Uses of Interface
org.strbio.io.Printf

Packages that use Printf

org.strbio	The StrBio library is a set of Java classes useful for development of software for computational structural biology research.
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	These classes are for running or exchanging data with local programs (other programs installed on your computer).
org.strbio.math	These classes perform functions related to mathematics and statistics.
org.strbio.mol	These classes represent objects or concepts useful to structural biologists.
org.strbio.mol.lib	These classes represent conceptual objects used in structural biology algorithms.
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	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	These classes are related to the RAF file format used by the ASTRAL database.
org.strbio.util	These classes perform general purpose utility functions.
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.ui	These classes are general purpose utility functions related to a program's user interface.

Uses of Printf in org.strbio

Methods in org.strbio with parameters of type Printf

static java.lang.String

IO.getURLData(java.net.URL url, java.lang.String query, java.lang.String serverName, Printf outfile) Get raw data from a web server, as a string.

Uses of Printf in org.strbio.io

Classes in org.strbio.io that implement Printf

class	OldBufferedPrintfTextArea A TextArea that you can do printf() on, like a civilized (C) programmer.
class	OldPrintfJLabel A JLabel that you can do printf() on, like a civilized (C) programmer.
class	OldPrintfJTextArea A JTextArea that you can do printf() on, like a civilized (C) programmer.
class	OldPrintfTextArea A TextArea that you can do printf() on, like a civilized (C) programmer.
class	PrintfJLabel A JLabel that you can do printf() on, like a civilized (C) programmer.
class	PrintfJTextArea A JTextArea that you can do printf() on, like a civilized (C) programmer.
class	PrintfStream A BufferedOutputStream that you can do printf() on, like a civilized (C) programmer.
class	PrintfTee A printf object that forwards output to 2 Printf's.
class	PrintfTextArea A TextArea that you can do printf() on, like a civilized (C) programmer.
class	PrintfWriter A Writer that you can do printf() on, like a civilized (C) programmer.

Methods in org.strbio.io with parameters of type Printf

void	Description.describe(Printf outfile) This should print info about the object to an output file.

Constructors in org.strbio.io with parameters of type Printf

PrintfTee(Printf x, Printf y)

Uses of Printf in org.strbio.local

Methods in org.strbio.local with parameters of type Printf

Profile	PSIBlastP2.blastAll(Printf outfile) Blast, and get the checkpoint info.
Profile	PSIBlastP.blastAll(Printf outfile) Blast, and get the checkpoint info.
Profile	BlastP.blastAll(Printf outfile) Return a profile containing responses to the blast query.
protected Profile	BlastP.blastPBlastAll(Printf outfile) kludge to allow super.super() reference to blastAll method.
Profile	BlastPAdapter.blastProfile(Printf outfile) Return a profile containing responses to the blast query.
ProteinSet	BlastPAdapter.blastProteinSet(Printf outfile) Returns a set of proteins in response to a blast query.
static java.lang.String	PDB.findPDBName(java.lang.String name, Printf outfile) Find PDB file corresponding to a given protein name.
static PDBInfo	PDB.getInfo(java.lang.String name, Printf outfile) Gets info on a PDB file for a given PDB code.

Uses of Printf in org.strbio.math

Methods in org.strbio.math with parameters of type Printf

void	FMatrix.print(Printf outfile) prints in ascii to an open Printf, with a nicer format than 'save'.
void	FVector.print(Printf outfile) prints in ascii to an open Printf, with a nicer format than 'save'.
void	FBin.print(Printf outfile) print out FBins to an open Printf.
void	Bin2D.print(Printf outfile) print out bins to an open Printf.
void	IMatrix.print(Printf outfile) prints in ascii to an open Printf, with a nicer format than 'save'.
void	Bin.print(Printf outfile) print out bins to an open Printf.
void	DMatrix.print(Printf outfile) prints in ascii to an open Printf, with a nicer format than 'save'.
void	IVector.print(Printf outfile) prints in ascii to an open Printf, with a nicer format than 'save'.
void	DVector.print(Printf outfile) prints in ascii to an open Printf, with a nicer format than 'save'.
void	FMatrix.save(Printf outfile) Save to an open Printf.
void	FVector.save(Printf outfile) Save to an open Printf.
void	IMatrix.save(Printf outfile) Save to an open Printf.
void	DMatrix.save(Printf outfile) Save to an open Printf.
void	IVector.save(Printf outfile) Save to an open PrintfStream.
void	DVector.save(Printf outfile) Save to an open Printf.

