org.strbio.mol.lib.pred2ary
Class PredClassProfile

java.lang.Object
  org.strbio.mol.Molecule
      org.strbio.mol.Polymer
          org.strbio.mol.Protein
              org.strbio.mol.Profile
                  org.strbio.mol.ProfilePSI
                      org.strbio.mol.lib.pred2ary.PredClassProfile

public class PredClassProfile
extends ProfilePSI

Class to represent a single protein, with class routines and lots of stats.

  Version 1.2, 6/7/99 - moved to org.strbio.mol.lib.pred2ary
  Version 1.1, 5/28/99 - made a child of JMCProtein
  Version 1.0, 5/11/98 - original version
  

Version:

1.2, 6/7/99

Author:

JMC

See Also:

PCPRes

Field Summary

Fields inherited from class org.strbio.mol.Profile

blastBits, blastLog10E, seqName

Fields inherited from class org.strbio.mol.Polymer

chainID, includeFile, includingFile, monDistance, monomers, properties

Fields inherited from class org.strbio.mol.Molecule

atoms, data, MAX_NAME_LENGTH, name

Constructor Summary

PredClassProfile()

PredClassProfile(Profile q)

PredClassProfile(Protein q)

PredClassProfile(ProteinSet q)

Method Summary

void	addClassPred(double[] dp, int offset) add class pred to that from an array.
void	addPred(double[] dp, int offset) add H and E from array.
void	addPred(PredClassProfile q) add H and E predictions together for 2 proteins.
void	addPredToArray(double[] dp, int offset) add h, e to array
static java.lang.String	className(int cl) Return the English name for class of type cl.
void	clearClassPred() clear class pred to zero
void	clearPred() clear H and E to zero
void	compute2arySM(int which, int sample)
void	deleteSM() Delete all stats matrices.
void	divideClassPred(double d) divide class pred by a number
void	dividePred(double d) divide h,e by a number
void	estAccy(IMatrix ea_h, IMatrix ea_e, IMatrix ea_c) estimate accuracy on this protein
int	findClass() find actual kneller class, and AA percentages.
void	findInputs(double cutoff) find network inputs for protein, after 2ary structure is predicted.
void	loadClassPred(double[] dp, int offset) take class pred from array
void	loadPred(double[] dp, int offset) take h, e from array
Monomer	newMonomer() This returns a new ProfResPSI.
Monomer	newMonomer(char t) This returns a new ProfResPSI.
Monomer	newMonomer(java.lang.String s) This returns a new ProfResPSI.
void	newSM(int n) Make n stats matrices, keeping existing ones also.
PCPRes	PR(int i)
int	predDiffs(PredClassProfile b) shows number of diff predictions between 2 proteins; should be another copy of same proteins.
void	predictClassDirectly() predict class directly from 2ary prediction.
void	print2ary(Printf outfile, int sample) print info on 2ary prediction.
void	printClass(Printf outfile) print class prediction info
void	printDirectClassPrediction(Printf outfile) show the class prediction from the 4-output network.
protected boolean	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	saveClassPred(double[] dp, int offset) save class pred to array
void	savePred(double[] dp, int offset) save h, e to array.
protected Polymer	splitCopy() When a Profile is split, sequence names should go to each child.

Methods inherited from class org.strbio.mol.ProfilePSI

blast, copy, deleteBackbonePotential, deletePSIBlastMatrix, getPSIBlastMatrix, processYAPF, setupBackbonePotential, setupBackbonePotential, setupFakePSIBlastMatrix, setupPSIBlastMatrix, writeYAPFInfo

Methods inherited from class org.strbio.mol.Profile

addKeySeq, addSeq, addSeqsDirectlyFrom, addSeqsFrom, allocSeqs, allocSeqsRes, blast, choose, clearSeqs, copySeqsDirectlyFrom, copySeqsFrom, doVarTom, ensureUniqueNames, ensureUniqueNames, findConsensus, findConservationWeights, findFrequencies, findNonZeroFrequencies, findSeqByName, firstNonGap, getSeqName, lastNonGap, printProfile, printProfile, readBLAST, readClustal, readHSSP, readMSF, removeRedundantSequences, removeSeq, removeSpacesInNames, seqPctCoverage, seqPctID, sequence, sequences, setSeqName, setSequence, splitCopy, truncateNames, writeClustal, writeFasta, writeMSF, writeProf, writeSAF, writeTDP

Methods inherited from class org.strbio.mol.Protein

AA, actualAccuracy, copyPredSSFrom, expectedAccuracy, filterPred, filterPred, filterReal, filterReal, findAccess, findDSSP, findDSSPResult, findPDB, firstRes, fixDistanceGaps, getDSSPResults, getInfo, hasGaps, isCATHMatch, makeMonDistance, makeMonDistanceCB, makeVirtualCB, molecularWeight, preCalculateAlphaTau, preCalculateAngles, preCalculatePhiPsi, predictSS, predictSS, readAccess, readCASP, readConv, readDSSP, readEA, readPDB, readPDBAtom, readProf, readSwissProt, readVar, readVar2, residues, reverse, runDSSP, showGaps, smoothHE, stripAllButCA, thread, thread, translateEA, writeCASP, writeConv, writeEA, writePDB, writePDB, writeVar2

