public class ParamAnalysis
extends java.lang.Object
Constructor and Description |
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ParamAnalysis() |
Modifier and Type | Method and Description |
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void |
calcPredictedExposeAnalysis(int howManyBuried,
int howManyUniqueBuried,
int howManyTotalBuried,
int howManyExposed,
int howManyUniqueExposed,
int howManyTotalExposed,
int howManyBurBur,
int howManyExpExp,
int howManyExpBur,
int top) |
double |
getAccBurBur() |
double |
getAccExpBur() |
double |
getAccExpExp() |
double |
getAccGlobal() |
double |
getAccHowManyCreateBuried() |
double |
getAccHowManyCreateExposed() |
double |
getAccIfCreateBuried() |
double |
getAccIfCreateExposed() |
double |
getAccVarCoeff() |
double |
getDcaSpread() |
double |
geteValAve() |
double |
getGapArea() |
double |
getGapBlockSizeAve() |
double |
getKurtosis() |
int |
getMSAseqNmb() |
double |
getOurScoreAve() |
double |
getpValAve() |
double |
getQuartileSpread() |
double |
getQuartileVarCoeff() |
double |
getRobVarCoeff() |
double |
getScoreAve() |
double |
getSepReduction() |
double |
getSkewness() |
double |
getSsHowManyCreate() |
double |
getSsIfCreate() |
double |
getStandDev() |
double |
getTPrate() |
double |
getVarCoeff() |
void |
mSAQualityFromHHRfileCheck(java.lang.String hhrPath)
Check e-values, p-values, and score of sequences in the MSA hhr file (pValAve, eValAve, scoreAve).
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void |
mSASeqNumberCheck_AligFragment(java.lang.String msaPath,
java.lang.String query,
java.util.List<java.lang.Integer> aliFragIndex,
boolean ifEachLine)
Check number of sequences in the MSA file and calculates some scores (mSASeqNmb, ourScoreZscore, gapArea, gapBlockSizeAve).
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void |
mSASeqNumberCheck(java.lang.String msaPath,
java.lang.String query,
boolean ifEachLine)
Check number of sequences in the MSA file and calculates some scores (mSASeqNmb, ourScoreZscore, gapArea, gapBlockSizeAve).
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void |
runAccAnalysis(int separation,
java.io.File file,
int top,
int pos1Col,
int pos2Col,
int acc1Col,
int acc2Col)
Analyze solvent accessibility coefficient of variation (accVarCoeff) in file.
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void |
runExposeAnalysis(int separation,
java.io.File file,
int top,
int pos1Col,
int pos2Col,
int acc1Col,
int acc2Col,
int aa1Col,
int aa2Col,
java.util.List<java.lang.Integer> accSeq,
java.lang.String seq)
Analyze exposition of residues (accIfCreateBuried, accHowManyCreateBuried, accIfCreateExposed, accHowManyCreateExposed, accBurBur, accExpExp, accExpBur, accGlobal).
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void |
runPredictedAccAnalysis(int separation,
java.io.File file,
int top,
int pos1Col,
int pos2Col,
java.util.List<java.lang.Integer> fastaPdbNmb,
java.util.List<java.lang.Integer> accSeq)
Analyze solvent accessibility coefficient of variation (accVarCoeff) for ACC predicted with ACCpro.
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void |
runPredictedAccAnalysis(int separation,
java.util.List<double[]> data,
int top,
int pos1Col,
int pos2Col,
java.util.List<java.lang.Integer> accSeq)
Analyze solvent accessibility coefficient of variation (accVarCoeff) for ACC predicted with ACCpro.
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void |
runPredictedExposeAnalysis(int separation,
java.io.File file,
int top,
int pos1Col,
int pos2Col,
java.util.List<java.lang.Integer> accSeq,
java.util.List<java.lang.Integer> fastaPdbNmb)
Analyze exposition of residues (accIfCreateBuried, accHowManyCreateBuried, accIfCreateExposed, accHowManyCreateExposed, accBurBur, accExpExp, accExpBur, accGlobal) on the basis of RSA predicted with ACCpro.
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void |
runPredictedExposeAnalysis(int separation,
java.util.List<double[]> data,
int top,
int pos1Col,
int pos2Col,
java.util.List<java.lang.Integer> accSeq)
Analyze exposition of residues (accIfCreateBuried, accHowManyCreateBuried, accIfCreateExposed, accHowManyCreateExposed, accBurBur, accExpExp, accExpBur, accGlobal) on the basis of RSA predicted with ACCpro.