Uses of Printf in org.strbio.mol

Methods in org.strbio.mol with parameters of type Printf

void	ThreadSet.alignmentStats(Printf outfile) compute stats on alignment.
void	ThreadSet.alignStrMatches(Printf outfile, boolean showAlignment, boolean showModeller) Aligns structural matches.
void	ProfileSet.blast(Printf outfile) Run BLAST on all proteins in the set, using NCBI's blast server.
void	Profile.blast(Printf outfile) Run BLAST on this profile, using NCBI's blast server.
void	ProfilePSI.blast(Printf outfile, Blast blastServer) Run BLAST on this profile, using a specified server.
void	ProfileSet.blast(Printf outfile, Blast blastServer) Run BLAST on all proteins in the set, using a specified blast server.
void	Profile.blast(Printf outfile, Blast blastServer) Run BLAST on this profile, using a specified server.
Protein	Profile.doVarTom(Printf outfile) Do var-tom on this profile.
Protein	Protein.findAccess(Printf outfile) find a protein in a PDB file which should be this one, based on the name.
Protein	Protein.findDSSP(Printf outfile) finds a protein in a PDB file which should be this one, based on the name.
static ProteinSet	ProteinSet.findDSSP(java.lang.String name, Printf outfile) find and load proteins from a DSSP file (do DSSP on PDB file)
protected Protein	Protein.findDSSPResult(ProteinSet q, Printf outfile) returns the appropriate protein from a set of DSSP results, aligned to this one.
Protein	Protein.findPDB(Printf outfile) find a protein in a PDB file which should be this one, based on the name.
static ProteinSet	ProteinSet.findPDB(java.lang.String name, Printf outfile) find and load proteins from a PDB file.
ProteinSet	Protein.getDSSPResults(Printf outfile) runs DSSP on a protein, returning a ProteinSet containing results from DSSP.
void	Protein.getInfo(Printf outfile, boolean getSequence, boolean getAngles, boolean getAtoms, boolean getStructure, boolean getEnv, boolean getPDB, boolean getCATH) Get info for a protein out of local databases.
void	ThreadSet.globalCompare(Printf outfile, boolean optZ, boolean optN) do global comparison of all sequences, showing scores and z-scores.
void	PolymerSet.load(java.lang.String filename, Printf outfile) Default load automatically figures out file type.
void	AlignmentSet.minareaInfo(Printf outfile) Shows some info from minarea: ratio score, RMS, and pct_id The minarea command is 'nw_minarea -A -g 0.1'.
void	ThreadSet.minareaInfo(Printf outfile) Show info on all structural matches.
void	ThreadSet.minareaInfoAll(Printf outfile) Show info on all seq/fold pairs.
void	ThreadSet.optimizeAlignment(Printf outfile) optimize the gap penalties for highest alignment accuracy.
void	ThreadSet.optimizeASns(Printf outfile) optimize the gap penalties for highest asns(1).
void	ThreadSet.optimizeMedianRank(Printf outfile) optimize the gap penalties for best median rank of known structural matches.
void	ThreadSet.optimizeRank(Printf outfile) optimize the gap penalties for best average rank of known structural matches.
void	ThreadSet.optimizeRankRW(Printf outfile) optimize the gap penalties for best reciprocal weighted average rank of known structural matches.
void	ThreadSet.optimizeTopN(int n, Printf outfile) optimize the gap penalties for most correct structural matches in the top N.
void	ThreadSet.optimizeZScore(Printf outfile) optimize the gap penalties for highest average Z score among structural matches.
java.util.Enumeration	PolymerSet.polymersInFile(java.io.BufferedReader infile, Printf outfile) Return an enumeration of polymers in a file.
java.util.Enumeration	PolymerSet.polymersInFile(java.lang.String filename, Printf outfile) Return an enumeration of polymers in a file.
void	ProteinSet.predictSS(Printf outfile) Predict the secondary structure of these proteins, using the default method (Pred2ary, with large jury).
