Database db = new Database(dbPath);
System.out.println(" Extracting input peptide sequences...");
// instantiate objects
JMotifXAroundSitePeptideObjectsMaker objsMaker = new JMotifXAroundSitePeptideObjectsMaker();
// data sequence....
MotifXPeptideSequenceExtractor sExtr = new MotifXPeptideSequenceExtractor();
ArrayList<String> inputBlockSequences = sExtr.extractInputPeptideSeqeunces(configMap, db);
nonRedundantAroundSitePeptideObjects = objsMaker.createSequencesAroundSiteFPeptideObjects(inputBlockSequences, configMap);
// background sequence....
// Two presupposition...
// (i) presuppose bg sequences are in block sequences
// (ii) presuppose bg sequences are non-redundant
MotifXBackgroundExtractor bGExtr = new MotifXBackgroundExtractor();
ArrayList<String> backgroundSequences = bGExtr.extractBGSequences(configMap, db);
backgroundAroundSitePeptideObjects = objsMaker.createSequencesAroundSiteFPeptideObjects(backgroundSequences, configMap);
motifs = new LinkedList<MotifXElucidatedMotif>();
ArrayList<MotifXMostSigResiduePosition> mSigRPs = new ArrayList<MotifXMostSigResiduePosition>();
seqOccurrence = nonRedundantAroundSitePeptideObjects.size();