should ignore the line if it doesn't know what it is.
processYAPF(String) - Method in class org.strbio.util.db.CATHInfo
Initialize this Info from a line in a YAPF file, if applicable.
processYAPF(String) - Method in class org.strbio.util.db.Data
process a line of info from a YAPF file.
processYAPF(String) - Method in class org.strbio.util.db.Info
Initialize this Info from a line in a YAPF file, if applicable.
processYAPF(String) - Method in class org.strbio.util.db.PDBInfo
Initialize this Info from a line in a YAPF file, if applicable.
processYAPF(String) - Method in class org.strbio.util.db.SCOPInfo
Initialize this Info from a line in a YAPF file, if applicable.
product - Variable in class org.strbio.mol.PrimerSet
product sequence
Profile - Class in org.strbio.mol
Class to represent a protein with profile information.
Profile() - Constructor for class org.strbio.mol.Profile
Make an empty Profile.
Profile(Protein) - Constructor for class org.strbio.mol.Profile
Make a Profile from a Protein, copying all data.
Profile(Profile) - Constructor for class org.strbio.mol.Profile
Copy a Profile, including all data in it.
Profile(ProteinSet) - Constructor for class org.strbio.mol.Profile
Make a Profile from a ProteinSet, copying all data.
ProfileDisplayArea - Class in org.strbio.mol.lib.pred2ary
This represents an area in object that will want to display some proteins in an area.
ProfileDisplayArea(ProfileSet, Component, int) - Constructor for class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
Initialize with given parent container.
ProfileDisplayArea.ClickedArea - Class in org.strbio.mol.lib.pred2ary
This class keeps track of rectangular areas of interest, and tells which one has been clicked on.
ProfileDisplayArea.ClickedArea() - Constructor for class org.strbio.mol.lib.pred2ary.ProfileDisplayArea.ClickedArea
 
ProfileGUIApp - Class in org.strbio.util.ui
A generic set of functions for GUI apps which deal with proteins to use, which should provide something of a common L&F.
ProfileGUIApp() - Constructor for class org.strbio.util.ui.ProfileGUIApp
 
ProfileGUIApp.LoadFormats - Class in org.strbio.util.ui
 
ProfileGUIApp.LoadFormats() - Constructor for class org.strbio.util.ui.ProfileGUIApp.LoadFormats
 
ProfileGUIApp.LoadProgressDialog - Class in org.strbio.util.ui
show load progress.
ProfileGUIApp.LoadProgressDialog(boolean) - Constructor for class org.strbio.util.ui.ProfileGUIApp.LoadProgressDialog
 
ProfilePSI - Class in org.strbio.mol
Class to represent a profile with position specific information (PSI), such as PSI-BLAST info and JMC's backbone potential.
ProfilePSI() - Constructor for class org.strbio.mol.ProfilePSI
Default constructor.
ProfilePSI(Protein) - Constructor for class org.strbio.mol.ProfilePSI
Create from a single protein.
ProfilePSI(Profile) - Constructor for class org.strbio.mol.ProfilePSI
Create from a regular profile.
ProfilePSI(ProteinSet) - Constructor for class org.strbio.mol.ProfilePSI
Create from a set of proteins.
ProfilePSISet - Class in org.strbio.mol
Class to represent a set of profiles with position specific information (PSI), such as PSI-BLAST info and JMC's backbone potential.
ProfilePSISet() - Constructor for class org.strbio.mol.ProfilePSISet
 
ProfileSet - Class in org.strbio.mol
Class to represent a set of proteins with profile information.
ProfileSet() - Constructor for class org.strbio.mol.ProfileSet
Create an empty set of Profiles.
ProfileSet(ProfileSet) - Constructor for class org.strbio.mol.ProfileSet
Copy another profile set, but not the profiles themselves.
ProfRes - Class in org.strbio.mol
Class to represent a single residue in a protein with profile information.
ProfRes() - Constructor for class org.strbio.mol.ProfRes
Most constructors just call the superclass one.
ProfRes(char) - Constructor for class org.strbio.mol.ProfRes
 
ProfRes(String) - Constructor for class org.strbio.mol.ProfRes
 
ProfRes(Residue) - Constructor for class org.strbio.mol.ProfRes
 
ProfRes(ProfRes) - Constructor for class org.strbio.mol.ProfRes
Constructor to copy another ProfRes.
ProfResPSI - Class in org.strbio.mol
Class to represent a single residue in a profile, with position specific information (PSI) added.
ProfResPSI() - Constructor for class org.strbio.mol.ProfResPSI
Most constructors just call the superclass one.
ProfResPSI(char) - Constructor for class org.strbio.mol.ProfResPSI
 
ProfResPSI(String) - Constructor for class org.strbio.mol.ProfResPSI
 
ProfResPSI(ProfResPSI) - Constructor for class org.strbio.mol.ProfResPSI
copy another residue, including the atoms.
Program - Class in org.strbio.local
Class to run a program on the local system.
Program() - Constructor for class org.strbio.local.Program
Default constructor doesn't know program name; must setProgramName to work
Program(String) - Constructor for class org.strbio.local.Program
constructor with program name
PROGRAM_NAME - Variable in class org.strbio.local.Program
What's the name of this program?
programName() - Method in class org.strbio.local.Access
 
programName() - Method in class org.strbio.local.BlastClient
 
programName() - Method in class org.strbio.local.BlastP
 
programName() - Method in class org.strbio.local.ClustalW
 
programName() - Method in class org.strbio.local.DSSP
 
programName() - Method in class org.strbio.local.Ls
 
programName() - Method in class org.strbio.local.Malfe
 
programName() - Method in class org.strbio.local.MaxSub
 
programName() - Method in class org.strbio.local.Melting
 
programName() - Method in class org.strbio.local.Mfold
 
programName() - Method in class org.strbio.local.Minarea
 
programName() - Method in class org.strbio.local.Modeller
 
programName() - Method in class org.strbio.local.Muscle
 
programName() - Method in class org.strbio.local.Primer3
 
programName() - Method in class org.strbio.local.Program
What's the name of this program?
programName() - Method in class org.strbio.local.PSIBlastP
 
programName() - Method in class org.strbio.local.TBlastN
 
programName() - Method in class org.strbio.local.VarTom
 
programTimer(Printf) - Static method in class org.strbio.util.JMC
Program timer routine.
programTimer() - Static method in class org.strbio.util.JMC
Program timer routine.
progress - Variable in class org.strbio.mol.lib.pred2ary.Jury
Indicator to update with verbose output, after every juror.
progressDialog - Variable in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
prop() - Method in class org.strbio.util.NeuralNet
propagate inputs forward through the network.
properties - Variable in class org.strbio.mol.Polymer
Integer that stores properties of the polymer.
propertyChange(PropertyChangeEvent) - Method in class org.strbio.util.ActionJButton
 
Protein - Class in org.strbio.mol
Class to represent a single protein.
Protein() - Constructor for class org.strbio.mol.Protein
Create a new protein with no information known about it.
Protein(Protein) - Constructor for class org.strbio.mol.Protein
Copy another Protein, making copies of all data fields.
Protein(String) - Constructor for class org.strbio.mol.Protein
Make a new protein from a string representing a sequence.
protein(int) - Method in class org.strbio.mol.ProteinSet
Return the i'th protein in the array.
protein - Variable in class org.strbio.util.db.ProteinInfo
A Protein object associated with this info, or null if it doesn't exist.
ProteinFilter - Class in org.strbio.mol.lib
A file filter for returning likely protein formats.
ProteinFilter() - Constructor for class org.strbio.mol.lib.ProteinFilter
 
ProteinInfo - Class in org.strbio.util.db
This is a parent class for all Info objects concerning proteins.
ProteinInfo() - Constructor for class org.strbio.util.db.ProteinInfo
 
proteinPane - Variable in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
ProteinSet - Class in org.strbio.mol
Class to represent a set of proteins to be acted on in a group.
ProteinSet() - Constructor for class org.strbio.mol.ProteinSet
Create an empty protein set.
ProteinSet(ProteinSet) - Constructor for class org.strbio.mol.ProteinSet
Copy another protein set, but not the proteins (only the pointers to them).
ProteinSet(Profile) - Constructor for class org.strbio.mol.ProteinSet
Make a protein set from a profile... the protein set will contain newly created Proteins, one per sequence in the profile.
ProteinStructureInfo - Class in org.strbio.util.db
This is a parent class for all Info objects concerning protein structure.
ProteinStructureInfo() - Constructor for class org.strbio.util.db.ProteinStructureInfo
 
ProteinTools - Class in org.strbio.util.ui
This contains a set of static routines for drawing information about Proteins into Graphics objects.
ProteinTools() - Constructor for class org.strbio.util.ui.ProteinTools
 
ProtParam - Class in org.strbio.net
Class to access expasy.ch's ProtParam over the web.
ProtParam() - Constructor for class org.strbio.net.ProtParam
 
psi - Variable in class org.strbio.mol.lib.MinareaResults
 
psi() - Method in class org.strbio.mol.Residue
Psi is the bond angle between N(n), CA(n), C(n), N(n+1).
PSI_BLAST_MATRIX - Static variable in class org.strbio.mol.PolymerProperties
ProfilePSI property: is there a psi-blast matrix?
PSIBlast - Interface in org.strbio.mol.lib
Interface for common PSI-blast related routines.
PSIBlastMatrices - Class in org.strbio.mol.lib
Matrix used in PSIBlast comparisons.
PSIBlastMatrices() - Constructor for class org.strbio.mol.lib.PSIBlastMatrices
Create an empty matrix; need to call setQuery.
PSIBlastMatrices(String) - Constructor for class org.strbio.mol.lib.PSIBlastMatrices
Create with given query sequence.
PSIBlastMatrices(Protein) - Constructor for class org.strbio.mol.lib.PSIBlastMatrices
Create with given protein as query.
PSIBlastNCBI - Class in org.strbio.net
Does a PSI-BLAST search in the NR database at NCBI, using the main web gateway.
PSIBlastNCBI() - Constructor for class org.strbio.net.PSIBlastNCBI
 
PSIBlastNCBI(String) - Constructor for class org.strbio.net.PSIBlastNCBI
Initialize with a given query sequence.
PSIBlastNCBI(Protein) - Constructor for class org.strbio.net.PSIBlastNCBI
Initialize with a given protein.
PSIBlastP - Class in org.strbio.local
Runs a local copy of psiblast.
PSIBlastP() - Constructor for class org.strbio.local.PSIBlastP
Initialize with no information; you still have to call setQuery before starting Blast.
PSIBlastP(String) - Constructor for class org.strbio.local.PSIBlastP
Initialize with a given query sequence.
PSIBlastP(Protein) - Constructor for class org.strbio.local.PSIBlastP
Initialize with a given protein.
PSIBlastP2 - Class in org.strbio.local
Runs a local copy of psiblast.
PSIBlastP2() - Constructor for class org.strbio.local.PSIBlastP2
Initialize with no information; you still have to call setQuery before starting Blast.
PSIBlastP2(String) - Constructor for class org.strbio.local.PSIBlastP2
Initialize with a given query sequence.
PSIBlastP2(Protein) - Constructor for class org.strbio.local.PSIBlastP2
Initialize with a given protein.
PSIBlastWeb - Class in org.strbio.net
Does a PSI-BLAST search in the NR database over the web.
PSIBlastWeb() - Constructor for class org.strbio.net.PSIBlastWeb
Initialize with no information; you still have to call setQuery before starting Blast.
PSIBlastWeb(String) - Constructor for class org.strbio.net.PSIBlastWeb
Initialize with a given query sequence.
PSIBlastWeb(Protein) - Constructor for class org.strbio.net.PSIBlastWeb
Initialize with a given protein.
ptype - Variable in class org.strbio.util.graph.ClickablePointPlot
type of point to draw.
ptype - Variable in class org.strbio.util.graph.PointPlot
type of point to draw.
PubMed - Class in org.strbio.net
Class to access PubMed over the web.
PubMed() - Constructor for class org.strbio.net.PubMed
 

Q

query - Variable in class org.strbio.local.BlastPAdapter
 
query - Variable in class org.strbio.mol.lib.BlastAdapter
 
quickAlign(Polymer, double, double) - Method in class org.strbio.mol.Polymer
standard needleman-wunch alignment algorithm, with identity matrix and given gap penalties
quickAlign(Polymer) - Method in class org.strbio.mol.Polymer
standard needleman-wunch alignment algorithm, with identity matrix, and constant gap penalty of 1.
quickCompare(Polymer, double, double) - Method in class org.strbio.mol.Polymer
standard needleman-wunch comparison algorithm, with identity matrix and given gap penalties.
quickCompare(Polymer) - Method in class org.strbio.mol.Polymer
standard needleman-wunch comparison algorithm, with identity matrix and a constant gap penalty of 1.

R

r_SM - Variable in class org.strbio.mol.lib.pred2ary.TPSet
 
RAFProtein - Class in org.strbio.raf
Modified version of org.strbio.mol.Protein... part of this might might be ported back to Protein.
RAFProtein() - Constructor for class org.strbio.raf.RAFProtein
 