void	Protein.predictSS(Printf outfile) Predict the secondary structure of this protein, using the default method (Pred2ary, with large jury).
void	ProteinSet.predictSS(Printf outfile, SSPredictor method) Predict the secondary structure of these proteins, using a specified prediction method.
void	Protein.predictSS(Printf outfile, SSPredictor method) Predict the secondary structure of this protein, using a specified prediction method.
void	Alignment.print(Printf outfile, boolean showgaps) prints out both sequences with alternating seq and fold lines.
void	AlignmentSet.printCalculated(Printf outfile, boolean showgaps) prints out both sequences in calculated alignment with alternating seq and fold lines.
void	AlignmentSet.printCalculatedOnCorrect(Printf outfile) prints out both sequences with alternating seq and fold lines, secondary structure information, relative shift info.
void	AlignmentSet.printCorrect(Printf outfile, boolean showgaps) prints out both sequences in correct alignment with alternating seq and fold lines.
void	Alignment.printModeller(Printf outfile) prints both sequences in a format Modeller likes.
void	AlignmentSet.printModeller(Printf outfile) prints both sequences in a format Modeller likes.
void	PolymerSet.printNames(int indent, Printf outfile) print names of Polymers in this set.
void	Profile.printProfile(Printf outfile) Print profile to output in a pretty format.
void	Profile.printProfile(Printf outfile, int pad) Print profile to output in a pretty format.
void	Alignment.printRelative(Alignment b, Printf outfile) prints out both sequences with alternating seq and fold lines, and also shows relation relative to another alignment (i.e. the correct alignment)
void	Polymer.printSequence(Printf outfile) print out the sequence in a nice 1-letter code format
void	Polymer.read(java.io.BufferedReader infile, Printf outfile) Find the first thing in a file that looks like a polymer, and read it.
void	PolymerSet.read(java.io.BufferedReader infile, Printf outfile) Read Polymers from unknown file type.
protected void	Polymer.read(java.io.BufferedReader infile, Printf outfile, boolean inc) This does the work in reading a protein, but should not be called directly.
void	PolymerSet.read(java.lang.String filename, Printf outfile) Read Polymers from unknown file type.
void	Protein.readAccess(java.io.BufferedReader infile, Printf outfile) read a protein out of an Access file.
void	Profile.readBLAST(java.io.BufferedReader infile, Printf outfile) This reads a profile from BLASTP 2.0.11 output.
void	Protein.readCASP(java.io.BufferedReader infile, Printf outfile) read a protein out of a CASP file.
void	Profile.readClustal(java.io.BufferedReader infile, Printf outfile) read a protein out of a CLUSTAL format file.
void	Protein.readConv(java.io.BufferedReader infile, Printf outfile) read a protein out of a Conv file.
void	Protein.readDSSP(java.io.BufferedReader infile, Printf outfile) read a protein out of a DSSP file.
void	Protein.readEA(java.io.BufferedReader infile, Printf outfile) read a protein out of an EA file.
void	Polymer.readFasta(java.io.BufferedReader infile, Printf outfile) read a polymer out of a Fasta file.
void	Profile.readHSSP(java.io.BufferedReader infile, Printf outfile) read a protein out of a HSSP (Sander & Schneider format) file.
void	Polymer.readList(java.io.BufferedReader infile, Printf outfile) read a polymer out of a 'list' file.
void	PolymerSet.readList(java.lang.String filename, Printf outfile) Read Polymers from a list file (a list of the Polymer names).
void	Profile.readMSF(java.io.BufferedReader infile, Printf outfile) read a protein out of a MSF (GCG's format) file.
void	Protein.readPDB(java.io.BufferedReader infile, Printf outfile) read a protein out of a PDB file.
