Examples of jmotifx.sequenceobjects.AroundSitePeptideObject

            //ArrayList<Protein> proteins = db.getProteins();
            //for(Protein prot: proteins){
            
                //if(prot.getTitleLine().contains(bestAccn)){
                    //int nxstIndex = getIndex(pep);
                    AroundSitePeptideObject aroundSitePeptide = new AroundSitePeptideObject(pep, center);
                    //String protSeq = prot.getSequence();
                    String protSeq = protTitleLine2ProtSequenceMap.get(bestTLine);
                    int seq_length = protSeq.length();
                    int indexOf = protSeq.indexOf(pep);
                    int protPeptideCenterIndex = indexOf + aroundSitePeptide.getCenterIndex();
                    
                    String blockPeptide = null;
                    if (protPeptideCenterIndex > preNPostCenterResidues && 
                            (((seq_length-1) - protPeptideCenterIndex) >= preNPostCenterResidues) ){ // pre > 50 and post >= 50
                        blockPeptide = protSeq.substring(protPeptideCenterIndex - preNPostCenterResidues,

    
    public ArrayList<AroundSitePeptideObject> getMatchesHelper(ArrayList<AroundSitePeptideObject> aroundSitePeptideObjs){
        ArrayList<AroundSitePeptideObject> matches = new ArrayList<AroundSitePeptideObject>();
        Iterator<AroundSitePeptideObject> itr = aroundSitePeptideObjs.iterator();
        while(itr.hasNext()){
            AroundSitePeptideObject aroundSitePeptideObj = itr.next();
            if(this.getMatchesHelperHelper(aroundSitePeptideObj)){
                matches.add(aroundSitePeptideObj);
            }
        }       
        return matches;

Related Classes of jmotifx.sequenceobjects.AroundSitePeptideObject

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