RAFResidue - Class in org.strbio.raf
Class to handle modified residues.
RAFResidue() - Constructor for class org.strbio.raf.RAFResidue
 
randomlyLocateFrame(Frame) - Static method in class org.strbio.util.JMC
Randomly locate a frame somewhere on the screen where it fits.
rankNoMatch() - Method in class org.strbio.mol.lib.ThreadResults
Calculate where 'no match' would rank among the folds (starting at 0).
ratio - Variable in class org.strbio.mol.lib.MinareaResults
 
read() - Method in class org.strbio.io.EOFStringReader
 
read(char[], int, int) - Method in class org.strbio.io.EOFStringReader
 
read(BufferedReader, Printf) - Method in class org.strbio.mol.lib.UserFoldLibrary
Reads proteins in, making sure they have the correct info.
read(BufferedReader, Printf, boolean) - Method in class org.strbio.mol.Polymer
This does the work in reading a protein, but should not be called directly.
read(BufferedReader) - Method in class org.strbio.mol.Polymer
Find the first thing in a file that looks like a polymer, and read it.
read(BufferedReader, Printf) - Method in class org.strbio.mol.Polymer
Find the first thing in a file that looks like a polymer, and read it.
read(BufferedReader, Printf) - Method in class org.strbio.mol.PolymerSet
Read Polymers from unknown file type.
read(String, Printf) - Method in class org.strbio.mol.PolymerSet
Read Polymers from unknown file type.
read(String) - Method in class org.strbio.mol.PolymerSet
Read Polymers from unknown file type (figures out what kind of Polymers they are).
readAccess(BufferedReader, Printf) - Method in class org.strbio.mol.Protein
read a protein out of an Access file.
readAccess(BufferedReader) - Method in class org.strbio.mol.Residue
Read this residue out of an Access format file (Scott Presnell's format).
readAccessRecord(String) - Method in class org.strbio.mol.Residue
Read Access record out of YAPF file.
readAngleRecord(String) - Method in class org.strbio.mol.Residue
Read pre-calc angles out of YAPF file.
readAtom(String, Printf) - Static method in class org.strbio.raf.RAFProtein
 
readAtomRecord(String) - Method in class org.strbio.mol.Monomer
Reads one PDB/YAPF atom record out of a buffer string, and inserts it into the list of atoms.
readBLAST(BufferedReader, Printf) - Method in class org.strbio.mol.Profile
This reads a profile from BLASTP 2.0.11 output.
readCASP(BufferedReader, Printf) - Method in class org.strbio.mol.Protein
read a protein out of a CASP file.
readClustal(BufferedReader, Printf) - Method in class org.strbio.mol.Profile
read a protein out of a CLUSTAL format file.
readConv(BufferedReader, Printf) - Method in class org.strbio.mol.Protein
read a protein out of a Conv file.
readConv(BufferedReader) - Method in class org.strbio.mol.Residue
Read this residue out of a Conv format file (Tom Defay's format).
readCWRecord(String) - Method in class org.strbio.mol.ProfRes
Read CW record out of YAPF file.
readDSSP(BufferedReader, Printf) - Method in class org.strbio.mol.Protein
read a protein out of a DSSP file.
readDSSP(BufferedReader) - Method in class org.strbio.mol.Residue
Read this residue out of a DSSP (Dictionary of Secondary Structure for Proteins) format file (Kabsch & Sander's format).
readDSSPRecord(String) - Method in class org.strbio.mol.Residue
Read DSSP record out of YAPF file.
readEA(BufferedReader, Printf) - Method in class org.strbio.mol.Protein
read a protein out of an EA file.
readEA(BufferedReader) - Method in class org.strbio.mol.Residue
Read this residue out of a EA (Estimated Accuracy) format file (JMC's format).
readFasta(BufferedReader) - Method in class org.strbio.mol.Monomer
Read this monomer out of a Fasta format file.
readFasta(BufferedReader, Printf) - Method in class org.strbio.mol.Polymer
read a polymer out of a Fasta file.
readFREQRecord(String) - Method in class org.strbio.mol.ProfRes
Read FREQ record out of YAPF file.
readHSSP(BufferedReader, Printf) - Method in class org.strbio.mol.Profile
read a protein out of a HSSP (Sander & Schneider format) file.
readHSSPSeqs(BufferedReader, int, int) - Method in class org.strbio.mol.ProfRes
Read sequence info for this residue out of a HSSP format file.
readJMCSTR(String) - Method in class org.strbio.mol.Residue
Get info for this residue out of a JMCSTR line in a PDB or YAPF file.
readList(BufferedReader, Printf) - Method in class org.strbio.mol.Polymer
read a polymer out of a 'list' file.
readList(String, Printf) - Method in class org.strbio.mol.PolymerSet
Read Polymers from a list file (a list of the Polymer names).
readMSF(BufferedReader, Printf) - Method in class org.strbio.mol.Profile
read a protein out of a MSF (GCG's format) file.
readPDB(String) - Method in class org.strbio.mol.Atom
Read an atom out of a PDB file.
readPDB(BufferedReader, Printf) - Method in class org.strbio.mol.Protein
read a protein out of a PDB file.
readPDBAtom(BufferedReader, Printf) - Method in class org.strbio.mol.Protein
read a protein out of a PDB file with no SEQRES records.
readPDBAtomRAF(BufferedReader, Printf) - Method in class org.strbio.raf.RAFProtein
read a protein out of a PDB file ATOM records.
readPDBSeqresRAF(BufferedReader, Printf) - Method in class org.strbio.raf.RAFProtein
read a protein out of a PDB SEQRES records
readPredSSRecord(String) - Method in class org.strbio.mol.Residue
Read predicted SS info out of YAPF file.
readProf(BufferedReader) - Method in class org.strbio.mol.ProfRes
Read this residue out of a Prof (sequence profile) format file (JMC's format).
readProf(BufferedReader, Printf) - Method in class org.strbio.mol.Protein
read a protein out of a Prof file.
readProf(BufferedReader) - Method in class org.strbio.mol.Residue
Read this residue out of a Prof (sequence profile) format file (JMC's format).
readPSIBlastRecord(String) - Method in class org.strbio.mol.ProfResPSI
Read PSI-BLAST info out of YAPF file.
readSeqRecord(String) - Method in class org.strbio.mol.Monomer
Read this monomer out of a YAPF (sequence profile) format file (JMC's format).
readSeqRecord(String) - Method in class org.strbio.mol.ProfRes
Read this residue out of a YAPF (sequence profile) format file (JMC's format).
readSeqres(String, Printf) - Static method in class org.strbio.raf.RAFProtein
 
readSequence(BufferedReader, Printf) - Method in class org.strbio.mol.Polymer
Read a polymer from a file containing just the sequence (all non-whitespace chars)
readSwissProt(BufferedReader, Printf) - Method in class org.strbio.mol.Protein
read a protein out of a SwissProt file.
readVar(BufferedReader, Printf) - Method in class org.strbio.mol.Protein
read a protein out of a Var file.
readVar(BufferedReader) - Method in class org.strbio.mol.Residue
Read this residue out of a Var format file (Tom Defay's format).
readVar2(BufferedReader, Printf) - Method in class org.strbio.mol.Protein
read a protein out of a Var2 file.
readVar2(BufferedReader) - Method in class org.strbio.mol.Residue
Read this residue out of a Var2 format file (Tom Defay's format).
readVarTomRecord(String) - Method in class org.strbio.mol.Residue
Read VarTom record out of YAPF file.
ready() - Method in class org.strbio.io.EOFStringReader
 
readYAPF(BufferedReader, Printf) - Method in class org.strbio.mol.Polymer
read a polymer out of a YAPF file.
readYAPF(BufferedReader) - Method in class org.strbio.util.db.Data
read info from a YAPF file.
readYAPF(String) - Method in class org.strbio.util.db.Data
read info from a YAPF file.
recognizeAndRead(String, BufferedReader, Printf) - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
This looks for a protein and reads it in, and also figures out what class it belongs to.
recognizeAndRead(String, BufferedReader, Printf) - Method in class org.strbio.mol.Polymer
This routine checks to see if the current buffer looks like the beginning of a polymer in a known file format.
recognizeAndRead(String, BufferedReader, Printf) - Method in class org.strbio.mol.Profile
This looks for a profile and reads it in.
recognizeAndRead(String, BufferedReader, Printf) - Method in class org.strbio.mol.Protein
This looks for a protein and reads it in.
redrawNow() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.ProgressDialog
 
redScale - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
Color scales to draw things in.
reduce_A - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
reduce_AB - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
reduce_B - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
reduce_O - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
reduceTrain(Printf, double, double, double, double, double, double, DataInputStream) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
Setup reduced training sets based on p_set.
reduceTrain(Printf, double, double, double, double, double, double) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
This sets the defaults properly, for backward compatibility.
reduceTrain(Printf, DataInputStream) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
This sets the defaults properly.
reduceTrain(Printf) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
This sets the defaults properly, for backward compatibility.
ref - Variable in class org.strbio.mol.lib.BackbonePotential
reference state.
related - Variable in class org.strbio.util.db.Info
Related data, or null if there is none.
rememberCurrentURL() - Method in class org.strbio.util.ui.HelpFrame
save the current URL to the history list.
remove(DVector) - Method in class org.strbio.math.DVectorSet
Remove a DVector from the set.
remove(int) - Method in class org.strbio.math.DVectorSet
Remove DVector number i from the set, and return it.
remove(Polymer) - Method in class org.strbio.mol.PolymerSet
Remove a polymer from the set.
remove(int) - Method in class org.strbio.mol.PolymerSet
Remove polymer number i from the set, and return it.
remove(DLinkedList.Node) - Method in class org.strbio.util.DLinkedList
Remove an object from the list.
remove(int) - Method in class org.strbio.util.DLinkedList
Remove the n'th object from the list.
removeGraph(Graphable2D) - Method in class org.strbio.util.graph.Graph2D
Remove a graph.
removeQuickly() - Method in class org.strbio.mol.AtomNode
Removes this atom from the linked list, without going through the DLinkedList routines.
removeRedundantSequences(boolean) - Method in class org.strbio.mol.PolymerSet
Eliminate redundant sequences (or subsequences) from the set.
removeRedundantSequences(boolean) - Method in class org.strbio.mol.Profile
Eliminate redundant sequences (or subsequences) from the set.
removeSeq(int) - Method in class org.strbio.mol.Profile
Remove one of the sequences.
removeSeq(int) - Method in class org.strbio.mol.ProfRes
Remove one sequence from the ProfRes.
removeSpacesInNames() - Method in class org.strbio.mol.Profile
This changes all spaces in sequence names to _
removeStrMatchesOver(double) - Method in class org.strbio.mol.ThreadSet
Remove structural matches over a certain minarea score.
removeStrMatchesUnder(double) - Method in class org.strbio.mol.ThreadSet
Remove structural matches under a certain minarea score.
renumberMonomers(int) - Method in class org.strbio.mol.Polymer
Renumbers the monomers starting with a given integer.
renumberValidNonGapMonomers(int) - Method in class org.strbio.mol.Polymer
Like renumberMonomers, but only does the valid, non-gap monomers.
reOptimize(Hooke.Optimizable, double, double, int, int) - Static method in class org.strbio.util.Hooke
This call allows you to resume an interrupted optimization at a particular point; it allows the initial step size to still be very small while keeping a large rho.
repaint() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.ProteinPane
when we repaint, we also want to revalidate things.
replace(String, String, String) - Static method in class org.strbio.util.StringUtil
replace all occurences of String 'a' in a template with String 'b', returning a new String.
replaceEOL(String) - Static method in class org.strbio.util.StringUtil
Converts a string to another string with \n replaced by the local EOL character.
reRender() - Method in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
 
reRender() - Method in class org.strbio.util.BarLegend
 
reRender() - Method in class org.strbio.util.DensityPlot
 
reRender() - Method in class org.strbio.util.graph.Graph2D
Repaint everything.
res2Num(char) - Static method in class org.strbio.mol.Residue
Convert an amino acid one letter code to a number (0-20), in the order shown in Residue.oneLetter.
res2NumBLAST(char) - Static method in class org.strbio.mol.lib.BlastConstants
Convert an amino acid one letter code to a number (0-25), in the order shown in Residue.oneLetterBLAST.
res2NumDefay(char) - Static method in class org.strbio.mol.Residue
Convert an amino acid one letter code to a number (0-20), in the order shown in Residue.oneLetterDefay.
rescale(double, double) - Method in class org.strbio.math.DMatrix
Rescales every value in this DMatrix: data[i][j] -> (data[i][j] + offset) * scale
rescale(float, float) - Method in class org.strbio.math.FMatrix
Rescales every value in this FMatrix: data[i][j] -> (data[i][j] + offset) * scale
rescale() - Method in class org.strbio.util.graph.Graph2D
Rescale, if autoscaling.
rescale() - Method in class org.strbio.util.graph.PointColorPlot
Rescales, updates the legend.
rescaleTo(double, double) - Method in class org.strbio.math.DMatrix
Rescales to a given mean and standard deviation.
rescaleTo(float, float) - Method in class org.strbio.math.FMatrix
Rescales to a given mean and standard deviation.
reset() - Method in class org.strbio.io.EOFStringReader
 
Residue - Class in org.strbio.mol
Class to represent a single residue in a protein.
Residue() - Constructor for class org.strbio.mol.Residue
Constructor makes structure and predStructure '?'.
Residue(char) - Constructor for class org.strbio.mol.Residue
Make a new residue of a given type.
Residue(String) - Constructor for class org.strbio.mol.Residue
Make a new residue of a given type (3-letter code).
Residue(Residue) - Constructor for class org.strbio.mol.Residue
copy another residue, including the atoms.
residues() - Method in class org.strbio.mol.Protein
How many residues do we have?
residues() - Method in class org.strbio.mol.ProteinSet
total # of residues in the set
restrictK(int, int) - Method in class org.strbio.mol.lib.ScoreSippl90
Restrict scoring to a range of k values.
restrictK(int, int) - Method in class org.strbio.mol.lib.ScoreUFSippl90
Restrict scoring to a range of k values.
revalidate() - Method in class org.strbio.util.JMCScrollPane
should be called if the image or the size of the window are changed.
reverse() - Method in class org.strbio.math.DVector
reverses the order of data in the vector.
reverse(DVector) - Static method in class org.strbio.math.DVector
returns a vector which is the reverse of this one.
reverse() - Method in class org.strbio.math.FVector
reverses the order of data in the vector.
reverse(FVector) - Static method in class org.strbio.math.FVector
returns a vector which is the reverse of this one.
reverse() - Method in class org.strbio.math.IVector
reverses the order of data in the vector.
reverse(IVector) - Static method in class org.strbio.math.IVector
returns a vector which is the reverse of this one.
reverse(String) - Static method in class org.strbio.mol.Nucleotide
reverse
reverse() - Method in class org.strbio.mol.Polymer
Reverse yourself.
reverse() - Method in class org.strbio.mol.Protein
Reverse yourself.
reverse() - Method in class org.strbio.util.DLinkedList
Reverse yourself.
reverseComplement(String) - Static method in class org.strbio.mol.Nucleotide
reverse complement
reverseComplement() - Method in class org.strbio.mol.Primer
returns complement of this one
reverseCopy() - Method in class org.strbio.mol.Polymer
Return a reversed copy of yourself.
reverseEndian(int) - Static method in class org.strbio.util.JMC
byte-reverse an integer
reverseEndian(long) - Static method in class org.strbio.util.JMC
byte-reverse a long
reverseEndian(double) - Static method in class org.strbio.util.JMC
byte-reverse a double
reverseIndex(int) - Method in class org.strbio.mol.Primer
reset index to be the index from the other end of the DNA (usueful if you reverse complement)
reverseIndex(int) - Method in class org.strbio.mol.PrimerSet
reset index to be the index from the other end of the DNA (usueful if you reverse complement)
rightActually(int) - Method in class org.strbio.math.CorrectMatrix
How many of the items that actually belonged to category A were predicted correctly?
rightActually(int) - Method in class org.strbio.math.SimMatrix
How many of the items that actually belonged to category A were predicted correctly?
rightActually(int) - Method in class org.strbio.math.StatsMatrix
How many of the items that actually belonged to category A were predicted correctly?
rightPred(int) - Method in class org.strbio.math.SimMatrix
How many of the items predicted to be in category A were predicted correctly?
rms - Variable in class org.strbio.local.MaxSub.Results
 
