public class Filters
extends java.lang.Object
Constructor and Description |
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Filters() |
Modifier and Type | Method and Description |
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private static boolean |
checkIfFound(java.util.List<java.lang.String> alreadyFound,
java.lang.String toFind) |
private static void |
createReport(java.lang.String resPath,
int top,
int separation,
java.lang.String notAllowed,
java.lang.String ssPredPath,
java.lang.String accPredPath,
java.lang.String fastaSeq,
int fragSizeIntra,
int anyfragSize,
java.lang.String whichSS,
java.util.List<java.lang.String> raport,
boolean ifIntraSS,
boolean ifInterNextSS,
int interSSsep,
int loopSize,
int endSize,
boolean ifBetweenEnds,
boolean ifDiffSS,
boolean ifDiffSSBegEnd,
int howMany,
boolean ifEntropy,
boolean ifBoth,
double entCutoff,
boolean ifGaps,
java.lang.String aliPath,
boolean ifGapsFreq,
boolean ifBothGapsFreq,
double gapFreq,
boolean ifIntraSSMarks,
boolean ifConservMarks,
boolean ifConservGaps,
boolean ifFirstCysMarks,
boolean ifSeqSep,
double seqSep,
boolean ifACCpasser,
boolean ifBothACC,
double accThres,
boolean ifBurExpDCA,
double aBE,
double bBE)
Run filtering and create report of filtered-out contacts.
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private static void |
getFragsForPredicted(java.lang.String ssPredPath,
java.lang.String fastaSeq,
int fragSize,
java.util.List<int[]> frags,
java.util.List<java.lang.String> fragSS,
java.lang.String notAllowed,
java.util.List<java.lang.Character> ssPred) |
private static boolean |
getNmbOfContacts(int pos1,
int pos2,
int s1,
int e1,
int s2,
int e2,
boolean ifDiffSS,
java.util.List<java.lang.Character> ssPred) |
private static boolean |
ifACCPass(int pos1,
int pos2,
java.util.List<java.lang.Integer> accPred,
double accThres,
boolean ifBoth) |
private static boolean |
ifBurExpDCAPass(int pos1,
int pos2,
java.util.List<java.lang.Integer> accPred,
double aBE,
double bBE,
double dcaScore) |
private static boolean |
ifConservMarksPass(MSAanalysis msaAnalysis,
int pos1,
int pos2,
java.lang.String aa1,
java.lang.String aa2,
boolean ifConservGaps) |
private static boolean |
ifEntropyPass(MSAanalysis msaAnalysis,
int pos1,
int pos2,
double entCutoff,
boolean ifBoth,
boolean ifGaps) |
private static boolean |
ifFirstCysMarksPass(int pos1,
int pos2,
java.lang.String aa1,
java.lang.String aa2,
java.util.List<java.lang.String> alreadyFound) |
private static boolean |
ifGapsFreqPass(MSAanalysis msaAnalysis,
int pos1,
int pos2,
boolean ifBothGapsFreq,
double gapFreq) |
private static boolean |
ifPassInterNextSS(java.util.List<int[]> frags,
int pos1,
int pos2,
int interSSsep,
int loopSize,
int endSize) |
private static boolean |
ifPassIntraSS(java.util.List<int[]> frags,
java.util.List<java.lang.String> fragSS,
int pos1,
int pos2,
java.lang.String whichSS,
int fragSizeIntra) |
private static boolean |
ifPassIntraSSMarks(java.util.List<int[]> frags,
java.util.List<java.lang.String> fragSS,
int pos1,
int pos2,
int separation) |
private static boolean |
ifSeqSepPass(int pos1,
int pos2,
double seqSep,
int seqLen) |
static void |
main(java.lang.String[] args) |
public static void main(java.lang.String[] args)
private static void createReport(java.lang.String resPath, int top, int separation, java.lang.String notAllowed, java.lang.String ssPredPath, java.lang.String accPredPath, java.lang.String fastaSeq, int fragSizeIntra, int anyfragSize, java.lang.String whichSS, java.util.List<java.lang.String> raport, boolean ifIntraSS, boolean ifInterNextSS, int interSSsep, int loopSize, int endSize, boolean ifBetweenEnds, boolean ifDiffSS, boolean ifDiffSSBegEnd, int howMany, boolean ifEntropy, boolean ifBoth, double entCutoff, boolean ifGaps, java.lang.String aliPath, boolean ifGapsFreq, boolean ifBothGapsFreq, double gapFreq, boolean ifIntraSSMarks, boolean ifConservMarks, boolean ifConservGaps, boolean ifFirstCysMarks, boolean ifSeqSep, double seqSep, boolean ifACCpasser, boolean ifBothACC, double accThres, boolean ifBurExpDCA, double aBE, double bBE)
resPath
- - path to the file with DCA resultstop
- - number of of predicted contacts N to apply filtration onseparation
- - separation parameter for contact definitionnotAllowed
- - these secondary structure will not be taken under consideration when list of secondary structure fragments is created for a sequencessPredPath
- - path to the file with SSpro resultsaccPredPath