void	Protein.readPDBAtom(java.io.BufferedReader infile, Printf outfile) read a protein out of a PDB file with no SEQRES records.
void	Protein.readProf(java.io.BufferedReader infile, Printf outfile) read a protein out of a Prof file.
void	Polymer.readSequence(java.io.BufferedReader infile, Printf outfile) Read a polymer from a file containing just the sequence (all non-whitespace chars)
void	Protein.readSwissProt(java.io.BufferedReader infile, Printf outfile) read a protein out of a SwissProt file.
void	Protein.readVar(java.io.BufferedReader infile, Printf outfile) read a protein out of a Var file.
void	Protein.readVar2(java.io.BufferedReader infile, Printf outfile) read a protein out of a Var2 file.
void	Polymer.readYAPF(java.io.BufferedReader infile, Printf outfile) read a polymer out of a YAPF file.
protected boolean	Profile.recognizeAndRead(java.lang.String buffer, java.io.BufferedReader infile, Printf outfile) This looks for a profile and reads it in.
protected boolean	Protein.recognizeAndRead(java.lang.String buffer, java.io.BufferedReader infile, Printf outfile) This looks for a protein and reads it in.
protected boolean	Polymer.recognizeAndRead(java.lang.String buffer, java.io.BufferedReader infile, Printf outfile) This routine checks to see if the current buffer looks like the beginning of a polymer in a known file format.
void	Protein.runDSSP(Printf outfile) Runs DSSP on this protein (which must have atomic coordinates).
void	AlignmentStats.save(Printf outfile) Write these results to an output file.
void	AlignmentSet.save(Printf outfile) Saves correct,calculated,nail alignments to a file in new format.
void	AlignmentSet.saveCalculatedCASP(Printf outfile) Save calculated alignment in CASP format, to open file
void	Alignment.saveCASP(Printf outfile) Save alignment in CASP format, to open file.
void	ThreadSet.showFRAll(Printf outfile) show comparison results for all proteins.
void	ThreadSet.showFRMatches(Printf outfile) show comparison results for str matches.
void	Protein.showGaps(Printf outfile) Print out possible gaps in the sequence.
void	ThreadSet.showPMatch(Printf outfile) shows probability of a structural match for various Z score ranges.
void	Alignment.stats(Printf outfile) get statistics on the alignment.
void	AlignmentSet.stats(Printf outfile) get statistics on the alignment.
ThreadResults[]	ProteinSet.thread(Printf outfile) Thread, using the default method.
ThreadResults	Protein.thread(Printf outfile) Thread, using the default method.
ThreadResults[]	ProteinSet.thread(Printf outfile, ThreadMethod method) Thread the proteins, using a specified threading method.
ThreadResults	Protein.thread(Printf outfile, ThreadMethod method) Thread the protein, using a specified threading method.
void	Residue.writeAccessRecord(Printf outfile) Write ACCESS record to YAPF file.
void	Residue.writeAngleRecord(Printf outfile) Write ANGLE record to YAPF file.
void	ProteinSet.writeCASP(Printf outfile) Write set to CASP file.
void	Residue.writeCASP(Printf outfile) Writes out this residue in CASP format.
void	Protein.writeCASP(Printf outfile) Write in CASP format.
void	ProfileSet.writeClustal(Printf outfile) Write set to Clustal file.
void	Profile.writeClustal(Printf outfile) Write in CLUSTAL format.
void	ProteinSet.writeConv(Printf outfile) Write set to Conv file.
void	Residue.writeConv(Printf outfile) Writes out this residue in Conv format.
void	Protein.writeConv(Printf outfile) Write in Conv format.
void	ProfRes.writeCWRecord(Printf outfile) Write CW info for this residue in JMC's YAPF format.
void	Residue.writeDSSPRecord(Printf outfile) Write DSSP record to YAPF file.
void	ProteinSet.writeEA(Printf outfile) Write set to EA file.
void	Residue.writeEA(Printf outfile) Writes out this residue in EA format.
