public class NonStrongestCysCys
extends java.lang.Object
Constructor and Description |
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NonStrongestCysCys() |
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 fastaSeq,
java.util.List<java.lang.String> raport)
Run filtering and create report of filtered-out contacts.
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private static boolean |
ifFirstCysMarksPass(int pos1,
int pos2,
java.lang.String aa1,
java.lang.String aa2,
java.util.List<java.lang.String> alreadyFound) |
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]: number of predicted contacts (N; default = 200);
[3]: 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 [2] is ignored);
[4]: for number of predicted contacts value of 'd' in 'm*L/d' where 'L' is sequence length (default = 1);
[5]: 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)
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 contactsprivate 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)