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void |
runPredictedSsAnalysis(int separation,
java.io.File file,
int top,
int pos1Col,
int pos2Col,
java.lang.String ssSymbols,
java.util.List<java.lang.Character> ssSeq,
java.util.List<java.lang.Integer> fastaPdbNmb)
Analyze occurrence of chosen SS in top results on the basis of SSpro prediction.
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void |
runPredictedSsAnalysis(int separation,
java.util.List<double[]> data,
int top,
int pos1Col,
int pos2Col,
java.lang.String ssSymbols,
java.util.List<java.lang.Character> ssSeq)
Analyze occurrence of chosen SS in top results on the basis of SSpro prediction.
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void |
runRelatAccAnalysis(int separation,
java.io.File file,
int top,
int pos1Col,
int pos2Col,
int acc1Col,
int acc2Col,
int aa1Col,
int aa2Col)
Analyze relative solvent accessibility coefficient of variation (accVarCoeff).
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void |
runSeparationAnalysis(int separation,
java.io.File file,
int top,
int pos1Col,
int pos2Col)
Analyze separation reduction in a file (sepReduction).
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void |
runSeparationAnalysis(int separation,
java.util.List<double[]> data,
int top,
int pos1Col,
int pos2Col)
Analyze separation reduction in a list with data (sepReduction).
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void |
runSpreadAnalysis(int separation,
java.io.File file,
int top,
int pos1Col,
int pos2Col,
int resCol)
Analyze several statistics of the data column in a file (variationCoeff, quartileSpread, standDev, dcaSpread, robVariationCoeff, quartileVarCoeff).
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void |
runSpreadAnalysis(int separation,
java.util.List<double[]> data,
int top,
int pos1Col,
int pos2Col,
int resCol)
Analyze several statistics of the data column in a list with data (variationCoeff, quartileSpread, standDev, dcaSpread, robVariationCoeff, quartileVarCoeff).
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void |
runSsAnalysis(int separation,
java.io.File file,
int top,
int pos1Col,
int pos2Col,
int ss1Col,
int ss2Col,
java.lang.String ssSymbols,
java.util.List<java.lang.Character> ssSeq)
Analyze occurrence of chosen SS in top results.
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void |
runTpAnalysis(int separation,
java.io.File file,
int top,
int pos1Col,
int pos2Col,
int tpCol)
Analyze TP rate in a set of files (TPrates).
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void |
runTpAnalysis(int separation,
java.io.File file,
int top,
int pos1Col,
int pos2Col,
int resCol,
double resCutoff)
Analyze TP rate in a set of files (TPrates).
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public double getOurScoreAve()
public double getGapArea()
public double getGapBlockSizeAve()
public double getSkewness()
public double getKurtosis()
public double getAccBurBur()
public double getAccExpExp()
public double getAccExpBur()
public double getAccGlobal()
public double getAccIfCreateExposed()
public double getAccHowManyCreateExposed()
public double getAccIfCreateBuried()
public double getAccHowManyCreateBuried()
public double getSsIfCreate()
public double getSsHowManyCreate()
public double getAccVarCoeff()
public double getpValAve()
public double geteValAve()
public double getScoreAve()
public int getMSAseqNmb()
public double getQuartileVarCoeff()
public double getRobVarCoeff()
public double getTPrate()
public double getDcaSpread()
public double getVarCoeff()
public double getQuartileSpread()
public double getStandDev()
public double getSepReduction()
public void mSAQualityFromHHRfileCheck(java.lang.String hhrPath)
hhrPath
- - path to the MSA filepublic void mSASeqNumberCheck_AligFragment(java.lang.String msaPath, java.lang.String query, java.util.List<java.lang.Integer> aliFragIndex, boolean ifEachLine)
msaPath
- - path to the MSA filequery
- - query sequencealiFragIndex
- - indexes of alignment which are related to the query (start from 1)ifEachLine
- - true if there is no '>' sequence separator but each sequence is in another linepublic void mSASeqNumberCheck(java.lang.String msaPath, java.lang.String query, boolean ifEachLine)
msaPath
- - path to the MSA filequery
- - query sequenceifEachLine
- - true if there is no '>' sequence separator but each sequence is in another linepublic void runAccAnalysis(int separation, java.io.File file, int top, int pos1Col, int pos2Col, int acc1Col, int acc2Col) throws java.lang.Exception
separation
- - difference between to columns' values which will be taken under consideration (pos1Col and pos2Col)file
- - file to analyzetop
- - how many top results will be analyzedpos1Col
- - number of first column of position to analyze (start with 0)pos2Col
- - number of second column of position to analyze (start with 0)acc1Col
- - number of first column with solvent ACC to analyze (start with 0)acc2Col
- - number of second column with solvent ACC to analyze (start with 0)java.lang.Exception