void	Protein.writeEA(Printf outfile) Write in EA format.
void	Profile.writeFasta(Printf outfile) Write each sequence in the profile in Fasta format.
void	Polymer.writeFasta(Printf outfile) Write in Fasta format.
void	PolymerSet.writeFasta(Printf outfile) Write set to Fasta file.
void	ProfRes.writeFREQRecord(Printf outfile) Write FREQ info for this residue in JMC's YAPF format.
void	PolymerSet.writeList(Printf outfile) create a file with a list of protein names in it.
void	ProfileSet.writeMSF(Printf outfile) Write set to MSF file.
void	Profile.writeMSF(Printf outfile) Write in MSF format.
void	ProteinSet.writePDB(Printf outfile) Write set to PDB file, including all SEQRES, JMCSTR, and ATOM records.
void	Protein.writePDB(Printf outfile) Write in PDB format, including SEQRES, JMCSTR, and ATOM records.
void	Polymer.writePDB(Printf outfile) Write in PDB format, which includes SEQRES and ATOM records.
void	PolymerSet.writePDB(Printf outfile) Write set to PDB file.
void	ProteinSet.writePDB(Printf outfile, boolean vanillaPDB) Write set to PDB file.
void	Protein.writePDB(Printf outfile, boolean vanillaPDB) Write in PDB format, which includes SEQRES and ATOM records.
void	Atom.writePDB(Printf outfile, java.lang.String protname, char chainid, java.lang.String restype, int resnum) Write the atom to a file in PDB format.
void	Polymer.writePDBAtom(Printf outfile) Write PDB ATOM records for this polymer.
void	Monomer.writePDBAtom(Printf outfile, java.lang.String polyname, char chainid) Writes out PDB ATOM records for all atoms belonging to this monomer.
void	Polymer.writePDBSeqres(Printf outfile) Write PDB SEQRES records for this polymer.
void	Residue.writePDBStr(Printf outfile) Writes out PDB JMCSTR records for this residue.
void	Residue.writePredSSRecord(Printf outfile) Write PREDSS record to YAPF file.
void	ProfRes.writeProf(Printf outfile) Write this residue in JMC's .prof format.
void	ProfileSet.writeProf(Printf outfile) Write set to Prof file.
void	Profile.writeProf(Printf outfile) Write in Prof format.
void	ProfResPSI.writePSIBlastRecord(Printf outfile) Write PSIBLAST record to YAPF file.
void	Monomer.writePts(Printf outfile) Writes out this monomer in PTS (Jon Blake's) format.
void	Polymer.writePTS(Printf outfile) Write in PTS format.
void	PolymerSet.writePTS(Printf outfile) Write set to PTS file.
void	ProfileSet.writeSAF(Printf outfile) Write set to SAF file.
void	Profile.writeSAF(Printf outfile) Write in Burkhard Rost's SAF format.
void	ProfRes.writeSeqRecord(Printf outfile) Write this residue in JMC's YAPF format.
void	Monomer.writeSeqRecord(Printf outfile) Write this monomer in JMC's YAPF format.
void	Profile.writeTDP(Printf outfile) A simple way of printing the profile, that var-tom uses as input.
void	ProteinSet.writeVar2(Printf outfile) Write set to Var2 file.
void	Residue.writeVar2(Printf outfile) Writes out this residue in Var2 format.
void	Protein.writeVar2(Printf outfile) Write in Var2 format.
void	Residue.writeVarTomRecord(Printf outfile) Write VarTom record to YAPF file.
void	Polymer.writeYAPF(Printf outfile) A portable way of writing a polymer, which is expandable to include protein/profile info also.
void	PolymerSet.writeYAPF(Printf outfile) Write set to YAPF file.
void	Polymer.writeYAPFAtom(Printf outfile) Write YAPF ATOM records for this polymer.
void	Monomer.writeYAPFAtom(Printf outfile, char chainid) Writes out YAPF ATOM records for all atoms belonging to this monomer.
protected void	ProfilePSI.writeYAPFInfo(Printf outfile) Write applicable sections of YAPF info.
protected void	Profile.writeYAPFInfo(Printf outfile) Write applicable sections of YAPF info.
protected void	Protein.writeYAPFInfo(Printf outfile) Write applicable sections of YAPF info.
protected void	Polymer.writeYAPFInfo(Printf outfile) Write applicable sections of YAPF info.

