public class Terminus
extends java.lang.Object
Constructor and Description |
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Terminus() |
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 accPredPath,
java.lang.String fastaSeq,
java.util.List<java.lang.String> raport,
int howMany,
boolean ifACCpasser,
boolean ifBothACC,
double accThres)
Run filtering and create report of filtered-out contacts.
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private static boolean |
getNmbOfContacts(int pos1,
int pos2,
int s1,
int e1,
int s2,
int e2) |
private static boolean |
ifACCPass(int pos1,
int pos2,
java.util.List<java.lang.Integer> accPred,
double accThres,
boolean ifBoth) |
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 ACCpro20 results;
[3]: value of t parameter (int; default = 15);
[4]: value of TRSA parameter (double; default = 35);
[5]: number of predicted contacts (N; default = 200);
[6]: 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 [5] is ignored);
[7]: for number of predicted contacts value of 'd' in 'm*L/d' where 'L' is sequence length (default = 1);
[8]: chosen sub-name for the output file;private static void createReport(java.lang.String resPath, int top, int separation, java.lang.String accPredPath, java.lang.String fastaSeq, java.util.List<java.lang.String> raport, int howMany, boolean ifACCpasser, boolean ifBothACC, double accThres)
resPath
- - path to the file with DCA resultstop
- - number of of predicted contacts N to apply filtration onseparation
- - separation parameter for contact definitionaccPredPath
- - path to the file with ACCpro20 resultsfastaSeq
- - FASTA sequenceraport
- - variable which will contain the list of filtered-out contactshowMany
- - value of t parameter for 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 filterprivate static boolean ifACCPass(int pos1, int pos2, java.util.List<java.lang.Integer> accPred, double accThres, boolean ifBoth)
private static boolean getNmbOfContacts(int pos1, int pos2, int s1, int e1, int s2, int e2)