RMS() - Method in class org.strbio.mol.Alignment
RMS of aligned CA positions.
RMS - Variable in class org.strbio.mol.AlignmentStats
RMS, correct alignment.
rotate(DMatrix) - Method in class org.strbio.mol.Atom
rotate an atom by multiplying by a 3x3 rotation matrix.
rotate(DMatrix) - Method in class org.strbio.mol.Molecule
rotate all atoms by multiplying by a 3x3 rotation matrix.
rotate(DMatrix) - Method in class org.strbio.mol.Monomer
rotate all atoms by multiplying by a 3x3 rotation matrix.
rotate(DMatrix) - Method in class org.strbio.mol.Polymer
rotate all monomers by multiplying by a 3x3 rotation matrix.
rounds - Variable in class org.strbio.local.PSIBlastP
How many rounds to do?
rows() - Method in class org.strbio.math.DHalfMatrix
Returns the number of rows (of the theoretical whole matrix, not just the upper triangular part.
rows() - Method in class org.strbio.math.DMatrix
returns the number of rows in the encapsulated array.
rows() - Method in class org.strbio.math.FHalfMatrix
Returns the number of rows (of the theoretical whole matrix, not just the upper triangular part.
rows() - Method in class org.strbio.math.FMatrix
returns the number of rows in the encapsulated array.
rows() - Method in class org.strbio.math.IMatrix
returns the number of rows in the encapsulated array.
run(Protein, Protein) - Method in class org.strbio.local.MaxSub
Run maxsub on two proteins, default cutoff is 3.5
run(Protein, Protein, double) - Method in class org.strbio.local.MaxSub
Run maxsub on two proteins
run(String) - Method in class org.strbio.local.Program
Run program with specified arguments, in foreground; both stdout and stdin are redirected to the
runBackground(String) - Method in class org.strbio.local.Program
Run program with specified arguments, in background, quietly.
runDSSP(Printf) - Method in class org.strbio.mol.Protein
Runs DSSP on this protein (which must have atomic coordinates).
runOnPolymerSet(PolymerSet, String) - Method in class org.strbio.local.Muscle
return a protein set resulting from running muscle on a protein set, with optional options to Muscle
runOnPolymerSet(PolymerSet) - Method in class org.strbio.local.Muscle
 
runOnProteins(Protein, Protein) - Method in class org.strbio.local.Malfe
Return a set of results, including alignment.
runOnProteins(Protein, Protein) - Method in class org.strbio.local.Minarea
Return a set of results, including alignment.
runOnProteinSet(ProteinSet) - Method in class org.strbio.local.ClustalW
return a string containing the raw output (aln file) from running clustalw on a protein set
runSilent(String) - Method in class org.strbio.local.Program
Run program with specified arguments, quietly.
rvs - Variable in class org.strbio.mol.PrimerSet
reverse primer

S

sample(double) - Method in class org.strbio.math.Bin
Sample a value.
sample(double, double) - Method in class org.strbio.math.Bin2D
 
sample(float) - Method in class org.strbio.math.FBin
Sample a value.
sample(double) - Method in class org.strbio.math.Sampler
 
Sampler - Class in org.strbio.math
This is a special case of Bin that samples data and can later return statistics like average, standard deviation.
Sampler() - Constructor for class org.strbio.math.Sampler
 
samples() - Method in class org.strbio.math.Bin
how many values have I sampled?
samples() - Method in class org.strbio.math.FBin
how many values have I sampled?
Sander() - Static method in class org.strbio.mol.lib.DayhoffMatrices
Some Sander matrix, for which I don't have the reference.
save(Printf) - Method in class org.strbio.math.DMatrix
Save to an open Printf.
save(String) - Method in class org.strbio.math.DMatrix
Saves to a new text file.
save(Printf) - Method in class org.strbio.math.DVector
Save to an open Printf.
save(String) - Method in class org.strbio.math.DVector
Saves to a new text file.
save(Printf) - Method in class org.strbio.math.FMatrix
Save to an open Printf.
save(String) - Method in class org.strbio.math.FMatrix
Saves to a new text file.
save(Printf) - Method in class org.strbio.math.FVector
Save to an open Printf.
save(String) - Method in class org.strbio.math.FVector
Saves to a new text file.
save(Printf) - Method in class org.strbio.math.IMatrix
Save to an open Printf.
save(String) - Method in class org.strbio.math.IMatrix
Saves to a new text file.
save(Printf) - Method in class org.strbio.math.IVector
Save to an open PrintfStream.
save(String) - Method in class org.strbio.math.IVector
Saves to a new text file.
save(Printf) - Method in class org.strbio.mol.AlignmentSet
Saves correct,calculated,nail alignments to a file in new format.
save(String) - Method in class org.strbio.mol.AlignmentSet
Saves correct,calculated,nail alignments to a file in new format.
save(Printf) - Method in class org.strbio.mol.AlignmentStats
Write these results to an output file.
save(String) - Method in class org.strbio.mol.lib.BackbonePotential
save histograms from a file... format is be all_raw, all_h, all_e, all_c, gly_raw, gly_h...
save(Printf) - Method in class org.strbio.mol.lib.MinareaResults
This should save all the results, except alignment, to one line in a file.
save(String) - Method in class org.strbio.mol.lib.PSIBlastMatrices
Save scoring matrix to a file.
save(Printf) - Method in class org.strbio.mol.lib.PSIBlastMatrices
Save scoring matrix to a file.
save(Printf) - Method in class org.strbio.mol.lib.Sippl90
Saved tabulated values to a file.
save(String) - Method in class org.strbio.mol.lib.Sippl90
Saves to a new text file.
save(String) - Method in class org.strbio.mol.PolymerSet
Save is equivalent to write.
save(PrintfStream) - Method in class org.strbio.util.NeuralNet
save weights in an open text file, for portability (to C) and readability.
save(String) - Method in class org.strbio.util.NeuralNet
save weights in text file, for portability (to C) and readability.
saveBinary(DataOutputStream) - Method in class org.strbio.math.DMatrix
Save in binary format to an open DataOutputStream.
saveBinary(String) - Method in class org.strbio.math.DMatrix
Saves to a new binary file.
saveBinary(DataOutputStream) - Method in class org.strbio.math.FMatrix
Save in binary format to an open DataOutputStream.
saveBinary(String) - Method in class org.strbio.math.FMatrix
Saves to a new binary file.
saveBinary(DataOutputStream) - Method in class org.strbio.math.IMatrix
Save in binary format to an open DataOutputStream
saveBinary(String) - Method in class org.strbio.math.IMatrix
Saves to a new binary file.
saveBinary(DataOutputStream) - Method in class org.strbio.util.NeuralNet
save weights in an open binary file, for speed.
saveBinary(String) - Method in class org.strbio.util.NeuralNet
save weights in binary file, for speed.
saveCalculated(String) - Method in class org.strbio.mol.AlignmentSet
Saves the calculated alignment to a file in old format.
saveCalculatedCASP(String) - Method in class org.strbio.mol.AlignmentSet
Save calculated alignment in CASP format
saveCalculatedCASP(Printf) - Method in class org.strbio.mol.AlignmentSet
Save calculated alignment in CASP format, to open file
saveCASP(String) - Method in class org.strbio.mol.Alignment
Save alignment in CASP format, creating new file.
saveCASP(Printf) - Method in class org.strbio.mol.Alignment
Save alignment in CASP format, to open file.
saveCASP() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.SaveWindow
 
saveCheckpoint(DataOutputStream) - Method in class org.strbio.mol.lib.PSIBlastMatrices
Save everything to a file, to be used with 'blastpgp -R filename'.
saveCheckpoint(String) - Method in class org.strbio.mol.lib.PSIBlastMatrices
Save everything to a file with a given name.
saveClassPred(double[]) - Method in class org.strbio.mol.lib.pred2ary.PCPSet
 
saveClassPred(double[], int) - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
save class pred to array
saveClassWeights() - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
save weights for all 5 class nets
saveCorrect(String) - Method in class org.strbio.mol.AlignmentSet
Saves the correct alignment to a file in old format.
savedBlastCheckpoint - Variable in class org.strbio.local.PSIBlastP
output file name to save BLAST checkpoint
savedBlastOutfile - Variable in class org.strbio.local.BlastP
output file name to save BLAST output
savedBlastOutfile2 - Variable in class org.strbio.local.PSIBlastP2
output file name to save BLAST output from 2nd search
saveDplot(String) - Method in class org.strbio.math.DMatrix
Saves in Dplot (ASGL) format to a new text file.
saveDplot(String) - Method in class org.strbio.math.FMatrix
Saves in Dplot (ASGL) format to a new text file.
saveEA() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.SaveWindow
 
saveEstAAStats(String) - Method in class org.strbio.mol.lib.AlignmentParametersEA
Save alignment accuracy stats to a file.
saveEstAAStats(Printf) - Method in class org.strbio.mol.lib.AlignmentParametersEA
Save accuracy stats to a file.
saveEstAAStats(String) - Method in class org.strbio.mol.ThreadSet
save the stats needed for alignment accuracy estimation to a file.
saveEstFRStats(String) - Method in class org.strbio.mol.lib.AlignmentParametersEA
Save alignment accuracy stats to a file.
saveEstFRStats(Printf) - Method in class org.strbio.mol.lib.AlignmentParametersEA
Save accuracy stats to a file.
saveEstFRStats(String) - Method in class org.strbio.mol.lib.FRParameters
Save alignment accuracy stats to a file.
saveEstFRStats(Printf) - Method in class org.strbio.mol.lib.FRParameters
Save accuracy stats to a file.
saveEstFRStats(String) - Method in class org.strbio.mol.ThreadSet
save the stats needed for FR accuracy estimation to a file.
saveFasta() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.SaveWindow
 
saveMSF() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.SaveWindow
 
saveOld(String) - Method in class org.strbio.mol.Alignment
Saves alignment to a file in old format.
savePDB(boolean) - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.SaveWindow
 
savePred(double[]) - Method in class org.strbio.mol.lib.pred2ary.PCPSet
 
savePred(double[], int) - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
save h, e to array.
saveProteins() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
open up a new save window and save in ea format to it.
saveProteinsB - Variable in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
saveProteinsMI - Variable in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
saveRaw(Printf) - Method in class org.strbio.mol.lib.Sippl90
Saved raw values to a file.
saveRaw(String) - Method in class org.strbio.mol.lib.Sippl90
Saves raw values to a new text file.
saveResultAS(Printf, AlignmentParametersEA, int) - Method in class org.strbio.mol.lib.ThreadResults
save one alignment in AS-readable format.
saveResultModeller(Printf, AlignmentParametersEA, int) - Method in class org.strbio.mol.lib.ThreadResults
save one result in AlignmentSet-readable format to a file.
saveResultsAS(Printf, AlignmentParametersEA, double) - Method in class org.strbio.mol.lib.ThreadResults
save results in AlignmentSet-readable format to a file.
saveResultsEnglish(Printf, AlignmentParametersEA, double) - Method in class org.strbio.mol.lib.ThreadResults
save results in english to a file.
saveResultsModeller(Printf, AlignmentParametersEA, double) - Method in class org.strbio.mol.lib.ThreadResults
save results in AlignmentSet-readable format to a file.
saveStrMatches(String) - Method in class org.strbio.mol.ThreadSet
Save structural matches to a file.
saveStrMatchesModeller(String) - Method in class org.strbio.mol.ThreadSet
Save structural matches to a modeller format file.
saveWindow - Variable in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
scg(int, Printf) - Method in class org.strbio.util.NeuralNet
Train using the scaled conjugate gradient algorithm for n cycles, from moller (1993).
SCOP - Class in org.strbio.net
Class to access SCOP over the web.
SCOP() - Constructor for class org.strbio.net.SCOP
 
SCOPInfo - Class in org.strbio.util.db
This is a class containing info that is found in SCOP.
SCOPInfo() - Constructor for class org.strbio.util.db.SCOPInfo
 
score - Variable in class org.strbio.local.MaxSub.Results
 
score - Variable in class org.strbio.mol.lib.MinareaResults
 
score(Residue, Residue) - Method in class org.strbio.mol.lib.Score2ary
 
score(Monomer, Monomer) - Method in class org.strbio.mol.lib.Score2ary
 
score(ProfResPSI, ProfResPSI) - Method in class org.strbio.mol.lib.ScoreAlphaTau
 
score(Monomer, Monomer) - Method in class org.strbio.mol.lib.ScoreAlphaTau
 
score(ProfResPSI, ProfResPSI) - Method in class org.strbio.mol.lib.ScoreAveragePSIBlast
 
score(Monomer, Monomer) - Method in class org.strbio.mol.lib.ScoreAveragePSIBlast
 
score(ProfResPSI, ProfResPSI) - Method in class org.strbio.mol.lib.ScoreAverageReversePSIBlast
 
score(Monomer, Monomer) - Method in class org.strbio.mol.lib.ScoreAverageReversePSIBlast
 
score(Residue, Residue) - Method in class org.strbio.mol.lib.ScoreBlosum62
 
score(Monomer, Monomer) - Method in class org.strbio.mol.lib.ScoreBlosum62
 
score(Residue, Residue) - Method in class org.strbio.mol.lib.ScoreDefay
 
score(Monomer, Monomer) - Method in class org.strbio.mol.lib.ScoreDefay
 
score(Residue, Residue) - Method in class org.strbio.mol.lib.ScoreFischer
 
score(Monomer, Monomer) - Method in class org.strbio.mol.lib.ScoreFischer
 
score(Monomer, Monomer) - Method in interface org.strbio.mol.lib.ScoreFunction
This function should return a score for aligning two monomers of a polymer, preferably with low = good, high = bad.
score(char, char) - Method in class org.strbio.mol.lib.ScoreID
This scoring function depends only on the residue type
score(Monomer, Monomer) - Method in class org.strbio.mol.lib.ScoreID
Returns EQUAL if residue types are the same, otherwise NOTEQUAL.
score(Residue, Residue) - Method in class org.strbio.mol.lib.ScoreJDB10
 
score(Monomer, Monomer) - Method in class org.strbio.mol.lib.ScoreJDB10
 
score(Residue, Residue) - Method in class org.strbio.mol.lib.ScorePairwiseDistance
Score is the distance between the residues' CA atoms.
score(Monomer, Monomer) - Method in class org.strbio.mol.lib.ScorePairwiseDistance
 
score(ProfResPSI, ProfResPSI) - Method in class org.strbio.mol.lib.ScorePhiPsi
 
score(Monomer, Monomer) - Method in class org.strbio.mol.lib.ScorePhiPsi
 
score(Residue, Residue) - Method in class org.strbio.mol.lib.ScorePred2ary
 
score(Monomer, Monomer) - Method in class org.strbio.mol.lib.ScorePred2ary
 
score(Residue, Residue) - Method in class org.strbio.mol.lib.ScorePredFreq
 
score(Monomer, Monomer) - Method in class org.strbio.mol.lib.ScorePredFreq
 
score(ProfResPSI, ProfResPSI) - Method in class org.strbio.mol.lib.ScorePSIBlast
 
score(Monomer, Monomer) - Method in class org.strbio.mol.lib.ScorePSIBlast
 
score(ProfResPSI, ProfResPSI) - Method in class org.strbio.mol.lib.ScoreReversePSIBlast
 
score(Monomer, Monomer) - Method in class org.strbio.mol.lib.ScoreReversePSIBlast
 
score(char, char) - Method in class org.strbio.mol.lib.ScoreScaledID
This scoring function depends only on the residue type
score(Monomer, Monomer) - Method in class org.strbio.mol.lib.ScoreScaledID
Returns EQUAL if monomer types are the same, otherwise NOTEQUAL.
score(Monomer, Monomer) - Method in class org.strbio.mol.lib.ScoreSippl90
 
score(Residue, Residue) - Method in class org.strbio.mol.lib.ScoreSippl90
This is somewhat hard to read; it is written for speed.
score(Monomer, Monomer) - Method in class org.strbio.mol.lib.ScoreUFSippl90
 
score(Residue, Residue) - Method in class org.strbio.mol.lib.ScoreUFSippl90
Restrict scoring to a range of k values.
Score2ary - Class in org.strbio.mol.lib
A scoring function that checks if the real 2ary structure matches.
Score2ary() - Constructor for class org.strbio.mol.lib.Score2ary
 