Constructors in org.strbio.mol with parameters of type Printf

PolymerSet.PolymerEnumeration(java.io.BufferedReader inf, Printf outf, PolymerSet ps)
create an enumeration on a given file, with a given polymer set.

Uses of Printf in org.strbio.mol.lib

Methods in org.strbio.mol.lib with parameters of type Printf

Profile	Blast.blastAll(Printf outfile) Return a profile containing responses to the blast query.
Profile	BlastAdapter.blastProfile(Printf outfile) Return a profile containing responses to the blast query.
Profile	Blast.blastProfile(Printf outfile) Return a profile containing responses to the blast query.
ProteinSet	BlastAdapter.blastProteinSet(Printf outfile) Returns a set of proteins in response to a blast query.
ProteinSet	Blast.blastProteinSet(Printf outfile) Returns a set of proteins in response to a blast query.
void	UserFoldLibrary.describe(Printf outfile) The default fold library description just prints the name of the class.
void	TOMFoldLibrary.describe(Printf outfile)
void	ScoreUFSippl90.describe(Printf outfile)
void	ScoreSippl90.describe(Printf outfile)
void	ScoreReversePSIBlast.describe(Printf outfile)
void	ScorePhiPsi.describe(Printf outfile)
void	ScorePSIBlast.describe(Printf outfile)
void	ScoreAverageReversePSIBlast.describe(Printf outfile)
void	ScoreAveragePSIBlast.describe(Printf outfile)
void	GapDistanceDependent.describe(Printf outfile)
void	GapModelAdapter.describe(Printf outfile) the default function describes only ends.
void	GapConstant.describe(Printf outfile)
void	GapAffine.describe(Printf outfile)
void	FRParametersNode.describe(Printf outfile) Describe prints parameters of the components, if they support it
void	FRParameters.describe(Printf outfile) Describe prints parameters of the components, if they support it
void	FoldLibrary.describe(Printf outfile) The default fold library description just prints the name of the class.
void	ScoreList.describe(Printf outfile) Tell scoring functions to describe themselves, if possible.
void	AlignmentParameters.describe(Printf outfile) Describe prints parameters of the components, if they support it
void	GapDistanceDependent.describeBriefly(Printf outfile)
void	GapConstant.describeBriefly(Printf outfile)
void	GapModelAdapter.describeEnds(Printf outfile) describe how ends are treated.
void	ThreadResults.makeAlignment(Printf outfile, AlignmentParameters ap, int i) make one alignment to a given fold.
void	ThreadResults.makeAlignments(Printf outfile, AlignmentParameters ap, double cutoff) make alignments for all folds >= a certain pMatch value.
void	Pred2ary.predict(Protein p, Printf outfile) Predicts on a given protein.
void	SSPredictor.predict(Protein p, Printf outfile) Predicts on a given protein.
void	Pred2ary.predict(ProteinSet ps, Printf outfile) Predicts on a given set of proteins.
void	SSPredictor.predict(ProteinSet p, Printf outfile) Predicts on a given set of proteins.
void	ThreadResults.printAlignment(Printf outfile, AlignmentParametersEA ap, int i) print one alignment in a standard format.
void	ThreadResults.printAlignments(Printf outfile, AlignmentParametersEA ap, double cutoff) print alignments in a standard format.
void	PSIBlastMatrices.printFreqs(Printf outfile) Print frequencies for debugging.
void	ThreadResults.printMatches(Printf outfile, boolean showAll) print fold rankings in a standard format.
void	GapModelAdapter.printParameters(Printf outfile) default printParameters function does nothing.
void	GapAffine.printParameters(Printf outfile)
void	GapModel.printParameters(Printf outfile) Briefly print the gap parameters, for inclusion in a line of output.
void	PSIBlastMatrices.printScores(Printf outfile) Print scores for debugging.
void	UserFoldLibrary.read(java.io.BufferedReader infile, Printf outfile) Reads proteins in, making sure they have the correct info.
void	Sippl90.save(Printf outfile) Saved tabulated values to a file.
void	PSIBlastMatrices.save(Printf outfile) Save scoring matrix to a file.
void	MinareaResults.save(Printf outfile) This should save all the results, except alignment, to one line in a file.
void	AlignmentParametersEA.saveEstAAStats(Printf outfile) Save accuracy stats to a file.
void	FRParameters.saveEstFRStats(Printf outfile) Save accuracy stats to a file.
void	AlignmentParametersEA.saveEstFRStats(Printf outfile) Save accuracy stats to a file.
void	Sippl90.saveRaw(Printf outfile) Saved raw values to a file.
void	ThreadResults.saveResultAS(Printf outfile, AlignmentParametersEA ap, int i) save one alignment in AS-readable format.
void	ThreadResults.saveResultModeller(Printf outfile, AlignmentParametersEA ap, int i) save one result in AlignmentSet-readable format to a file.
void	ThreadResults.saveResultsAS(Printf outfile, AlignmentParametersEA ap, double cutoff) save results in AlignmentSet-readable format to a file.
void	ThreadResults.saveResultsEnglish(Printf outfile, AlignmentParametersEA ap, double cutoff) save results in english to a file.
void	ThreadResults.saveResultsModeller(Printf outfile, AlignmentParametersEA ap, double cutoff) save results in AlignmentSet-readable format to a file.
ThreadResults	JMCThreadMethod2.thread(Protein p, Printf outfile) Thread a given protein, returning a ThreadResults object.
ThreadResults	JMCThreadMethod.thread(Protein p, Printf outfile) Thread a given protein, returning a ThreadResults object.
ThreadResults	ThreadMethod.thread(Protein p, Printf outfile) Thread a given protein, returning a ThreadResults object.
ThreadResults[]	JMCThreadMethod2.thread(ProteinSet ps, Printf outfile) Thread a given protein set, returning an array of ThreadResults objects.
ThreadResults[]	JMCThreadMethod.thread(ProteinSet ps, Printf outfile) Thread a given protein set, returning an array of ThreadResults objects.
ThreadResults[]	ThreadMethod.thread(ProteinSet ps, Printf outfile) Thread a given protein set, returning an array of ThreadResults objects.