public void runPredictedAccAnalysis(int separation, java.util.List<double[]> data, int top, int pos1Col, int pos2Col, java.util.List<java.lang.Integer> accSeq) throws java.lang.Exception
separation
- - difference between to columns' values which will be taken under consideration (pos1Col and pos2Col)data
- - list with data to analyzetop
- - how many top results will be analyzedpos1Col
- - number in data of first column of position to analyze (start with 0)pos2Col
- - number in data of second column of position to analyze (start with 0)accSeq
- - predicted values of ACCjava.lang.Exception
public void runPredictedAccAnalysis(int separation, java.io.File file, int top, int pos1Col, int pos2Col, java.util.List<java.lang.Integer> fastaPdbNmb, java.util.List<java.lang.Integer> accSeq) throws java.lang.Exception
separation
- - difference between to columns' values which will be taken under consideration (pos1Col and pos2Col)file
- - file to analyzetop
- - how many top results will be analyzedpos1Col
- - number of first column of position to analyze (start with 0)pos2Col
- - number of second column of position to analyze (start with 0)fastaPdbNmb
- - PDB numbers of sequence for which ACC was predicted (if null then mapping is equal)accSeq
- - predicted values of ACCjava.lang.Exception
public void runRelatAccAnalysis(int separation, java.io.File file, int top, int pos1Col, int pos2Col, int acc1Col, int acc2Col, int aa1Col, int aa2Col) throws java.lang.Exception
separation
- - difference between to columns' values which will be taken under consideration (pos1Col and pos2Col)file
- - file to analyzetop
- - how many top results will be analyzedpos1Col
- - number of first column of position to analyze (start with 0)pos2Col
- - number of second column of position to analyze (start with 0)acc1Col
- - number of first column with solvent ACC to analyze (start with 0)acc2Col
- - number of second column with solvent ACC to analyze (start with 0)aa1Col
- - number of first column with residue type to analyze (start with 0)aa2Col
- - number of second column with residue type to analyze (start with 0)java.lang.Exception
public void runPredictedExposeAnalysis(int separation, java.util.List<double[]> data, int top, int pos1Col, int pos2Col, java.util.List<java.lang.Integer> accSeq) throws java.lang.Exception
separation
- - difference between to columns' values which will be taken under consideration (pos1Col and pos2Col)data
- - list with data to analyzetop
- - how many top results will be analyzedpos1Col
- - number in data of first column of position to analyze (start with 0)pos2Col
- - number in data of second column of position to analyze (start with 0)accSeq
- - predicted with ACCpro relative solvent accessibility for each residuejava.lang.Exception
public void runPredictedExposeAnalysis(int separation, java.io.File file, int top, int pos1Col, int pos2Col, java.util.List<java.lang.Integer> accSeq, java.util.List<java.lang.Integer> fastaPdbNmb) throws java.lang.Exception
separation
- - difference between to columns' values which will be taken under consideration (pos1Col and pos2Col)file
- - file to analyzetop
- - how many top results will be analyzedpos1Col
- - number of first column of position to analyze (start with 0)pos2Col
- - number of second column of position to analyze (start with 0)accSeq
- - predicted with ACCpro relative solvent accessibility for each residuefastaPdbNmb
- - PDB numbers of sequence for which ACC was predictedjava.lang.Exception
public void calcPredictedExposeAnalysis(int howManyBuried, int howManyUniqueBuried, int howManyTotalBuried, int howManyExposed, int howManyUniqueExposed, int howManyTotalExposed, int howManyBurBur, int howManyExpExp, int howManyExpBur, int top)
public void runExposeAnalysis(int separation, java.io.File file, int top, int pos1Col, int pos2Col, int acc1Col, int acc2Col, int aa1Col, int aa2Col, java.util.List<java.lang.Integer> accSeq, java.lang.String seq) throws java.lang.Exception
separation
- - difference between to columns' values which will be taken under consideration (pos1Col and pos2Col)file
- - file to analyzetop
- - how many top results will be analyzedpos1Col
- - number of first column of position to analyze (start with 0)pos2Col
- - number of second column of position to analyze (start with 0)acc1Col
- - number of first column with solvent ACC to analyze (start with 0)acc2Col
- - number of second column with solvent ACC to analyze (start with 0)aa1Col
- - number of first column with residue type to analyze (start with 0)aa2Col
- - number of second column with residue type to analyze (start with 0)accSeq
- - solvent accessibility for each residueseq
- - residue sequencejava.lang.Exception
public void runTpAnalysis(int separation, java.io.File file, int top, int pos1Col, int pos2Col, int resCol, double resCutoff) throws java.lang.Exception
separation
- - difference between to columns' values which will be taken under considerationfile
- - file to analyzetop
- - how many top results will be analyzedpos1Col