ScoreAlphaTau - Class in org.strbio.mol.lib
A scoring function that uses the 2ary prediction pseudopotential and alpha/tau angles of the fold.
ScoreAlphaTau(String, int, boolean, double) - Constructor for class org.strbio.mol.lib.ScoreAlphaTau
load potential in from a file.
ScoreAveragePSIBlast - Class in org.strbio.mol.lib
A scoring function that uses PSI-BLAST matrices, averaging the score over all residues in the fold.
ScoreAveragePSIBlast() - Constructor for class org.strbio.mol.lib.ScoreAveragePSIBlast
 
ScoreAverageReversePSIBlast - Class in org.strbio.mol.lib
A scoring function that uses PSI-BLAST matrices.
ScoreAverageReversePSIBlast() - Constructor for class org.strbio.mol.lib.ScoreAverageReversePSIBlast
 
scoreBackboneAlphaTau(double, double) - Method in class org.strbio.mol.ProfResPSI
the BackbonePotential score for putting this residue into a given alpha/tau.
scoreBackbonePhiPsi(double, double) - Method in class org.strbio.mol.ProfResPSI
the BackbonePotential score for putting this residue into a given phi/psi.
ScoreBlosum62 - Class in org.strbio.mol.lib
A scoring function that uses the default Blosum62 matrix Version 1.0, 1/28/99 - original version
ScoreBlosum62() - Constructor for class org.strbio.mol.lib.ScoreBlosum62
 
ScoreDefay - Class in org.strbio.mol.lib
A scoring function from Tom Defay's algorithm.
ScoreDefay(String) - Constructor for class org.strbio.mol.lib.ScoreDefay
 
ScoreDefay() - Constructor for class org.strbio.mol.lib.ScoreDefay
If no filename is specified, use the default table.
ScoreFischer - Class in org.strbio.mol.lib
A scoring function that checks if the predicted 2ary structure in the sequence matches the real secondary structure in the fold, while weighting a match by the predicted frequency.
ScoreFischer() - Constructor for class org.strbio.mol.lib.ScoreFischer
 
ScoreFunction - Interface in org.strbio.mol.lib
Interface for scoring functions.
ScoreID - Class in org.strbio.mol.lib
A scoring function that returns a non-scaled identity matrix.
ScoreID() - Constructor for class org.strbio.mol.lib.ScoreID
 
ScoreJDB10 - Class in org.strbio.mol.lib
A scoring function that uses JDB's 10% ID matrix.
ScoreJDB10(String) - Constructor for class org.strbio.mol.lib.ScoreJDB10
 
ScoreJDB10() - Constructor for class org.strbio.mol.lib.ScoreJDB10
If no filename is specified, use the default table.
scoreList - Variable in class org.strbio.mol.lib.AlignmentParameters
The scoring functions used.
ScoreList - Class in org.strbio.mol.lib
A scoring function return a identity matrix; this is set up so that a sampling of all calls to score() over a large set of sequences and folds will average 0.0 with a standard deviation of 1.0.
ScoreList() - Constructor for class org.strbio.mol.lib.ScoreList
make an empty ScoreList node.
ScoreList(ScoreFunction) - Constructor for class org.strbio.mol.lib.ScoreList
make a ScoreList node with a ScoreFunction.
ScoreList(ScoreFunction, double) - Constructor for class org.strbio.mol.lib.ScoreList
make a ScoreList node with a ScoreFunction and a weight.
scoreMatch - Variable in class org.strbio.mol.lib.FRParameters
composite score for each match (weighted sum of scores from all methods)
scoreNonMatch - Variable in class org.strbio.mol.lib.FRParameters
scores for each non-match
ScorePairwiseDistance - Class in org.strbio.mol.lib
A scoring function based on the CA distance between 2 residues.
ScorePairwiseDistance() - Constructor for class org.strbio.mol.lib.ScorePairwiseDistance
 
ScorePhiPsi - Class in org.strbio.mol.lib
A scoring function that uses the 2ary prediction pseudopotential and phi/psi angles of the fold.
ScorePhiPsi(String, int, boolean, double) - Constructor for class org.strbio.mol.lib.ScorePhiPsi
load potential in from a file.
ScorePhiPsi(BackbonePotential) - Constructor for class org.strbio.mol.lib.ScorePhiPsi
initialize scoring system from a pre-initialized BackbonePotential
ScorePhiPsi() - Constructor for class org.strbio.mol.lib.ScorePhiPsi
initialize scoring system with default BackbonePotential.
ScorePred2ary - Class in org.strbio.mol.lib
A scoring function that checks if the predicted 2ary structure in the sequence matches the real secondary structure in the fold.
ScorePred2ary() - Constructor for class org.strbio.mol.lib.ScorePred2ary
 
ScorePredFreq - Class in org.strbio.mol.lib
A scoring function that checks if the predicted 2ary structure in the sequence matches the real secondary structure in the fold, while weighting things by the predicted frequencies.
ScorePredFreq() - Constructor for class org.strbio.mol.lib.ScorePredFreq
 
ScorePSIBlast - Class in org.strbio.mol.lib
A scoring function that uses PSI-BLAST matrices.
ScorePSIBlast() - Constructor for class org.strbio.mol.lib.ScorePSIBlast
 
ScoreReversePSIBlast - Class in org.strbio.mol.lib
A scoring function that uses PSI-BLAST matrices.
ScoreReversePSIBlast() - Constructor for class org.strbio.mol.lib.ScoreReversePSIBlast
 
ScoreScaledDefay - Class in org.strbio.mol.lib
A scoring function from Tom Defay's algorithm, but rescaled.
ScoreScaledDefay(String) - Constructor for class org.strbio.mol.lib.ScoreScaledDefay
 
ScoreScaledDefay() - Constructor for class org.strbio.mol.lib.ScoreScaledDefay
 
ScoreScaledID - Class in org.strbio.mol.lib
A scoring function that returns a scaled identity matrix.
ScoreScaledID() - Constructor for class org.strbio.mol.lib.ScoreScaledID
 
ScoreSetup - Interface in org.strbio.mol.lib
Interface for scoring functions that need to be set up before being used on a given polymer.
ScoreSetup2 - Interface in org.strbio.mol.lib
Interface for scoring functions that need to be set up before being used on a given seq/fold pair.
ScoreSippl90 - Class in org.strbio.mol.lib
A scoring function that uses Sippl's 90 parameters, with the frozen approximation.
ScoreSippl90(String) - Constructor for class org.strbio.mol.lib.ScoreSippl90
load potential in from a file.
ScoreSippl90(Sippl90) - Constructor for class org.strbio.mol.lib.ScoreSippl90
initialize scoring system from a pre-initialized potential.
ScoreSippl90() - Constructor for class org.strbio.mol.lib.ScoreSippl90
initialize scoring system with default BackbonePotential.
ScoreUFSippl90 - Class in org.strbio.mol.lib
A scoring function that uses Sippl's 90 parameters, without the frozen approximation.
ScoreUFSippl90(String) - Constructor for class org.strbio.mol.lib.ScoreUFSippl90
load potential in from a file.
ScoreUFSippl90(Sippl90) - Constructor for class org.strbio.mol.lib.ScoreUFSippl90
initialize scoring system from a pre-initialized potential.
ScoreUFSippl90() - Constructor for class org.strbio.mol.lib.ScoreUFSippl90
initialize scoring system with default BackbonePotential.
scrollPanel - Variable in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
sd(int, Printf) - Method in class org.strbio.util.NeuralNet
Train using steepest descent for n cycles, unless stopped by low_error or max_error.
search(String, int, Printf) - Static method in class org.strbio.net.PubMed
returns array of Strings, each of which contains one complete MEDLINE search result
search(int, Printf) - Static method in class org.strbio.net.PubMed
returns String which contains one complete MEDLINE search result for a given accession code.
searchByName(String) - Method in class org.strbio.mol.PolymerSet
return a Polymer matching a given name, or null if not in set
searchByNameFuzzy(String, int) - Method in class org.strbio.mol.PolymerSet
Find a Polymer matching a given name, using fuzzy matching.
searchByNameFuzzy(String) - Method in class org.strbio.mol.PolymerSet
Find a Polymer matching a given name, using fuzzy matching.
searchByNameFuzzyIndex(String, int) - Method in class org.strbio.mol.PolymerSet
Find a Polymer matching a given name, using fuzzy matching, Returns the index, or -1 if nothing close is found.
searchByNameFuzzyIndex(String) - Method in class org.strbio.mol.PolymerSet
Find a Polymer matching a given name, using fuzzy matching, Returns the index, or -1 if nothing close is found.
searchByNameIndex(String) - Method in class org.strbio.mol.PolymerSet
return index of Polymer matching a given name, or -1 if not in set
seed - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
selfEnergy(Protein, int, int) - Method in class org.strbio.mol.lib.Sippl90
return the self-energy for a protein for a range of k's (including both ends of the range)
selfEnergy(Protein) - Method in class org.strbio.mol.lib.Sippl90
return the total self energy for a protein.
selfEnergyLR1(Protein) - Method in class org.strbio.mol.lib.Sippl90
return the long range (1) energy for a protein (k=31..60)
selfEnergyLR2(Protein) - Method in class org.strbio.mol.lib.Sippl90
return the long range (2) energy for a protein (k=61..100)
selfEnergyLR3(Protein) - Method in class org.strbio.mol.lib.Sippl90
return the long range (3) energy for a protein (k=101..150)
selfEnergyLR4(Protein) - Method in class org.strbio.mol.lib.Sippl90
return the long range (4) energy for a protein (k=151+)
selfEnergyMR(Protein) - Method in class org.strbio.mol.lib.Sippl90
return the medium range energy for a protein (k=11..30)
selfEnergySR(Protein) - Method in class org.strbio.mol.lib.Sippl90
return the short range energy for a protein (k=1..10)
separate - Variable in class org.strbio.mol.lib.BackbonePotential
separate GPN?
seq - Variable in class org.strbio.mol.Alignment
the sequence in the alignment.
seq - Variable in class org.strbio.mol.AlignmentSet
The sequence being aligned.
seq - Variable in class org.strbio.mol.ProfRes
Info on sequences in the profile, if available.
seqName - Variable in class org.strbio.mol.Profile
Name of each of the sequences in the profile, if sequence information is available; otherwise, null.
seqPctCoverage(int, int) - Method in class org.strbio.mol.Profile
Find pct coverage of second sequence by first.
seqPctID(int, int) - Method in class org.strbio.mol.Profile
Find pct id between 2 sequences, w/o gap penalties.
seqs - Variable in class org.strbio.mol.ThreadSet
Sequences being threaded.
seqToFold() - Method in class org.strbio.mol.Alignment
Returns a copy of the seq to fold array.
sequence() - Method in class org.strbio.mol.Polymer
Return the sequence as a string.
sequence(int) - Method in class org.strbio.mol.Profile
Return a string containing one of the sequences in the profile.
sequenceClicked - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
 
sequenceNonGap() - Method in class org.strbio.mol.Polymer
Return the sequence (only non-gap monomers) as a string.
sequences() - Method in class org.strbio.mol.Profile
Number of sequences in the profile, if known; otherwise, zero.
sequences() - Method in class org.strbio.mol.ProfRes
Number of sequences in the profile, if known; otherwise, zero.
sequenceValidNonGap() - Method in class org.strbio.mol.Polymer
Return the sequence (only valid non-gap monomers) as a string.
setAligned(int, int) - Method in class org.strbio.mol.Alignment
Sets seq monomer i to be aligned to fold monomer j.
setAlignment(Alignment) - Method in interface org.strbio.mol.lib.AlignmentDependent
This function is called to provide the alignment.
setAlignment(Alignment) - Method in class org.strbio.mol.lib.AlignmentParameters
Set the alignment for scoring functions that require it.
setAlignment(Alignment) - Method in class org.strbio.mol.lib.ScoreList
Set up scoring functions with a given Alignment functions that implement AlignmentDependent
setAlignment(Alignment) - Method in class org.strbio.mol.lib.ScoreUFSippl90
 
setBackground(Color) - Method in class org.strbio.util.JMCScrollPane
Sets the background of the viewport, not the scroll bars
setBars(DVector) - Method in class org.strbio.util.graph.BarPlot
Sets the bars being drawn.
setBaseLibrary(FoldLibrary) - Method in class org.strbio.mol.lib.JMCThreadMethod2
Set a custom BASE fold library.
setBaseURL(String) - Method in class org.strbio.net.BlastWeb
Sets the base url; i.e. to "http://www.ncbi.nlm.nih.gov/cgi-bin/BLAST/"
setBias(int, int, double) - Method in class org.strbio.util.NeuralNet
set the bias of a given neuron.
setBox(int) - Method in class org.strbio.util.graph.Graph2D
Sets box drawing style.
setCheckpointFile(String) - Method in class org.strbio.local.PSIBlastP
set output file name to save BLAST checkpoint, or null to use a temporary file
setColorScale(ColorScale) - Method in class org.strbio.util.BarLegend
Set the color scale to use.
setColorScale(ColorScale) - Method in class org.strbio.util.DensityPlot
Set the color scale to use.
setColorScale(ColorScale) - Method in class org.strbio.util.graph.ColorScaleLegend
Set the color scale to use.
setColorScale(ColorScale) - Method in class org.strbio.util.graph.PointColorPlot
Set the color scale to use.
setError(OutputStream) - Method in class org.strbio.local.Program
redirect process error to a given stream
setFlipped(boolean) - Method in interface org.strbio.util.graph.AxisScale
Flip this axis from normal java orientation (left->right, top->bottom).
setFlipped(boolean) - Method in class org.strbio.util.graph.XAxisScale
Flip this axis from normal java orientation (left->right, top->bottom).
setFlipped(boolean) - Method in class org.strbio.util.graph.YAxisScale
Flip this axis from normal java orientation (left->right, top->bottom).
setFont(String, int) - Method in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
Set font to draw labels.
setFont(Font, FontMetrics) - Method in interface org.strbio.util.graph.AxisScale
set the font labels will be printed in.
setFont(Font, FontMetrics) - Method in class org.strbio.util.graph.ColorScaleLegend
set the font labels will be printed in.
setFont(Font) - Method in class org.strbio.util.graph.Graph2D
Sets the font for all labels / titles.
setFont(Font, FontMetrics) - Method in interface org.strbio.util.graph.Legend
set the font labels will be printed in.
setFont(Font, FontMetrics) - Method in class org.strbio.util.graph.PointLegend
set the font labels will be printed in.
setFont(Font, FontMetrics) - Method in class org.strbio.util.graph.XAxisScale
set the font labels will be printed in.
setFont(Font, FontMetrics) - Method in class org.strbio.util.graph.YAxisScale
set the font labels will be printed in.
setFontSize(int) - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
setFontSize(int) - Method in class org.strbio.util.ui.GUIApp
Set the font size.
setFormat(String) - Method in class org.strbio.util.BarLegend
Sets the format string for printing min, max; i.e. "%.2f".
setFormat(String) - Method in interface org.strbio.util.graph.AxisScale
set the format labels will be printed in.
setFormat(String) - Method in class org.strbio.util.graph.ColorScaleLegend
Sets the format string for printing min, max; i.e. "%.2f".
setFormat(String) - Method in class org.strbio.util.graph.Graph2D
Sets the format string for printing axis scales.
setFormat(String) - Method in class org.strbio.util.graph.XAxisScale
set the format labels will be printed in.
setFormat(String) - Method in class org.strbio.util.graph.YAxisScale
set the format labels will be printed in.
setGraphSize(int, int) - Method in class org.strbio.util.graph.Graph2D
Set the preferred size of the graph window.
setHookeParameters(double, double, int, int) - Method in class org.strbio.mol.ThreadSet
used to set optimizing parameters for optimize* functions; these are the Hooke parameters.
setInput(InputStream) - Method in class org.strbio.local.Program
redirect process input from a given stream
setInput(int, double) - Method in class org.strbio.util.NeuralNet
set a network input
setLabel(String) - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
give user a short message.
setLabel(String) - Method in class org.strbio.util.graph.ColorScaleLegend
set the label for this legend.
setLabel(String) - Method in interface org.strbio.util.graph.Legend
set the label for this legend.
setLabel(String) - Method in class org.strbio.util.graph.PointLegend
set the label for this legend.
setLegend(ColorScaleLegend) - Method in class org.strbio.util.graph.PointColorPlot
sets legend.
setLegend(PointLegend) - Method in class org.strbio.util.graph.PointPlot
sets legend.
setListener(ClickablePointPlot.ClickListener) - Method in class org.strbio.util.graph.ClickablePointPlot
 