Constructors in org.strbio.mol.lib with parameters of type Printf

UserFoldLibrary(java.lang.String filename, Printf outfile)

Uses of Printf in org.strbio.mol.lib.pred2ary

Fields in org.strbio.mol.lib.pred2ary declared as Printf

Printf

Jury.outfile File to print output to.

Methods in org.strbio.mol.lib.pred2ary with parameters of type Printf

double	TrainingSet.fcut2ary(int sample, Printf outfile)
double	PredictionSet.fcut2ary(int sample, Printf outfile)
double	TPSet.fcut2ary(NeuralNet net, int sample, Printf outfile) find best 2ary cutoff
void	TPSet.fcutClass(NeuralNet cnet4, NeuralNet[] cnet1, Printf outfile) find cutoff, and compute class stats
void	TrainingSet.fcutClass(Printf outfile)
double	TrainingSet.fcutLvl2(int sample, Printf outfile)
double	PredictionSet.fcutLvl2(int sample, Printf outfile)
double	TPSet.fcutLvl2(NeuralNet net, int sample, Printf outfile) find cutoff, and compute stats on a training set.
void	TrainingSet.jackknife(int sets, Printf outfile) split up a set using jackknife procedure
void	PredictionSet.predict2ary(int sample, Printf outfile) do 2ary prediction; train and find cutoff if necessary.
void	TPSet.predict2ary(NeuralNet net, int sample, Printf outfile) do a 2ary prediction
void	TPSet.predictClass(NeuralNet cnet4, NeuralNet[] cnet1, Printf outfile) do class prediction
void	PredictionSet.predictClass(Printf outfile) cutoff = 0.0 -> find correct cutoff.
void	TPSet.predictClassDirectly(Printf outfile) do class prediction directly from 2ary prediction
void	PredictionSet.predictLvl1(int sample, Printf outfile) cutoff = 0.0 -> find correct cutoff.
void	PredictionSet.predictLvl2(int sample, Printf outfile) cutoff = 0.0 -> find correct cutoff.
void	TPSet.predictLvl2(NeuralNet net, int sample, Printf outfile) do a prediction
void	PredClassProfile.print2ary(Printf outfile, int sample) print info on 2ary prediction.
void	TPSet.print2ary(Printf outfile, int sample)
void	TPSet.print2aryByClass(Printf outfile)
void	TPSet.print2aryStats(Printf outfile)
void	TPSet.print2aryUnreduced(Printf outfile)
void	PredClassProfile.printClass(Printf outfile) print class prediction info
void	TPSet.printClass(Printf outfile)
void	TPSet.printClassStats(Printf outfile)
void	PredClassProfile.printDirectClassPrediction(Printf outfile) show the class prediction from the 4-output network.
void	TPSet.printDirectClassPrediction(Printf outfile)
void	TPSet.printDirectClassStats(Printf outfile)
protected boolean	PredClassProfile.recognizeAndRead(java.lang.String buffer, java.io.BufferedReader infile, Printf outfile) This looks for a protein and reads it in, and also figures out what class it belongs to.
void	TrainingSet.reduceTrain(Printf outfile) This sets the defaults properly, for backward compatibility.
void	TrainingSet.reduceTrain(Printf outfile, java.io.DataInputStream binary_input) This sets the defaults properly.
void	TrainingSet.reduceTrain(Printf outfile, double cutoff_r_a, double cutoff_r_b, double cutoff_r_a_b, double cutoff_lvl2_r_a, double cutoff_lvl2_r_b, double cutoff_lvl2_r_a_b) This sets the defaults properly, for backward compatibility.
void	TrainingSet.reduceTrain(Printf outfile, double cutoff_r_a, double cutoff_r_b, double cutoff_r_a_b, double cutoff_lvl2_r_a, double cutoff_lvl2_r_b, double cutoff_lvl2_r_a_b, java.io.DataInputStream binary_input) Setup reduced training sets based on p_set.
boolean	TrainingSet.setup2aryNet(java.lang.String weight_file, Printf outfile) set up networks... returns true if loaded in old weights.
boolean	TrainingSet.setupClassNet(java.lang.String weight_file, Printf outfile) set up class networks... returns true if loaded in old weights.
boolean	TrainingSet.setupLvl2Net(java.lang.String weight_file, Printf outfile) set up lvl 2 network... returns true if loaded in old weights.
void	TrainingSet.train2ary(Printf outfile) do the whole 2ary training procedure
void	TrainingSet.train2aryLoop(Printf outfile) train one net as much as needed, including finding cutoff and predicting prediction set, if we're testing.
int	TrainingSet.train2aryNet(int nsteps, Printf outfile) train a few steps, return actual number trained
double[]	TrainingSet.train2aryTcp(int nsteps, int sample, Printf outfile) train, cutoff, predict for a single training set, or group of them... returns actual number of steps taken, and the average error.
void	TrainingSet.trainClass(Printf outfile) do the whole class training procedure
void	TrainingSet.trainClassLoop(Printf outfile) train one net as much as needed, including finding cutoff and predicting prediction set, if we're testing.
int	TrainingSet.trainClassNet(int nsteps, boolean[] train_net, Printf outfile) train a few steps, return actual number trained
double[]	TrainingSet.trainClassTcp(int nsteps, boolean[] train_net, Printf outfile) 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.
void	TrainingSet.trainLvl2(Printf outfile) do the whole 2ary training procedure on lvl2 net
void	TrainingSet.trainLvl2Loop(Printf outfile) train one net as much as needed, including finding cutoff and predicting prediction set, if we're testing.
int	TrainingSet.trainLvl2Net(int nsteps, Printf outfile) train a few steps, return actual number trained
double[]	TrainingSet.trainLvl2Tcp(int nsteps, int sample, Printf outfile) train, cutoff, predict for a single training set, or group of them... returns actual number of steps taken, and average error.