- - path to the file with ACCpro20 resultsfastaSeq
- - FASTA sequencefragSizeIntra
- - value of Sintra parameter for intra-secondary structure filteranyfragSize
- - only secondary structure fragments of minimally that length will be used when list of secondary structure fragments is created for a sequencewhichSS
- - which secondary structure elements should be checked by intra-secondary structure filterraport
- - variable which will contain the list of filtered-out contactsifIntraSS
- - turn on/off (true/false) the intra-secondary structure filterifInterNextSS
- - turn on/off (true/false) the inter-secondary structure filterinterSSsep
- - value of Sinter parameter for inter-secondary structure filterloopSize
- - value of Sloop parameter for inter-secondary structure filterendSize
- - value of e parameter for inter-secondary structure filterifBetweenEnds
- - turn on/off (true/false) the terminus filterifDiffSS
- - true if contacts between one end of the protein and the rest should be between different secondary structures to be filtered-outifDiffSSBegEnd
- - True if contacts between two ends of the protein should be between different secondary structures to be filtered-outhowMany
- - value of t parameter for terminus filterentCutoff
- - value of Tent parameter for low entropy filterifBoth
- - True if both residues in pair should be in agreement with Tent parameterifEntropy
- - turn on/off (true/false) the low entropy filterifGaps
- - True if gaps should be counted as symbols during entropy calculationaliPath
- - path to the file with alignmentifGapsFreq
- - turn on/off (true/false) the frequent gap filterifBothGapsFreq
- - True if both residues in pair should be in agreement with Tgaps parametergapFreq
- - value of Tgaps parameter for frequent gap filterifIntraSSMarks
- - turn on/off (true/false) the secondary structure straddling filterifConservMarks
- - turn on/off (true/false) the highly conserved filterifConservGaps
- - True if gaps should be counted as symbols during conservation calculationifFirstCysMarks
- - turn on/off (true/false) the the non-strongest Cys-Cys filterifSeqSep
- - turn on/off (true/false) the inter-terminus filterseqSep
- - value of Snt parameter for inter-terminus filterifACCpasser
- - True if TRSA parameter should be used for terminus filterifBothACC
- - True if both residues in pair should be in agreement with TRSA parameteraccThres
- - value of TRSA parameter for terminus filterifBurExpDCA
- - turn on/off (true/false) the buried-exposed filteraBE
- - value of a parameter for buried-exposed filterbBE
- - value of b parameter for buried-exposed filterprivate static boolean ifBurExpDCAPass(int pos1, int pos2, java.util.List<java.lang.Integer> accPred, double aBE, double bBE, double dcaScore)
private static boolean ifACCPass(int pos1, int pos2, java.util.List<java.lang.Integer> accPred, double accThres, boolean ifBoth)
private static boolean ifSeqSepPass(int pos1, int pos2, double seqSep, int seqLen)
private static boolean ifFirstCysMarksPass(int pos1, int pos2, java.lang.String aa1, java.lang.String aa2, java.util.List<java.lang.String> alreadyFound)
private static boolean checkIfFound(java.util.List<java.lang.String> alreadyFound, java.lang.String toFind)
private static boolean ifConservMarksPass(MSAanalysis msaAnalysis, int pos1, int pos2, java.lang.String aa1, java.lang.String aa2, boolean ifConservGaps)
private static boolean ifPassIntraSSMarks(java.util.List<int[]> frags, java.util.List<java.lang.String> fragSS, int pos1, int pos2, int separation)
private static boolean ifGapsFreqPass(MSAanalysis msaAnalysis, int pos1, int pos2, boolean ifBothGapsFreq, double gapFreq)
private static boolean ifEntropyPass(MSAanalysis msaAnalysis, int pos1, int pos2, double entCutoff, boolean ifBoth, boolean ifGaps)
private static boolean getNmbOfContacts(int pos1, int pos2, int s1, int e1, int s2, int e2, boolean ifDiffSS, java.util.List<java.lang.Character> ssPred)
private static void getFragsForPredicted(java.lang.String ssPredPath, java.lang.String fastaSeq, int fragSize, java.util.List<int[]> frags, java.util.List<java.lang.String> fragSS, java.lang.String notAllowed, java.util.List<java.lang.Character> ssPred)
private static boolean ifPassIntraSS(java.util.List<int[]> frags, java.util.List<java.lang.String> fragSS, int pos1, int pos2, java.lang.String whichSS, int fragSizeIntra)
private static boolean ifPassInterNextSS(java.util.List<int[]> frags, int pos1, int pos2, int interSSsep, int loopSize, int endSize)