setListener(Graph2D.ClickListener) - Method in class org.strbio.util.graph.Graph2D
Sets the object that listens for clicks on the graph.
setMajorTics(int) - Method in class org.strbio.util.graph.XAxisScale
Sets the number of major tics on the axis.
setMajorTics(int) - Method in class org.strbio.util.graph.YAxisScale
Sets the number of major tics on the axis.
setMajorTicsOn(double) - Method in class org.strbio.util.graph.XAxisScale
puts major tics everywhere on the axis that's divisible by this number.
setMajorTicsOn(double) - Method in class org.strbio.util.graph.YAxisScale
puts major tics everywhere on the axis that's divisible by this number.
setMask(boolean[][]) - Method in class org.strbio.util.DensityPlot
Sets the current mask matrix; does not make a copy.
setMatrix(DMatrix) - Method in class org.strbio.util.DensityPlot
Set the matrix being drawn.
setMatrixFile(String) - Method in class org.strbio.local.PSIBlastP
set output file name to save BLAST matrix (text), or null to not save it
setMax(double) - Method in class org.strbio.util.DensityPlot
Set the maximum value to plot... turns off autoscaling of the maximum.
setMax(double) - Method in interface org.strbio.util.graph.AxisScale
set the maximum value that will be graphed.
setMax(double) - Method in class org.strbio.util.graph.XAxisScale
set the maximum value that will be graphed.
setMax(double) - Method in class org.strbio.util.graph.YAxisScale
set the maximum value that will be graphed.
setMaxX(double) - Method in class org.strbio.util.graph.Graph2D
Set the maximum x value to plot... turns off autoscaling of the maximum.
setMaxY(double) - Method in class org.strbio.util.graph.Graph2D
Set the maximum y value to plot... turns off autoscaling of the maximum.
setMin(double) - Method in class org.strbio.util.DensityPlot
Set the minimum value to plot... turns off autoscaling of the minimum.
setMin(double) - Method in interface org.strbio.util.graph.AxisScale
set the minimum value that will be graphed.
setMin(double) - Method in class org.strbio.util.graph.XAxisScale
set the minimum value that will be graphed.
setMin(double) - Method in class org.strbio.util.graph.YAxisScale
set the minimum value that will be graphed.
setMinMax(double, double) - Method in class org.strbio.util.BarLegend
Sets the min anx max values for the scale.
setMinMax(double, double) - Method in class org.strbio.util.graph.ColorScaleLegend
Sets the min anx max values for the scale.
setMinorTics(int) - Method in class org.strbio.util.graph.XAxisScale
sets the number of minor tics between each major tic.
setMinorTics(int) - Method in class org.strbio.util.graph.YAxisScale
sets the number of minor tics between each major tic.
setMinX(double) - Method in class org.strbio.util.graph.Graph2D
Set the minimum X value to plot... turns off autoscaling.
setMinY(double) - Method in class org.strbio.util.graph.Graph2D
Set the minimum Y value to plot... turns off autoscaling.
setNext(DLinkedList.Node) - Method in class org.strbio.mol.AtomNode
set the next AtomNode
setNext(DLinkedList.Node) - Method in class org.strbio.mol.Monomer
set the next monomer in the polymer.
setNext(DLinkedList.Node) - Method in interface org.strbio.util.DLinkedList.Node
This should set the next node in the list to a given linkable object.
setNJurors(int) - Method in interface org.strbio.mol.lib.pred2ary.Jury.ProgressIndicator
Tell the progress indicator how many jurors there are total.
setNJurors(int) - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.ProgressDialog
 
setNNodes(int) - Method in class org.strbio.util.DLinkedList
Tell the list that it now has N objects.
setOptimizableParameters(double[]) - Method in class org.strbio.mol.lib.GapAffine
set all the optimizable (double) parameters from a vector.
setOptimizableParameters(double[]) - Method in class org.strbio.mol.lib.GapConstant
set all the optimizable (double) parameters from a vector.
setOptimizableParameters(double[]) - Method in class org.strbio.mol.lib.GapDistanceDependent
set all the optimizable (double) parameters from a vector.
setOptimizableParameters(double[]) - Method in interface org.strbio.mol.lib.GapModel
set all the optimizable (double) parameters from a vector.
setOptimizableParameters(double[]) - Method in class org.strbio.mol.lib.GapModelAdapter
by default, nothing is optimizable.
setOrientation(int) - Method in class org.strbio.util.DensityPlot
Set the preferred orientation.
setOrientation(int) - Method in class org.strbio.util.graph.Graph2D
Set the preferred orientation.
setOriginal(boolean) - Method in class org.strbio.mol.lib.JMCThreadMethod2
Use the original fold library in addition to the other library?
setOutput(OutputStream) - Method in class org.strbio.local.Program
redirect process output to a given stream
setOutput(int, double) - Method in class org.strbio.util.NeuralNet
set a network output
setOutputFile(String) - Method in class org.strbio.local.BlastP
set output file name to save BLAST output, or null to use a temporary file
setOutputFile2(String) - Method in class org.strbio.local.PSIBlastP2
set output file name to save BLAST output from 2nd search, or null to use a temporary file
setPatternPresenter(NeuralNet.Trainable) - Method in class org.strbio.util.NeuralNet
set the pattern presentation object.
setPointAt(int, DVector) - Method in class org.strbio.math.DVectorSet
set the i'th point in the set.
setPointAtFast(int, DVector) - Method in class org.strbio.math.DVectorSet
set the i'th point in the set.
setPoints(DVectorSet) - Method in class org.strbio.util.graph.ClickablePointPlot
Sets the points being drawn.
setPoints(DVectorSet) - Method in class org.strbio.util.graph.PointColorPlot
Set the points being drawn.
setPoints(DVectorSet) - Method in class org.strbio.util.graph.PointPlot
Sets the points being drawn.
setPointType(PointType) - Method in class org.strbio.util.graph.ClickablePointPlot
Set point type to draw.
setPointType(PointType) - Method in class org.strbio.util.graph.PointPlot
Set point type to draw.
setPolymerAt(int, Polymer) - Method in class org.strbio.mol.PolymerSet
set the i'th polymer in the set.
setPotential(BackbonePotential) - Method in class org.strbio.mol.lib.ScorePhiPsi
Use a pre-initialized BackbonePotential.
setPrev(DLinkedList.Node) - Method in class org.strbio.mol.AtomNode
set the previous AtomNode
setPrev(DLinkedList.Node) - Method in class org.strbio.mol.Monomer
set the previous monomer in the polymer.
setPrev(DLinkedList.Node) - Method in interface org.strbio.util.DLinkedList.Node
This should set the previous node in the list to a given linkable object.
setProgramName(String) - Method in class org.strbio.local.Program
Set the name of this program
setProperty(int) - Method in class org.strbio.mol.Polymer
sets one property.
setProperty(int) - Method in class org.strbio.mol.PolymerSet
sets one property.
setProteins(ProfilePSISet) - Method in class org.strbio.app.JThread
 
setProteins(ProfilePSISet) - Method in class org.strbio.app.JThreadText
 
setProteins(ProfileSet) - Method in class org.strbio.util.ui.ProfileGUIApp
set the current protein set.
setPSIBlastMatrices(PSIBlastMatrices) - Method in class org.strbio.local.PSIBlastP
Get scoring matrix.
setQuery(Protein) - Method in class org.strbio.local.BlastPAdapter
Sets a query protein.
setQuery(String) - Method in class org.strbio.local.BlastPAdapter
Sets a query sequence (just protein for now).
setQuery(Protein) - Method in interface org.strbio.mol.lib.Blast
Sets a query protein.
setQuery(String) - Method in interface org.strbio.mol.lib.Blast
 
setQuery(Protein) - Method in class org.strbio.mol.lib.BlastAdapter
Sets a query protein.
setQuery(String) - Method in class org.strbio.mol.lib.BlastAdapter
Sets a query sequence (just protein for now).
setQuery(String) - Method in class org.strbio.mol.lib.PSIBlastMatrices
Set the query sequence to a given string.
setQuery(Protein) - Method in class org.strbio.mol.lib.PSIBlastMatrices
Set the query sequence to a given string.
sets - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
sets_2 - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
setSeqName(int, String) - Method in class org.strbio.mol.Profile
set the name of sequence i
setSequence(int, String) - Method in class org.strbio.mol.Profile
Set the sequence for one of the sequences in the profile.
setShownAl(int) - Method in class org.strbio.app.JThread
called when row N in the table is clicked.
setShownProtein(int) - Method in class org.strbio.app.JThread
 
setSize(int, int) - Method in class org.strbio.util.DensityPlot
Set the preferred size.
setTitle(String) - Method in class org.strbio.util.graph.Graph2D
Sets title.
setUnaligned(int) - Method in class org.strbio.mol.Alignment
Sets seq monomer i to be unaligned.
setup(Polymer, Polymer) - Method in class org.strbio.mol.lib.AlignmentParameters
Set up everything for doing an alignment on a given seq and fold.
setup(Polymer, Polymer) - Method in class org.strbio.mol.lib.GapDistanceDependent
Calculate distance matrix.
setup(Polymer, Polymer) - Method in interface org.strbio.mol.lib.GapModel
Perform any last minute setup before align/comparison.
setup(Polymer, Polymer) - Method in class org.strbio.mol.lib.GapModelAdapter
Default is no setup.
setup(Polymer, Polymer) - Method in class org.strbio.mol.lib.OptimalAAParameters
kludge to set up precalculated phi/psi angles in the fold
setup(Polymer, Polymer) - Method in class org.strbio.mol.lib.OptimalAAParametersFR
kludge to set up precalculated phi/psi angles in the fold
setup(Polymer) - Method in class org.strbio.mol.lib.ScoreAlphaTau
 
setup(Polymer) - Method in class org.strbio.mol.lib.ScoreAveragePSIBlast
 
setup(Polymer, Polymer) - Method in class org.strbio.mol.lib.ScoreAveragePSIBlast
 
setup(Polymer) - Method in class org.strbio.mol.lib.ScoreAverageReversePSIBlast
 
setup(Polymer) - Method in class org.strbio.mol.lib.ScoreList
Set up scoring functions for a given protein, for all scoring functions that implement ScoreSetup.
setup(Polymer, Polymer) - Method in class org.strbio.mol.lib.ScoreList
Set up scoring functions for a given protein pair, for all scoring functions that implement ScoreSetup2.
setup(Polymer) - Method in class org.strbio.mol.lib.ScorePhiPsi
 
setup(Polymer) - Method in class org.strbio.mol.lib.ScorePSIBlast
 
setup(Polymer) - Method in class org.strbio.mol.lib.ScoreReversePSIBlast
 
setup(Polymer) - Method in interface org.strbio.mol.lib.ScoreSetup
This function is to set up the scoring function for use on a polymer.
setup(Polymer, Polymer) - Method in interface org.strbio.mol.lib.ScoreSetup2
This function is to set up the scoring function for use on a pair.
setup(Polymer, Polymer) - Method in class org.strbio.mol.lib.ScoreSippl90
 
setup(Polymer, Polymer) - Method in class org.strbio.mol.lib.ScoreUFSippl90
 
setup2aryNet(String, Printf) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
set up networks... returns true if loaded in old weights.
setup2aryNet(DataInputStream) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
Setup 2ary network from a binary input stream.
setupActions() - Method in class org.strbio.app.JThread
 
setupActions() - Method in class org.strbio.util.ui.ProfileGUIApp
set up what each Action is supposed to do.
setupBackbonePotential(boolean, BackbonePotential, double, double) - Method in class org.strbio.mol.ProfilePSI
set up the BackbonePotential scoring matrices for all residues
setupBackbonePotential(boolean, BackbonePotential) - Method in class org.strbio.mol.ProfilePSI
set up the BackbonePotential scoring matrices for all residues.
setupBackbonePotential(boolean, BackbonePotential, double, double) - Method in class org.strbio.mol.ProfResPSI
set up the BackbonePotential scoring matrices
setupBackbonePotential(boolean, BackbonePotential) - Method in class org.strbio.mol.ProfResPSI
set up the BackbonePotential scoring matrices
setupClassNet(String, Printf) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
set up class networks... returns true if loaded in old weights.
setupClassNet(DataInputStream) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
Setup class networks from a binary input stream.
setupFakePSIBlastMatrix() - Method in class org.strbio.mol.ProfilePSI
Set up fake PSI-blast matrices at each position, using the BLAST (blosum62) matrix.
setupFontSizeMenu() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
setupFontSizeMenu() - Method in class org.strbio.util.ui.GUIApp
Set up a font size menu.
setupFontSizeMenuItem(int, Menu) - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
setupFrame(URL, Point, Dimension) - Method in class org.strbio.util.ui.HelpFrame
Create a help frame with the given index url.
setupLvl2Net(String, Printf) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
set up lvl 2 network... returns true if loaded in old weights.
setupLvl2Net(DataInputStream) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
Setup lvl2 network from a binary input stream.
setupPSIBlastMatrix(PSIBlastMatrices) - Method in class org.strbio.mol.ProfilePSI
Set up PSI-blast matrices at each position.
setValue(double) - Method in class org.strbio.math.DMatrix
Sets every value in the matrix to a specified double.
setValue(double) - Method in class org.strbio.math.DVector
Sets every value in the array to a specified double.
setValue(float) - Method in class org.strbio.math.FMatrix
Sets every value in the matrix to a specified float.
setValue(float) - Method in class org.strbio.math.FVector
Sets every value in the array to a specified float.
setValue(int) - Method in class org.strbio.math.IMatrix
Sets every value in the matrix to a specified int.
setValue(int) - Method in class org.strbio.math.IVector
Sets every value in the matrix to a specified int.
setValueAt(int, int, double) - Method in class org.strbio.math.DHalfMatrix
This allows you to set a value at column x, row y in the theoretical whole matrix.
setValueAt(int, int, double) - Method in class org.strbio.math.DMatrix
Sets the data at a given column/row.
setValueAt(int, double) - Method in class org.strbio.math.DVector
Sets the data at a given index.
setValueAt(int, int, float) - Method in class org.strbio.math.FHalfMatrix
This allows you to set a value at column x, row y in the theoretical whole matrix.
setValueAt(int, int, float) - Method in class org.strbio.math.FMatrix
Sets the data at a given column/row.
setValueAt(int, float) - Method in class org.strbio.math.FVector
Sets the data at a given index.
setValueAt(int, int, int) - Method in class org.strbio.math.IMatrix
Sets the data at a given column/row.
setValueAt(int, int) - Method in class org.strbio.math.IVector
Sets the data at a given index.
setVars(double[]) - Method in interface org.strbio.util.CGOptimizer.Optimizable
This should set the optimizable variables to values from the array.
setVars(double[]) - Method in interface org.strbio.util.Hooke.Optimizable
This should set the optimizable variables to values from the array.
setWeight(int, int, int, double) - Method in class org.strbio.util.NeuralNet
Set a given weight.
setXAxisLabel(String) - Method in class org.strbio.util.graph.Graph2D
Sets x axis label
setYAxisLabel(String) - Method in class org.strbio.util.graph.Graph2D
Sets y axis label
sfArray - Variable in class org.strbio.mol.Alignment
A vector containing the current alignment.
shift(Alignment) - Method in class org.strbio.mol.Alignment
calculate average alignment shift, as in CASP2.
shift() - Method in class org.strbio.mol.AlignmentSet
calculate average alignment shift, as in CASP2.
shift - Variable in class org.strbio.mol.AlignmentStats
average alignment shift
shiftToChar(int) - Static method in class org.strbio.mol.Alignment
Convert an alignment shift to an ascii character for printing.
SHORTEST_ALIGNMENT_LENGTH - Static variable in class org.strbio.mol.Alignment
The smallest number of consecutive monomers that can be aligned: currently 2.
show_individual - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
show_reduce - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
showAboutDialog() - Method in class org.strbio.app.JThread
show the "about" dialog.
showCorrect - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
 
