//Extract block sequences....
JMotifXBlockSequenceExtractor bseqExt = new JMotifXBlockSequenceExtractor();
int peptideWindow = Integer.parseInt(configMap.get("peptideWindow"));
String centerResidue = configMap.get("centerResidue");
ArrayList<String> inseqsBlock =
bseqExt.extractBlockSequenceThisWindow(inseqs, peptideWindow, db, centerResidue); //window defaults to 13
//Remove redundant Peptides
MotifXPeptideSequenceFilter filter = new MotifXPeptideSequenceFilter();
inputPeptideSequences = filter.removeRedundancy(inseqsBlock);