Uses of Printf in org.strbio.net

Methods in org.strbio.net with parameters of type Printf

Profile	BlastWeb.blastAll(Printf outfile) Returns a profile with all responses to the query.
java.lang.String	BlastWeb.blastGetInitial(Printf outfile) Query the blast server for the queue data.
java.lang.String	BlastWeb.blastGetResult(Printf outfile) Query the blast server for the queue data.
java.lang.String	PSIBlastWeb.blastInitial(Printf outfile) Return a string containg initial results from the web server.
java.lang.String	PSIBlastWeb.blastRaw(Printf outfile) Return a string containing the raw HTML from the server.
java.lang.String	BlastNCBI2.blastRaw(Printf outfile) Return a stream containing the raw HTML from the NCBI server.
java.lang.String	BlastWeb.blastRaw(Printf outfile) Return a string containing the raw HTML from the server.
java.lang.String	PSIBlastWeb.blastStepN(int step, Printf outfile) Return a string containing the html from step N.
static java.lang.String	ProtParam.getAnnot(Protein p, Printf outfile) gets annot for a protein... returns null error processing or reading sequence.
static java.lang.String	ProtParam.getAnnot(java.lang.String seq, Printf outfile) gets annot for a protein... returns null error processing or reading sequence.
static java.lang.String	ProtParam.getCheckedAnnot(Protein p, Printf outfile) gets raw annot for a protein... returns null error processing or reading sequence
static java.lang.String	ProtParam.getCheckedAnnot(java.lang.String seq, Printf outfile) gets raw annot for a protein... returns null error processing or reading sequence
static CATHInfo[]	CATH.getInfo(java.lang.String name, Printf outfile) Gets all CATH entries for a given PDB code.
static Protein	Entrez.getProtein(java.lang.String id, Printf outfile) Searches on a given protein identifier.
static java.lang.String	FruitFly.getRawAnnot(int release, java.lang.String geneName, Printf outfile) Query the server for annotation data
static java.lang.String	SCOP.getRawAnnot(java.lang.String code, Printf outfile) Query the server for annotation data
static java.lang.String	ProtParam.getRawAnnot(java.lang.String sequence, Printf outfile) Query the server for annotation data
static java.lang.String	FruitFly.getRawAnnot(java.lang.String geneName, Printf outfile) Query the server for annotation data
static java.lang.String	Ecocyc.getRawAnnot(java.lang.String objName, Printf outfile) Query the server for annotation data
static java.lang.String	Alces.getRawAnnot(java.lang.String sequence, Printf outfile) Query the server for annotation data
static java.lang.String	SCOP.getRawAnnotNumeric(SCOPInfo si, Printf outfile) Query the server for annotation data, using numeric entries in SCOPInfo.
static java.lang.String	SCOP.getRawAnnotPDB(java.lang.String code, Printf outfile) Query the server for annotation data for a given pdb string
static java.lang.String	FruitFly.getRawAnnotSlow(int release, java.lang.String geneName, Printf outfile) Query the server for annotation data
static java.lang.String	TargetDB.getRawData(java.lang.String id, Printf outfile) Query the server for data on a given target
static void	PubMed.printRaw(java.lang.String term, int year, Printf outfile) prints raw query of an pubmed search
static void	ProtParam.printRaw(java.lang.String sequence, Printf outfile) prints raw result of a search
static void	FruitFly.printRaw(java.lang.String geneName, Printf outfile) prints raw result of a flybase search
static void	Entrez.printRaw(java.lang.String id, Printf outfile) prints raw query of an entrez search
static void	Ecocyc.printRaw(java.lang.String sequence, Printf outfile) prints raw result of a search
static void	PubMed.printRaw2(int accession, Printf outfile) prints raw query of an pubmed id search
static java.lang.String	PubMed.search(int accession, Printf outfile) returns String which contains one complete MEDLINE search result for a given accession code.
static java.lang.String[]	PubMed.search(java.lang.String term, int year, Printf outfile) returns array of Strings, each of which contains one complete MEDLINE search result
static java.lang.String	ThreeDPSSM.submit(Protein p, Printf outfile) Query the server

Uses of Printf in org.strbio.raf

Methods in org.strbio.raf with parameters of type Printf

void	GapRAF.describe(Printf outfile)
void	GapRAF.describeBriefly(Printf outfile)
static ProteinSet	RAFProtein.readAtom(java.lang.String filename, Printf outfile)
void	RAFProtein.readPDBAtomRAF(java.io.BufferedReader infile, Printf outfile) read a protein out of a PDB file ATOM records.
void	RAFProtein.readPDBSeqresRAF(java.io.BufferedReader infile, Printf outfile) read a protein out of a PDB SEQRES records
static ProteinSet	RAFProtein.readSeqres(java.lang.String filename, Printf outfile)

Uses of Printf in org.strbio.util

Methods in org.strbio.util with parameters of type Printf

static void	JMC.printArgs(java.lang.String[] argv, Printf outfile) Print out the arguments used to call the program to a given Printf.
static void	JMC.printTime(float seconds, Printf outfile) Given a time in seconds, prints it in hours:minutes:seconds format.
static void	JMC.programTimer(Printf outfile) Program timer routine.
int	NeuralNet.scg(int n, Printf outfile) Train using the scaled conjugate gradient algorithm for n cycles, from moller (1993).
int	NeuralNet.sd(int n, Printf outfile) Train using steepest descent for n cycles, unless stopped by low_error or max_error.

Uses of Printf in org.strbio.util.db

Methods in org.strbio.util.db with parameters of type Printf

void	SCOPInfo.writeYAPF(Printf outfile) write this info to a single line of a file, so it can be read later.
void	CATHInfo.writeYAPF(Printf outfile) write this info to a single line of a file, so it can be read later.
void	PDBInfo.writeYAPF(Printf outfile) write this info to a single line of a file, so it can be read later.
void	Info.writeYAPF(Printf outfile) write this info to a single line of a file, so it can be read later.
void	Data.writeYAPF(Printf outfile) write all info to a Printf.

Uses of Printf in org.strbio.util.ui

Classes in org.strbio.util.ui that implement Printf

class

ProfileGUIApp.LoadProgressDialog show load progress.