showFRAll(Printf) - Method in class org.strbio.mol.ThreadSet
show comparison results for all proteins.
showFRMatches(Printf) - Method in class org.strbio.mol.ThreadSet
show comparison results for str matches.
showGaps(Printf) - Method in class org.strbio.mol.Protein
Print out possible gaps in the sequence.
showHelp(String) - Method in class org.strbio.app.Pred2ary
shows help, located under lib/Pred2ary/, or the index if null filename given.
showHelp(String) - Method in class org.strbio.mol.lib.pred2ary.Pred2aryApplet
Display a file in the browser.
showHelp(String) - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
showHelp(String) - Method in class org.strbio.util.ui.GUIApp
shows help, located under appDataPath, or the index if null filename given.
showLastURL() - Method in class org.strbio.util.ui.HelpFrame
Show the last URL shown before this one, or index if nothing else.
showPMatch(Printf) - Method in class org.strbio.mol.ThreadSet
shows probability of a structural match for various Z score ranges.
showPrediction - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
 
showProfile - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
What exactly to show?
showProteins() - Method in class org.strbio.app.JThread
 
showProteins() - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
showProteins() - Method in class org.strbio.util.ui.ProfileGUIApp
 
showURL(URL) - Method in class org.strbio.util.ui.HelpFrame
Show a given URL in the help box.
sigma - Variable in class org.strbio.mol.lib.BackbonePotential
Scale GPN in Sippl-like manner?
SimMatrix - Class in org.strbio.math
This is a NxN matrix, where data[i][j] indicates the number of times something was actually i, but predicted to be j.
SimMatrix() - Constructor for class org.strbio.math.SimMatrix
 
SimMatrix(int) - Constructor for class org.strbio.math.SimMatrix
 
SimMatrix(IMatrix) - Constructor for class org.strbio.math.SimMatrix
 
SimMatrix(int[][]) - Constructor for class org.strbio.math.SimMatrix
 
Sippl90 - Class in org.strbio.mol.lib
Sippl scoring method, from JMB 90 papers.
Sippl90() - Constructor for class org.strbio.mol.lib.Sippl90
Don't initialize anything.
SM - Variable in class org.strbio.mol.lib.pred2ary.TPSet
 
SmallAppletJury - Class in org.strbio.mol.lib.pred2ary
The 'small' network set. 1 juror (level 1 and 2 networks), trained on training set 0 only.
SmallAppletJury(Pred2aryApplet) - Constructor for class org.strbio.mol.lib.pred2ary.SmallAppletJury
Create a new jury.
SmallJury - Class in org.strbio.mol.lib.pred2ary
The 'small' network set. 1 juror (level 1 and 2 networks), trained on training set 0 only.
SmallJury() - Constructor for class org.strbio.mol.lib.pred2ary.SmallJury
Create a new jury.
smithWaterman - Variable in class org.strbio.local.PSIBlastP
Do Smith-Waterman alignments?
smooth(double, int) - Method in class org.strbio.math.DMatrix
This function smooths the matrix by averaging over adjacent blocks.
smooth(float, int) - Method in class org.strbio.math.FMatrix
This function smooths the matrix by averaging over adjacent blocks.
smooth(int) - Method in class org.strbio.mol.lib.pred2ary.TPSet
smooth h and e
smoothHE() - Method in class org.strbio.mol.Protein
Do one round of 'diffusive smoothing' on the predH and predE values in a protein's residues.
smoothPeriodic(double, int) - Method in class org.strbio.math.DMatrix
This function smooths the matrix by averaging over adjacent blocks.
smoothPeriodic(float, int) - Method in class org.strbio.math.FMatrix
This function smooths the matrix by averaging over adjacent blocks.
sort() - Method in class org.strbio.math.DVector
returns a vector of indices to sort an DVector (small -> large).
sort() - Method in class org.strbio.math.FVector
returns a vector of indices to sort an FVector (small -> large).
sort() - Method in class org.strbio.math.IVector
returns a vector of indices to sort an IVector (small -> large).
sorted - Variable in class org.strbio.mol.lib.ThreadResults
A sorted vector of the probabilities, from highest to lowest.
source - Variable in class org.strbio.util.db.PDBInfo
Source, from the PDB's SOURCE records.
sparseBack(double[], int[], int) - Method in class org.strbio.util.NeuralNet
fast version of back for sparse inputs
sparseBoolBack(double[], int[], int) - Method in class org.strbio.util.NeuralNet
fast version of back for sparse inputs.
sparseBoolProp(int[], int) - Method in class org.strbio.util.NeuralNet
prop optimized for lots of zero inputs.
sparseDeltaProp(int[], int, int[], int) - Method in class org.strbio.util.NeuralNet
prop, but with a vector of inputs that have been added since the last call, and a vector that have been removed.
sparseProp(int[], int) - Method in class org.strbio.util.NeuralNet
prop, optimized for lots of zero inputs.
split(String, String) - Static method in class org.strbio.util.StringUtil
splits a string into an array of strings; wrapper for StringTokenizer null delimiter is the same as the default for ST.
split(String) - Static method in class org.strbio.util.StringUtil
splits a string into an array of strings; wrapper for StringTokenizer.
splitCopy() - Method in class org.strbio.mol.lib.pred2ary.PredClassProfile
 
splitCopy() - Method in class org.strbio.mol.Polymer
This should return a copy of all data which should be copied during AutoSplit (not including monomers, monDistance, name).
splitCopy(Profile) - Method in class org.strbio.mol.Profile
When a Profile is split, sequence names should go to each child.
splitCopy() - Method in class org.strbio.mol.Profile
When a Profile is split, sequence names should go to each child.
splitCopy() - Method in class org.strbio.mol.ProfilePSI
 
splitCopy() - Method in class org.strbio.mol.Protein
 
SplitProteins - Class in org.strbio.app
Split protein set into several.
SplitProteins() - Constructor for class org.strbio.app.SplitProteins
 
sprintf(char[], String, boolean) - Static method in class org.strbio.util.StringUtil
Formats a string without any parameter substitution, but with formatting (i.e.
sprintf(char[], String) - Static method in class org.strbio.util.StringUtil
default convertLF is true.
sprintf(char[], String, int, boolean) - Static method in class org.strbio.util.StringUtil
Formats an int.
sprintf(char[], String, int) - Static method in class org.strbio.util.StringUtil
default convertLF is true.
sprintf(char[], String, long, boolean) - Static method in class org.strbio.util.StringUtil
Formats a long.
sprintf(char[], String, long) - Static method in class org.strbio.util.StringUtil
default convertLF is true.
sprintf(char[], String, char, boolean) - Static method in class org.strbio.util.StringUtil
Formats a char.
sprintf(char[], String, char) - Static method in class org.strbio.util.StringUtil
default convertLF is true.
sprintf(char[], String, String, boolean) - Static method in class org.strbio.util.StringUtil
formats a String.
sprintf(char[], String, String) - Static method in class org.strbio.util.StringUtil
default convertLF is true.
sprintf(char[], String, double, boolean) - Static method in class org.strbio.util.StringUtil
formats a double.
sprintf(char[], String, double) - Static method in class org.strbio.util.StringUtil
default convertLF is true.
sprintf(char[], String, float, boolean) - Static method in class org.strbio.util.StringUtil
Formats a float.
sprintf(char[], String, float) - Static method in class org.strbio.util.StringUtil
default convertLF is true.
sqlDate() - Static method in class org.strbio.sql.SQLUtil
what's the date to use in sql queries?
SQLUtil - Class in org.strbio.sql
Utilities to use in SQL.
SQLUtil() - Constructor for class org.strbio.sql.SQLUtil
 
SSPredictor - Interface in org.strbio.mol.lib
Interface for common secondary structure prediction routines.
StandardJury - Class in org.strbio.mol.lib.pred2ary
Class that implements a jury of secondary structure prediction networks.
StandardJury(String) - Constructor for class org.strbio.mol.lib.pred2ary.StandardJury
Create a new jury, given the name of the binary input file.
standardProb() - Static method in class org.strbio.mol.lib.BlastConstants
What BLAST thinks are the standard probabilities of each residue occurring.
startRes - Variable in class org.strbio.util.db.CATHInfo
starting residue number in domain, or -1 for whole chain.
stats(Printf) - Method in class org.strbio.mol.Alignment
get statistics on the alignment.
stats(Printf) - Method in class org.strbio.mol.AlignmentSet
get statistics on the alignment.
StatsMatrix - Class in org.strbio.math
This class describes a special kind of integer matrix which is used for keeping stats on how well a predictive procedure is performing.
StatsMatrix() - Constructor for class org.strbio.math.StatsMatrix
 
StatsMatrix(int, int) - Constructor for class org.strbio.math.StatsMatrix
 
StatsMatrix(IMatrix) - Constructor for class org.strbio.math.StatsMatrix
 
StatsMatrix(int[][]) - Constructor for class org.strbio.math.StatsMatrix
 
statusLine - Variable in class org.strbio.util.ui.GUIApp
 
stdev() - Method in class org.strbio.math.Bin
Return the standard deviation of all values sampled.
stdev(int) - Method in class org.strbio.math.Bin2D
St dev of values sampled in a particular bin.
stdev() - Method in class org.strbio.math.DMatrix
Returns the standard deviation of a distribution containing all values in the matrix.
stdev() - Method in class org.strbio.math.DVector
Returns the standard deviation of a distribution containing all values in the array.
stdev() - Method in class org.strbio.math.FBin
Return the standard deviation of all values sampled.
stdev() - Method in class org.strbio.math.FMatrix
Returns the standard deviation of a distribution containing all values in the matrix.
stdev() - Method in class org.strbio.math.FVector
Returns the standard deviation of a distribution containing all values in the array.
stdevp() - Method in class org.strbio.math.Bin
Returns the standard deviation of all values sampled.
stdevp() - Method in class org.strbio.math.DMatrix
Returns the standard deviation of a distribution containing all values in the matrix.
stdevp() - Method in class org.strbio.math.DVector
Returns the standard deviation of a distribution containing all values in the array.
stdevp() - Method in class org.strbio.math.FMatrix
Returns the standard deviation of a distribution containing all values in the matrix.
stdevp() - Method in class org.strbio.math.FVector
Returns the standard deviation of a distribution containing all values in the array.
steps - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
steps_2 - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
sThread - Static variable in class org.strbio.app.JThreadServer
 
stringToScores(String) - Method in class org.strbio.mol.lib.PSIBlastMatrices
Get frequencies out of a string.
StringUtil - Class in org.strbio.util
Useful functions for doing stuff with strings.
StringUtil() - Constructor for class org.strbio.util.StringUtil
 
stripAllAtoms() - Method in class org.strbio.mol.Monomer
Strip away all atoms from this monomer.
stripAllAtoms() - Method in class org.strbio.mol.Polymer
Strip out all atoms from all monomers.
stripAllBut(String[]) - Method in class org.strbio.mol.Monomer
Strip away all atoms except ones named in an array.
stripAllBut(String[]) - Method in class org.strbio.mol.Polymer
Strip away all atoms except ones named in an array.
stripAllButCA() - Method in class org.strbio.mol.Protein
go to each residue, and remove all atoms except alpha carbons (CA).
stripAllButCA() - Method in class org.strbio.mol.Residue
Strip away all atoms except alpha carbons (atoms named "CA").
stripAllButFirstAtom() - Method in class org.strbio.mol.Monomer
Strip all but first atom from this monomer.
stripAllButFirstAtom() - Method in class org.strbio.mol.Polymer
Strip all but first atom from all monomers.
stripAtomsByName(String) - Method in class org.strbio.mol.Monomer
Strip away a named atom or atoms.
stripAtomsByName(String) - Method in class org.strbio.mol.Polymer
Strip away a named atom or atoms.
stripCommonGaps() - Method in class org.strbio.mol.Alignment
Strip common gaps in the two sequences
stripCommonGaps(Polymer) - Method in class org.strbio.mol.Polymer
strip out all gaps in 2 polymers which occur at the same location.
stripGaps() - Method in class org.strbio.mol.Alignment
Strip all gaps in the two sequences
stripGaps() - Method in class org.strbio.mol.AlignmentSet
Strip gaps from both seq and fold.
stripGaps() - Method in class org.strbio.mol.Polymer
strip out all gaps.
stripHTML(String) - Static method in class org.strbio.util.HTML
Strip all HTML in a string, returning a new String.
stripHTML(String) - Static method in class org.strbio.util.StringUtil
Deprecated. use HTML.stripHTML
stripInvalidAndGaps() - Method in class org.strbio.mol.Polymer
strip out all invalid monomers and gaps.
stripLeading0() - Method in class org.strbio.util.db.CATHInfo
strip leading 0's from the number.
stripLeading0() - Method in class org.strbio.util.db.SCOPInfo
strip leading 0's from the number.
stripNoAtoms() - Method in class org.strbio.mol.Polymer
strip out all monomers with no atoms.
stripNoAtoms() - Method in class org.strbio.mol.PolymerSet
strip out monomers without atomic coordinates, for all Polymers.
stripType(char) - Method in class org.strbio.mol.Polymer
strip out all monomers with a certain type.
structure - Variable in class org.strbio.mol.Residue
the structure, as defined by DSSP.
submit(Protein, Printf) - Static method in class org.strbio.net.ThreeDPSSM
Query the server
subtract(DMatrix) - Method in class org.strbio.math.DMatrix
Subtracts another DMatrix from this one.
subtract(double) - Method in class org.strbio.math.DMatrix
Subtracts a double to every value in this DMatrix.
subtract(DMatrix, DMatrix) - Static method in class org.strbio.math.DMatrix
Subtracts one DMatrix's from another returns a new DMatrix containing the difference.
subtract(DVector) - Method in class org.strbio.math.DVector
Subtracts another DVector from this one.
subtract(DVector, DVector) - Static method in class org.strbio.math.DVector
Subtracts one DVector's from another returns a new DVector containing the difference.
subtract(FMatrix) - Method in class org.strbio.math.FMatrix
Subtracts another FMatrix from this one.
subtract(float) - Method in class org.strbio.math.FMatrix
Subtracts a float to every value in this FMatrix.
subtract(FMatrix, FMatrix) - Static method in class org.strbio.math.FMatrix
Subtracts one FMatrix's from another returns a new FMatrix containing the difference.
subtract(FVector) - Method in class org.strbio.math.FVector
Subtracts another FVector from this one.
subtract(FVector, FVector) - Static method in class org.strbio.math.FVector
Subtracts one FVector's from another returns a new FVector containing the difference.
subtract(IMatrix) - Method in class org.strbio.math.IMatrix
Subtracts another IMatrix from this one.
subtract(IMatrix, IMatrix) - Static method in class org.strbio.math.IMatrix
Subtracts one IMatrix's from another returns a new IMatrix containing the difference.
subtract(IVector) - Method in class org.strbio.math.IVector
Subtracts another IVector from this one.
subtract(IVector, IVector) - Static method in class org.strbio.math.IVector
Subtracts one IVector's from another returns a new IVector containing the difference.
sum_x - Variable in class org.strbio.math.Bin
 