- - number of first column to analyze (start with 0)pos2Col
- - number of second column to analyze (start with 0)resCol
- - number of column with analyzed value (start with 0)resCutoff
- - cutoff for the analyzed valuejava.lang.Exception
public void runTpAnalysis(int separation, java.io.File file, int top, int pos1Col, int pos2Col, int tpCol) throws java.lang.Exception
separation
- - difference between to columns' values which will be taken under considerationfile
- - file to analyzetop
- - how many top results will be analyzedpos1Col
- - number of first column to analyze (start with 0)pos2Col
- - number of second column to analyze (start with 0)tpCol
- - number of column with indication true/false (start with 0)java.lang.Exception
public void runSeparationAnalysis(int separation, java.util.List<double[]> data, int top, int pos1Col, int pos2Col) throws java.lang.Exception
separation
- - difference between to columns' values which will be taken under considerationdata
- - list with data to analyzetop
- - how many top results will be analyzedpos1Col
- - number in data of first column to analyze (start with 0)pos2Col
- - number in data of second column to analyze (start with 0)java.lang.Exception
public void runSeparationAnalysis(int separation, java.io.File file, int top, int pos1Col, int pos2Col) throws java.lang.Exception
separation
- - difference between to columns' values which will be taken under considerationfile
- - file to analyzetop
- - how many top results will be analyzedpos1Col
- - number of first column to analyze (start with 0)pos2Col
- - number of second column to analyze (start with 0)java.lang.Exception
public void runSpreadAnalysis(int separation, java.util.List<double[]> data, int top, int pos1Col, int pos2Col, int resCol) throws java.lang.Exception
separation
- - difference between to columns' values which will be taken under considerationdata
- - list with data to analyzetop
- - how many top results will be analyzedpos1Col
- - number in data of first column of position to analyze (start with 0)pos2Col
- - number in data of second column of position to analyze (start with 0)resCol
- - number in data of column with analyzed result (start with 0)java.lang.Exception
public void runSpreadAnalysis(int separation, java.io.File file, int top, int pos1Col, int pos2Col, int resCol) throws java.lang.Exception
separation
- - difference between to columns' values which will be taken under considerationfile
- - file to analyzetop
- - how many top results will be analyzedpos1Col
- - number of first column of position to analyze (start with 0)pos2Col
- - number of second column of position to analyze (start with 0)resCol
- - number of column with analyzed result (start with 0)java.lang.Exception
public void runPredictedSsAnalysis(int separation, java.util.List<double[]> data, int top, int pos1Col, int pos2Col, java.lang.String ssSymbols, java.util.List<java.lang.Character> ssSeq) throws java.lang.Exception
separation
- - difference between to columns' values which will be taken under considerationdata
- - list with data to analyzetop
- - how many top results will be analyzedpos1Col
- - number in data of first column to analyze (start with 0)pos2Col
- - number in data of second column to analyze (start with 0)ssSymbols
- - string with secondary structure symbols of pairs to analyzessSeq
- - secondary structures of each residue in a sequencejava.lang.Exception
public void runPredictedSsAnalysis(int separation, java.io.File file, int top, int pos1Col, int pos2Col, java.lang.String ssSymbols, java.util.List<java.lang.Character> ssSeq, java.util.List<java.lang.Integer> fastaPdbNmb) throws java.lang.Exception
separation
- - difference between to columns' values which will be taken under considerationfile
- - file to analyzetop
- - how many top results will be analyzedpos1Col
- - number of first column to analyze (start with 0)pos2Col
- - number of second column to analyze (start with 0)ssSymbols
- - string with secondary structure symbols of pairs to analyzessSeq
- - secondary structures of each residue in a sequencefastaPdbNmb
- - PDB numbers of sequence for which ACC was predictedjava.lang.Exception
public void runSsAnalysis(int separation, java.io.File file, int top, int pos1Col, int pos2Col, int ss1Col, int ss2Col, java.lang.String ssSymbols, java.util.List<java.lang.Character> ssSeq) throws java.lang.Exception
separation
- - difference between to columns' values which will be taken under considerationfile
- - file to analyzetop
- - how many top results will be analyzedpos1Col
- - number of first column to analyze (start with 0)pos2Col
- - number of second column to analyze (start with 0)ss1Col
- - number of first column with secondary structure information to analyze (start with 0)ss2Col
- - number of second column with secondary structure information to analyze (start with 0)ssSymbols
- - string with secondary structure symbols of pairs to analyzessSeq
- - secondary structures of each residue in a sequencejava.lang.Exception