public class IntraSecondary
extends java.lang.Object
Constructor and Description |
---|
IntraSecondary() |
Modifier and Type | Method and Description |
---|---|
private static void |
createReport(java.lang.String resPath,
int top,
int separation,
java.lang.String notAllowed,
java.lang.String ssPredPath,
java.lang.String fastaSeq,
int fragSizeIntra,
int anyfragSize,
java.lang.String whichSS,
java.util.List<java.lang.String> raport)
Run filtering and create report of filtered-out contacts.
|
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) |
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 SSpro results;
[3]: value of Sintra parameter (int; default = 5);
[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 notAllowed, java.lang.String ssPredPath, java.lang.String fastaSeq, int fragSizeIntra, int anyfragSize, java.lang.String whichSS, 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 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 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 contactsprivate 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)