Methods inherited from class org.strbio.mol.Polymer

alignToArray, alignToInverseArray, autoSplit, centerOfMass, centerOfMass, clear, clearProperties, clearProperty, copyAtoms, correctAlignFold, correctAlignSeq, deleteMonDistance, firstMon, getGlobalAlignment, getMonomers, getNonGapMonomers, getProperty, getValidNonGapMonomers, globalAlign, globalAlign, globalCompare, globalCompare, keepMonomers, kludgeChainID, lastMon, length, makeMonDistanceAllAtomMin, minareaSuperimpose, monomer, nMonomers, nMonomers, nonGapMonomers, pad, printSequence, quickAlign, quickAlign, quickCompare, quickCompare, read, read, read, readFasta, readList, readSequence, readYAPF, renumberMonomers, renumberValidNonGapMonomers, reverseCopy, rotate, sequence, sequenceNonGap, sequenceValidNonGap, setProperty, stripAllAtoms, stripAllBut, stripAllButFirstAtom, stripAtomsByName, stripCommonGaps, stripGaps, stripInvalidAndGaps, stripNoAtoms, stripType, transform, translate, trimEnds, validNonGapMonomers, writePDBAtom, writePDBSeqres, writePTS, writeYAPF, writeYAPFAtom, YAPFGetNextMonomer

Methods inherited from class org.strbio.mol.Molecule

atomSearch, copyAtoms

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PredClassProfile

public PredClassProfile()

PredClassProfile

public PredClassProfile(ProteinSet q)

PredClassProfile

public PredClassProfile(Protein q)

PredClassProfile

public PredClassProfile(Profile q)

Method Detail

newMonomer

public Monomer newMonomer()

Description copied from class: ProfilePSI

This returns a new ProfResPSI.

Overrides:

newMonomer in class ProfilePSI

newMonomer

public Monomer newMonomer(char t)

Description copied from class: ProfilePSI

This returns a new ProfResPSI.

Overrides:

newMonomer in class ProfilePSI

newMonomer

public Monomer newMonomer(java.lang.String s)

Description copied from class: ProfilePSI

This returns a new ProfResPSI.

Overrides:

newMonomer in class ProfilePSI

splitCopy

protected Polymer splitCopy()

Description copied from class: Profile

When a Profile is split, sequence names should go to each child.

Overrides:

splitCopy in class ProfilePSI

PR

public PCPRes PR(int i)

findClass

public final int findClass()

find actual kneller class, and AA percentages.

recognizeAndRead

protected boolean recognizeAndRead(java.lang.String buffer,
                                   java.io.BufferedReader infile,
                                   Printf outfile)
                            throws java.io.IOException

This looks for a protein and reads it in, and also figures out what class it belongs to.

Overrides:

recognizeAndRead in class Profile

Throws:

java.io.IOException

See Also:

Profile.recognizeAndRead(java.lang.String, java.io.BufferedReader, org.strbio.io.Printf)

predictClassDirectly

public final void predictClassDirectly()

predict class directly from 2ary prediction.

findInputs

public final void findInputs(double cutoff)

find network inputs for protein, after 2ary structure is predicted. cutoff should be the same as that used to predict secondary structure.

newSM

public final void newSM(int n)

Make n stats matrices, keeping existing ones also.

deleteSM

public final void deleteSM()

Delete all stats matrices.

predDiffs

public final int predDiffs(PredClassProfile b)

shows number of diff predictions between 2 proteins; should be another copy of same proteins. Returns -1 if proteins are not the same.

compute2arySM

public final void compute2arySM(int which,
                                int sample)

addPred

public final void addPred(PredClassProfile q)

add H and E predictions together for 2 proteins.

addPred

public final void addPred(double[] dp,
                          int offset)

add H and E from array.

savePred

public final void savePred(double[] dp,
                           int offset)

save h, e to array.

addPredToArray

public final void addPredToArray(double[] dp,
                                 int offset)

add h, e to array

loadPred

public final void loadPred(double[] dp,
                           int offset)

take h, e from array

clearPred

public final void clearPred()

clear H and E to zero

dividePred

public final void dividePred(double d)

divide h,e by a number

addClassPred

public final void addClassPred(double[] dp,
                               int offset)

add class pred to that from an array.

saveClassPred

public final void saveClassPred(double[] dp,
                                int offset)

save class pred to array

loadClassPred

public final void loadClassPred(double[] dp,
                                int offset)

take class pred from array

clearClassPred

public final void clearClassPred()

clear class pred to zero

divideClassPred

public final void divideClassPred(double d)

divide class pred by a number

print2ary

public final void print2ary(Printf outfile,
                            int sample)

print info on 2ary prediction.

printClass

public final void printClass(Printf outfile)

print class prediction info

printDirectClassPrediction

public final void printDirectClassPrediction(Printf outfile)

show the class prediction from the 4-output network.

estAccy

public final void estAccy(IMatrix ea_h,
                          IMatrix ea_e,
                          IMatrix ea_c)

estimate accuracy on this protein

className

public static final java.lang.String className(int cl)

Return the English name for class of type cl.