public class LowEntropy
extends java.lang.Object
Constructor and Description |
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LowEntropy() |
Modifier and Type | Method and Description |
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private static void |
createReport(java.lang.String resPath,
int top,
int separation,
java.lang.String fastaSeq,
java.util.List<java.lang.String> raport,
boolean ifBoth,
double entCutoff,
boolean ifGaps,
java.lang.String aliPath)
Run filtering and create report of filtered-out contacts.
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private static boolean |
ifEntropyPass(MSAanalysis msaAnalysis,
int pos1,
int pos2,
double entCutoff,
boolean ifBoth,
boolean ifGaps) |
static void |
main(java.lang.String[] args) |
public static void main(java.lang.String[] args)
args
- -
[0]: path to FASTA file;
[1]: path to gplmDCA results;
[2]: path to MSA file;
[3]: value of Tent parameter (double; default = 0.02);
[4]: number of predicted contacts (N; default = 200);
[5]: for number of predicted contacts value of 'm' in 'm*L/d' where 'L' is sequence length (if 'm' is set to non-0 then [4] is ignored);
[6]: for number of predicted contacts value of 'd' in 'm*L/d' where 'L' is sequence length (default = 1);
[7]: chosen sub-name for the output file;private static void createReport(java.lang.String resPath, int top, int separation, java.lang.String fastaSeq, java.util.List<java.lang.String> raport, boolean ifBoth, double entCutoff, boolean ifGaps, java.lang.String aliPath)
resPath
- - path to the file with DCA resultstop
- - number of of predicted contacts N to apply filtration onseparation
- - separation parameter for contact definitionfastaSeq
- - FASTA sequenceraport
- - variable which will contain the list of filtered-out contactsentCutoff
- - value of Tent parameter for low entropy filterifBoth
- - True if both residues in pair should be in agreement with Tent parameterifGaps
- - True if gaps should be counted as symbols during entropy calculationaliPath
- - path to the file with alignmentprivate static boolean ifEntropyPass(MSAanalysis msaAnalysis, int pos1, int pos2, double entCutoff, boolean ifBoth, boolean ifGaps)