sum_x - Variable in class org.strbio.math.FBin
 
sum_x2 - Variable in class org.strbio.math.Bin
 
sum_x2 - Variable in class org.strbio.math.FBin
 
sum_xy - Variable in class org.strbio.math.Bin2D
 

T

tabbedPane - Variable in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
tail() - Method in class org.strbio.util.DLinkedList
returns the tail of the list.
target - Variable in class org.strbio.mol.lib.ThreadResults
The protein that was threaded.
TargetDB - Class in org.strbio.net
Class to access http://targetdb.pdb.org Version 1.0, 9/22/03 - original version
TargetDB() - Constructor for class org.strbio.net.TargetDB
 
tau() - Method in class org.strbio.mol.Residue
Tau is the dihedral angle between CA(n-1), CA(n), CA(n+1), CA(n+2).
TBlastN - Class in org.strbio.local
Runs a local copy of tblastn.
TBlastN() - Constructor for class org.strbio.local.TBlastN
Initialize with no information; you still have to call setQuery before starting Blast.
TBlastN(String) - Constructor for class org.strbio.local.TBlastN
Initialize with a given query sequence.
TBlastN(Protein) - Constructor for class org.strbio.local.TBlastN
Initialize with a given protein.
tempFactor - Variable in class org.strbio.mol.Atom
Temperature (B) factor.
test - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
test_2 - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
textArea - Variable in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.LoadWindow
 
textArea - Variable in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.SaveWindow
 
textCheckpointName - Variable in class org.strbio.local.PSIBlastP
 
theta - Variable in class org.strbio.mol.lib.MinareaResults
 
thread(Protein, Printf) - Method in class org.strbio.mol.lib.JMCThreadMethod
Thread a given protein, returning a ThreadResults object.
thread(ProteinSet, Printf) - Method in class org.strbio.mol.lib.JMCThreadMethod
Thread a given protein set, returning an array of ThreadResults objects.
thread(Protein, Printf) - Method in class org.strbio.mol.lib.JMCThreadMethod2
Thread a given protein, returning a ThreadResults object.
thread(ProteinSet, Printf) - Method in class org.strbio.mol.lib.JMCThreadMethod2
Thread a given protein set, returning an array of ThreadResults objects.
thread(Protein, Printf) - Method in interface org.strbio.mol.lib.ThreadMethod
Thread a given protein, returning a ThreadResults object.
thread(ProteinSet, Printf) - Method in interface org.strbio.mol.lib.ThreadMethod
Thread a given protein set, returning an array of ThreadResults objects.
thread(Printf, ThreadMethod) - Method in class org.strbio.mol.Protein
Thread the protein, using a specified threading method.
thread(Printf) - Method in class org.strbio.mol.Protein
Thread, using the default method.
thread(Printf, ThreadMethod) - Method in class org.strbio.mol.ProteinSet
Thread the proteins, using a specified threading method.
thread(Printf) - Method in class org.strbio.mol.ProteinSet
Thread, using the default method.
ThreadMethod - Interface in org.strbio.mol.lib
A method that does threading.
ThreadResults - Class in org.strbio.mol.lib
Threading results on one protein.
ThreadResults() - Constructor for class org.strbio.mol.lib.ThreadResults
 
ThreadSet - Class in org.strbio.mol
Class to keep track of two sets of proteins that are being used in threading algorithms.
ThreadSet() - Constructor for class org.strbio.mol.ThreadSet
Initialize everything to default values.
three2One(String) - Static method in class org.strbio.mol.Residue
Convert your 3-letter code into 1-letter code.
three2One(String) - Static method in class org.strbio.raf.RAFResidue
Convert your 3-letter code into 1-letter code.
ThreeDPSSM - Class in org.strbio.net
Class to submit jobs to 3dpssm server Version 1.0, 9/25/02 - original version
ThreeDPSSM() - Constructor for class org.strbio.net.ThreeDPSSM
 
threeLetter - Static variable in class org.strbio.mol.Residue
three letter code, in alphabetical order.
threeLetter - Static variable in class org.strbio.raf.RAFResidue
three letter code
title - Variable in class org.strbio.util.db.PDBInfo
Title, from the PDB's TITLE records.
tm(String) - Method in class org.strbio.local.Melting
return the melting temperature for a dna sequence
tm(String, String) - Method in class org.strbio.local.Melting
return the melting temperature for a dna sequence, with given complement.
tm - Variable in class org.strbio.mol.Primer
calculated melting temperature
tm(String) - Method in class org.strbio.net.Alces
return the melting temperature for a dna sequence
tmpnam() - Static method in class org.strbio.util.StringUtil
Like tmpnam() in C, but stupider... doesn't put the file into a /tmp directory or whatever the local equivalent is.
toCharArrays() - Method in class org.strbio.mol.Alignment
Saves alignment in 2 char[] arrays (sequence and fold), so it can be printed.
toDMatrix() - Method in class org.strbio.math.DVectorSet
Return the DVector set expressed as a matrix, with one row per point, and one column per dimension.
tolerance - Variable in class org.strbio.mol.ThreadSet
margin for error in evaluating alignments.
TOMFoldLibrary - Class in org.strbio.mol.lib
The TOM fold library.
TOMFoldLibrary() - Constructor for class org.strbio.mol.lib.TOMFoldLibrary
 
totalActually(int) - Method in class org.strbio.math.CorrectMatrix
How many items are there in category A?
totalActually(int) - Method in class org.strbio.math.SimMatrix
How many items are there in category A?
totalActually(int) - Method in class org.strbio.math.StatsMatrix
How many items are there in category A?
totalPred(int) - Method in class org.strbio.math.SimMatrix
How many items predicted to be in category A?
totalScore(Monomer, Monomer) - Method in class org.strbio.mol.lib.ScoreList
return the total score for a monomer pair, from all scoring functions at this point on.
totalZMatch - Variable in class org.strbio.mol.lib.AlignmentParametersEA
z score of total score for each match.
totalZNonMatch - Variable in class org.strbio.mol.lib.AlignmentParametersEA
z score of total score for each non-match.
TPSet - Class in org.strbio.mol.lib.pred2ary
Class to represent a set of profiles being used in 2ary structure prediction; this might be either a training or prediction set.
TPSet() - Constructor for class org.strbio.mol.lib.pred2ary.TPSet
 
TPSet(TPSet) - Constructor for class org.strbio.mol.lib.pred2ary.TPSet
 
TPSet.NetVars - Class in org.strbio.mol.lib.pred2ary
Class with variables used to configure the neural nets.
TPSet.NetVars() - Constructor for class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
train2ary(Printf) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
do the whole 2ary training procedure
train2aryLoop(Printf) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
train one net as much as needed, including finding cutoff and predicting prediction set, if we're testing.
train2aryNet(int, Printf) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
train a few steps, return actual number trained
train2aryTcp(int, int, Printf) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
train, cutoff, predict for a single training set, or group of them... returns actual number of steps taken, and the average error.
trainClass(Printf) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
do the whole class training procedure
trainClassLoop(Printf) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
train one net as much as needed, including finding cutoff and predicting prediction set, if we're testing.
trainClassNet(int, boolean[], Printf) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
train a few steps, return actual number trained
trainClassTcp(int, boolean[], Printf) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
train, cutoff, predict for a single training set, or group of them... returns actual number of steps taken, avg error on cnet4, and average error on cnet1's.
TrainingSet - Class in org.strbio.mol.lib.pred2ary
Class to represent a set of profiles being used in 2ary structure prediction as a training set.
TrainingSet() - Constructor for class org.strbio.mol.lib.pred2ary.TrainingSet
 
TrainingSet(TrainingSet) - Constructor for class org.strbio.mol.lib.pred2ary.TrainingSet
Copy the set, but don't dupicate any data/networks.
TrainingSet.Present2ary - Class in org.strbio.mol.lib.pred2ary
 
TrainingSet.Present2ary(TPSet.NetVars) - Constructor for class org.strbio.mol.lib.pred2ary.TrainingSet.Present2ary
 
TrainingSet.PresentClass1 - Class in org.strbio.mol.lib.pred2ary
class to show proteins to class prediction network (1-output) depends on training_class being set.
TrainingSet.PresentClass1(TPSet.NetVars) - Constructor for class org.strbio.mol.lib.pred2ary.TrainingSet.PresentClass1
 
TrainingSet.PresentClass4 - Class in org.strbio.mol.lib.pred2ary
class to show proteins to class prediction network (4-output)
TrainingSet.PresentClass4(TPSet.NetVars) - Constructor for class org.strbio.mol.lib.pred2ary.TrainingSet.PresentClass4
 
TrainingSet.PresentLvl2 - Class in org.strbio.mol.lib.pred2ary
 
TrainingSet.PresentLvl2(TPSet.NetVars) - Constructor for class org.strbio.mol.lib.pred2ary.TrainingSet.PresentLvl2
 
trainLvl2(Printf) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
do the whole 2ary training procedure on lvl2 net
trainLvl2Loop(Printf) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
train one net as much as needed, including finding cutoff and predicting prediction set, if we're testing.
trainLvl2Net(int, Printf) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
train a few steps, return actual number trained
trainLvl2Tcp(int, int, Printf) - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
train, cutoff, predict for a single training set, or group of them... returns actual number of steps taken, and average error.
transform(DMatrix) - Method in class org.strbio.math.DVector
transforms this vector using a transformation DMatrix.
transform(FMatrix) - Method in class org.strbio.math.FVector
transforms this vector using a transformation FMatrix.
transform(DMatrix) - Method in class org.strbio.mol.Atom
transform the position of an atom using a 3x4 (or 4x4 with the last column constant) transformation matrix.
transform(DMatrix) - Method in class org.strbio.mol.Molecule
transform the position of all atoms.
transform(DMatrix) - Method in class org.strbio.mol.Monomer
transform the position of all atoms.
transform(DMatrix) - Method in class org.strbio.mol.Polymer
transform the position of all monomers.
transform(double, double, Point) - Method in class org.strbio.util.graph.Graph2D
Transforms a given value (x,y) in real coordinates into a point to be plotted on the screen, considering min, max, etc.
translate(DVector) - Method in class org.strbio.mol.Atom
translate an atom by adding a DVector(3) to its coordinates.
translate(DVector) - Method in class org.strbio.mol.Molecule
translate all atoms by adding a DVector(3) to their coordinates.
translate(DVector) - Method in class org.strbio.mol.Monomer
translate all atoms by adding a DVector(3) to their coordinates.
translate(DVector) - Method in class org.strbio.mol.Polymer
translate all monomers by adding a DVector(3) to their coordinates.
translate2ary() - Method in class org.strbio.mol.lib.pred2ary.TPSet
translate he to predictions
translateClass() - Method in class org.strbio.mol.lib.pred2ary.TPSet
saved net outputs -> class predictions
translateEA() - Method in class org.strbio.mol.lib.pred2ary.TPSet
 
translateEA() - Method in class org.strbio.mol.Protein
Translates predH and predE into predStructure (directly).
translateEA() - Method in class org.strbio.mol.Residue
Translates predH and predE into predStructure (directly).
transpose() - Method in class org.strbio.math.DMatrix
Returns the transpose of this DMatrix.
transpose() - Method in class org.strbio.math.FMatrix
Returns the transpose of this FMatrix.
trimEnds(char) - Method in class org.strbio.mol.Polymer
strip out all monomers with a certain type from both ends of the sequence.
truncate(DLinkedList.Node) - Method in class org.strbio.util.DLinkedList
Truncate the list after a certain node.
truncate(int) - Method in class org.strbio.util.DLinkedList
Truncate the list after nth node.
truncateBefore(DLinkedList.Node) - Method in class org.strbio.util.DLinkedList
Truncate the list before a certain node.
truncateBefore(int) - Method in class org.strbio.util.DLinkedList
Truncate the list before nth node.
truncateNames(int) - Method in class org.strbio.mol.Profile
This truncates all names to a given length (or less).
type - Variable in class org.strbio.mol.Monomer
type of monomer, in a one-letter code
typeName() - Method in class org.strbio.mol.Monomer
Return a long name for this monomer, based on the type.
typeName() - Method in class org.strbio.mol.Residue
Return a long name for this monomer, based on the type.

