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gatherSortedGplmdca(String, int, int, int, String) - Method in class TopMethods
 
gatherSortedGplmdca(String) - Method in class TopMethods
 
gatherSortedGplmdcaFinal(String, int, int, int, String) - Method in class TopMethods
 
gdcaSortInd - Variable in class TopMethods
 
gdcaSortVal - Variable in class TopMethods
 
getAlignment() - Method in class MSAanalysis
Get alignment in the integer format.
getFastaSeqs() - Method in class FastaFileReader
Get fasta sequences.
getFastaTitles() - Method in class FastaFileReader
Get fasta sequences' titles.
getFragsForPredicted(String, String, int, List<int[]>, List<String>, String, List<Character>) - Static method in class Filters
 
getFragsForPredicted(String, String, int, List<int[]>, List<String>, String, List<Character>) - Static method in class InterSecondary
 
getFragsForPredicted(String, String, int, List<int[]>, List<String>, String, List<Character>) - Static method in class IntraSecondary
 
getFragsForPredicted(String, String, int, List<int[]>, List<String>, String, List<Character>) - Static method in class SecondaryStraddling
 
getFullText() - Method in class ReadFile
 
getGdcaSortInd() - Method in class TopMethods
 
getGdcaSortVal() - Method in class TopMethods
 
getIndex() - Method in class QS_double
 
getNmbOfContacts(int, int, int, int, int, int, boolean, List<Character>) - Static method in class Filters
 
getNmbOfContacts(int, int, int, int, int, int) - Static method in class Terminus
 
getPosDca1() - Method in class TopMethods
 
getPosDca2() - Method in class TopMethods
 
getQSciag() - Method in class QS_double
 
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