U

UnfilledCirclePoint - Class in org.strbio.util.graph
A point type that paints circles.
UnfilledCirclePoint(int) - Constructor for class org.strbio.util.graph.UnfilledCirclePoint
need radius of the point to draw
UNIFORM - Static variable in class org.strbio.mol.lib.BackbonePotential
Reference state is uniform probability.
unJackknife() - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
reverse jackknifing
unReduceTrain() - Method in class org.strbio.mol.lib.pred2ary.TrainingSet
remove training set reduction.
update(int) - Method in interface org.strbio.mol.lib.pred2ary.Jury.ProgressIndicator
Tell the progress indicator that we've done juror number N
update(int) - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.ProgressDialog
 
updateLoad(int) - Method in interface org.strbio.mol.lib.pred2ary.AppletJury.LoadProgressIndicator
Tell the progress indicator that we've loaded x percent of the jury from the web server.
updateLoad(int) - Method in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame.ProgressDialog
 
USE_LENGTH_INFO - Static variable in class org.strbio.mol.lib.pred2ary.TPSet
Set this to allow the class prediction algorith to know the length rules without learning them from the training set.
use_sd - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
UserFoldLibrary - Class in org.strbio.mol.lib
A standard fold library for threading, loaded in by the user.
UserFoldLibrary() - Constructor for class org.strbio.mol.lib.UserFoldLibrary
 
UserFoldLibrary(String) - Constructor for class org.strbio.mol.lib.UserFoldLibrary
 
UserFoldLibrary(String, Printf) - Constructor for class org.strbio.mol.lib.UserFoldLibrary
 

V

validNonGapMonomers() - Method in class org.strbio.mol.Polymer
How many valid non-gap monomers do we have?
valueAt(int, int) - Method in class org.strbio.math.DHalfMatrix
This allows you to get a value at column x, row y in the theoretical whole matrix.
valueAt(int, int) - Method in class org.strbio.math.DMatrix
Returns the data at a given column/row.
valueAt(int) - Method in class org.strbio.math.DVector
Returns the data at a given index.
valueAt(int, int) - Method in class org.strbio.math.FHalfMatrix
This allows you to get a value at column x, row y in the theoretical whole matrix.
valueAt(int, int) - Method in class org.strbio.math.FMatrix
Returns the data at a given column/row.
valueAt(int) - Method in class org.strbio.math.FVector
Returns the data at a given index.
valueAt(int, int) - Method in class org.strbio.math.IMatrix
Returns the data at a given column/row.
valueAt(int) - Method in class org.strbio.math.IVector
Returns the data at a given index.
VAR_TOM_INFO - Static variable in class org.strbio.mol.PolymerProperties
Protein property: is there TOM information on residue variability?
vars - Variable in class org.strbio.mol.lib.pred2ary.TPSet
 
VarTom - Class in org.strbio.local
Class to run var-tom on a protein.
VarTom() - Constructor for class org.strbio.local.VarTom
 
verify() - Method in class org.strbio.util.DLinkedList
Verify that the list is intact (for debugging purposes).
VERSION - Static variable in class org.strbio.app.BlastProtein
 
VERSION - Static variable in class org.strbio.app.ConvertProtein
 
version() - Method in class org.strbio.app.JThread
what's the version?
version() - Method in class org.strbio.app.JThreadText
what's the version?
VERSION - Static variable in class org.strbio.app.Modify2ary
 
VERSION - Static variable in class org.strbio.app.SplitProteins
 
VERSION - Static variable in class org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
 
version() - Method in class org.strbio.util.ui.GUIApp
what's the version?

W

w_w - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
w_w_2 - Variable in class org.strbio.mol.lib.pred2ary.TPSet.NetVars
 
waitForServerData(String, int) - Method in class org.strbio.mol.lib.pred2ary.Pred2aryApplet
Read a file on the server, and wait until the entire file is received.
warnUser(String) - Method in class org.strbio.app.Pred2ary
 
warnUser(String) - Method in class org.strbio.util.ui.GUIApp
 
weight - Variable in class org.strbio.mol.ProfRes
Conservation weight, as defined by Rost & Sander.
weight(int, int, int) - Method in class org.strbio.util.NeuralNet
Return a given weight.
weight_2ary - Variable in class org.strbio.mol.lib.pred2ary.TrainingSet
 
weight_class - Variable in class org.strbio.mol.lib.pred2ary.TrainingSet
 
weight_lvl2 - Variable in class org.strbio.mol.lib.pred2ary.TrainingSet
 
weightAverage - Variable in class org.strbio.mol.lib.FRParametersNode
How much to weight the average (gapped) score of the alignments?
weightCoverage - Variable in class org.strbio.mol.lib.FRParametersNode
How much to weight the alignment coverage of the alignments?
weightLength - Variable in class org.strbio.mol.lib.FRParameters
How much to weight the length ratio?
weightTotal - Variable in class org.strbio.mol.lib.FRParametersNode
How much to weight the total score of the alignments?
weightZScore - Variable in class org.strbio.mol.lib.FRParametersNode
How much to weight the Z score (of the total score) of the alignments?
wrapLines - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
 
wrapPos - Variable in class org.strbio.mol.lib.pred2ary.ProfileDisplayArea
 
write(String) - Method in class org.strbio.mol.PolymerSet
Write set to a file, with name determined by the suffix.
write(String) - Method in class org.strbio.mol.ProfileSet
Write set to a file, with name determined by the suffix.
write(String) - Method in class org.strbio.mol.ProteinSet
Write set to a file, with name determined by the suffix.
writeAccessRecord(Printf) - Method in class org.strbio.mol.Residue
Write ACCESS record to YAPF file.
writeAngleRecord(Printf) - Method in class org.strbio.mol.Residue
Write ANGLE record to YAPF file.
writeCASP(Printf) - Method in class org.strbio.mol.Protein
Write in CASP format.
writeCASP(String) - Method in class org.strbio.mol.ProteinSet
Write set to CASP file.
writeCASP(Printf) - Method in class org.strbio.mol.ProteinSet
Write set to CASP file.
writeCASP(Printf) - Method in class org.strbio.mol.Residue
Writes out this residue in CASP format.
writeClustal(Printf) - Method in class org.strbio.mol.Profile
Write in CLUSTAL format.
writeClustal(String) - Method in class org.strbio.mol.ProfileSet
Write set to Clustal file.
writeClustal(Printf) - Method in class org.strbio.mol.ProfileSet
Write set to Clustal file.
writeConv(Printf) - Method in class org.strbio.mol.Protein
Write in Conv format.
writeConv(String) - Method in class org.strbio.mol.ProteinSet
Write set to Conv file.
writeConv(Printf) - Method in class org.strbio.mol.ProteinSet
Write set to Conv file.
writeConv(Printf) - Method in class org.strbio.mol.Residue
Writes out this residue in Conv format.
writeCWRecord(Printf) - Method in class org.strbio.mol.ProfRes
Write CW info for this residue in JMC's YAPF format.
writeDSSPRecord(Printf) - Method in class org.strbio.mol.Residue
Write DSSP record to YAPF file.
writeEA(Printf) - Method in class org.strbio.mol.Protein
Write in EA format.
writeEA(String) - Method in class org.strbio.mol.ProteinSet
Write set to EA file.
writeEA(Printf) - Method in class org.strbio.mol.ProteinSet
Write set to EA file.
writeEA(Printf) - Method in class org.strbio.mol.Residue
Writes out this residue in EA format.
writeFasta(Printf) - Method in class org.strbio.mol.Polymer
Write in Fasta format.
writeFasta(String) - Method in class org.strbio.mol.PolymerSet
Write set to Fasta file.
writeFasta(Printf) - Method in class org.strbio.mol.PolymerSet
Write set to Fasta file.
writeFasta(Printf) - Method in class org.strbio.mol.Profile
Write each sequence in the profile in Fasta format.
writeFREQRecord(Printf) - Method in class org.strbio.mol.ProfRes
Write FREQ info for this residue in JMC's YAPF format.
writeList(Printf) - Method in class org.strbio.mol.PolymerSet
create a file with a list of protein names in it.
writeList(String) - Method in class org.strbio.mol.PolymerSet
create a file with a list of protein names in it.
writeMSF(Printf) - Method in class org.strbio.mol.Profile
Write in MSF format.
writeMSF(String) - Method in class org.strbio.mol.ProfileSet
Write set to MSF file.
writeMSF(Printf) - Method in class org.strbio.mol.ProfileSet
Write set to MSF file.
writePDB(Printf, String, char, String, int) - Method in class org.strbio.mol.Atom
Write the atom to a file in PDB format.
writePDB(Printf) - Method in class org.strbio.mol.Polymer
Write in PDB format, which includes SEQRES and ATOM records.
writePDB(String) - Method in class org.strbio.mol.PolymerSet
Write set to PDB file.
writePDB(Printf) - Method in class org.strbio.mol.PolymerSet
Write set to PDB file.
writePDB(Printf, boolean) - Method in class org.strbio.mol.Protein
Write in PDB format, which includes SEQRES and ATOM records.
writePDB(Printf) - Method in class org.strbio.mol.Protein
Write in PDB format, including SEQRES, JMCSTR, and ATOM records.
writePDB(String, boolean) - Method in class org.strbio.mol.ProteinSet
Write set to PDB file.
writePDB(Printf, boolean) - Method in class org.strbio.mol.ProteinSet
Write set to PDB file.
writePDB(String) - Method in class org.strbio.mol.ProteinSet
Write set to PDB file, including all SEQRES, JMCSTR, and ATOM records.
writePDB(Printf) - Method in class org.strbio.mol.ProteinSet
Write set to PDB file, including all SEQRES, JMCSTR, and ATOM records.
writePDBAtom(Printf, String, char) - Method in class org.strbio.mol.Monomer
Writes out PDB ATOM records for all atoms belonging to this monomer.
writePDBAtom(Printf) - Method in class org.strbio.mol.Polymer
Write PDB ATOM records for this polymer.
writePDBSeqres(Printf) - Method in class org.strbio.mol.Polymer
Write PDB SEQRES records for this polymer.
writePDBStr(Printf) - Method in class org.strbio.mol.Residue
Writes out PDB JMCSTR records for this residue.
writePredSSRecord(Printf) - Method in class org.strbio.mol.Residue
Write PREDSS record to YAPF file.
writeProf(Printf) - Method in class org.strbio.mol.Profile
Write in Prof format.
writeProf(String) - Method in class org.strbio.mol.ProfileSet
Write set to Prof file.
writeProf(Printf) - Method in class org.strbio.mol.ProfileSet
Write set to Prof file.
writeProf(Printf) - Method in class org.strbio.mol.ProfRes
Write this residue in JMC's .prof format.
writePSIBlastRecord(Printf) - Method in class org.strbio.mol.ProfResPSI
Write PSIBLAST record to YAPF file.
writePts(Printf) - Method in class org.strbio.mol.Monomer
Writes out this monomer in PTS (Jon Blake's) format.
writePTS(Printf) - Method in class org.strbio.mol.Polymer
Write in PTS format.
writePTS(String) - Method in class org.strbio.mol.PolymerSet
Write set to PTS file.
writePTS(Printf) - Method in class org.strbio.mol.PolymerSet
Write set to PTS file.
writeSAF(Printf) - Method in class org.strbio.mol.Profile
Write in Burkhard Rost's SAF format.
writeSAF(String) - Method in class org.strbio.mol.ProfileSet
Write set to SAF file.
writeSAF(Printf) - Method in class org.strbio.mol.ProfileSet
Write set to SAF file.
writeSeqRecord(Printf) - Method in class org.strbio.mol.Monomer
Write this monomer in JMC's YAPF format.
writeSeqRecord(Printf) - Method in class org.strbio.mol.ProfRes
Write this residue in JMC's YAPF format.
writeTDP(Printf) - Method in class org.strbio.mol.Profile
A simple way of printing the profile, that var-tom uses as input.
writeTDP(String) - Method in class org.strbio.mol.ProfileSet
A simple way of printing profiles, that var-tom uses as input.
writeVar2(Printf) - Method in class org.strbio.mol.Protein
Write in Var2 format.
writeVar2(String) - Method in class org.strbio.mol.ProteinSet
Write set to Var2 file.
writeVar2(Printf) - Method in class org.strbio.mol.ProteinSet
Write set to Var2 file.
writeVar2(Printf) - Method in class org.strbio.mol.Residue
Writes out this residue in Var2 format.
writeVarTomRecord(Printf) - Method in class org.strbio.mol.Residue
Write VarTom record to YAPF file.
writeYAPF(Printf) - Method in class org.strbio.mol.Polymer
A portable way of writing a polymer, which is expandable to include protein/profile info also.
writeYAPF(String) - Method in class org.strbio.mol.PolymerSet
Write set to YAPF file.
writeYAPF(Printf) - Method in class org.strbio.mol.PolymerSet
Write set to YAPF file.
writeYAPF(Printf) - Method in class org.strbio.util.db.CATHInfo
write this info to a single line of a file, so it can be read later.
writeYAPF(Printf) - Method in class org.strbio.util.db.Data
write all info to a Printf.
writeYAPF(String) - Method in class org.strbio.util.db.Data
write all info to a file.
writeYAPF(Printf) - Method in class org.strbio.util.db.Info
write this info to a single line of a file, so it can be read later.
writeYAPF(Printf) - Method in class org.strbio.util.db.PDBInfo
write this info to a single line of a file, so it can be read later.
writeYAPF(Printf) - Method in class org.strbio.util.db.SCOPInfo
write this info to a single line of a file, so it can be read later.
writeYAPFAtom(Printf, char) - Method in class org.strbio.mol.Monomer
Writes out YAPF ATOM records for all atoms belonging to this monomer.
writeYAPFAtom(Printf) - Method in class org.strbio.mol.Polymer
Write YAPF ATOM records for this polymer.
writeYAPFInfo(Printf) - Method in class org.strbio.mol.Polymer
Write applicable sections of YAPF info.
writeYAPFInfo(Printf) - Method in class org.strbio.mol.Profile
Write applicable sections of YAPF info.
writeYAPFInfo(Printf) - Method in class org.strbio.mol.ProfilePSI
Write applicable sections of YAPF info.
writeYAPFInfo(Printf) - Method in class org.strbio.mol.Protein
Write applicable sections of YAPF info.
wrongActually(int) - Method in class org.strbio.math.CorrectMatrix
How many of the items that actually belonged to category A were predicted incorrectly?
wrongActually(int) - Method in class org.strbio.math.SimMatrix
How many of the items that actually belonged to category A were predicted incorrectly?
wrongActually(int) - Method in class org.strbio.math.StatsMatrix
How many of the items that actually belonged to category A were predicted incorrectly?
wrongPred(int) - Method in class org.strbio.math.SimMatrix
How many of the items predicted to be in category A were predicted incorrectly?

X

x() - Method in class org.strbio.mol.Atom
returns the first coordinate, or Double.NaN if unknown
x - Variable in class org.strbio.mol.lib.MinareaResults
 
XAxisScale - Class in org.strbio.util.graph
A scale to go along the x axis of a graph.
XAxisScale(Font, FontMetrics) - Constructor for class org.strbio.util.graph.XAxisScale
 

Y

y() - Method in class org.strbio.mol.Atom
returns the second coordinate, or Double.NaN if unknown
y - Variable in class org.strbio.mol.lib.MinareaResults
 
YAPFGetNextMonomer(int) - Method in class org.strbio.mol.Polymer
Return the next non-gap residue with number 'n', or null if there is none.
YAxisScale - Class in org.strbio.util.graph
A scale to go along the y axis of a graph.
YAxisScale(Font, FontMetrics) - Constructor for class org.strbio.util.graph.YAxisScale
 
ySampler - Variable in class org.strbio.math.Bin2D
 

Z

z() - Method in class org.strbio.mol.Atom
returns the third coordinate, or Double.NaN if unknown
z - Variable in class org.strbio.mol.lib.MinareaResults
 
zScore(double) - Method in class org.strbio.math.Bin
Shows how many standard deviations a given double is below the average.
zScore(double) - Method in class org.strbio.math.DMatrix
Shows how many standard deviations (of this matrix) a given double is below the average (of this matrix)
zScore(double) - Method in class org.strbio.math.DVector
Shows how many standard deviations (of this array) a given double is below the average (of this array)
zScore(float) - Method in class org.strbio.math.FMatrix
Shows how many standard deviations (of this matrix) a given float is below the average (of this matrix)
zScore(float) - Method in class org.strbio.math.FVector
Shows how many standard deviations (of this array) a given float is below the average (of this array)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z