Package database

Examples of database.Protein

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        ArrayList<AroundSiteFPeptideObject> bGFPep = new ArrayList<AroundSiteFPeptideObject>();
       
        ArrayList<Protein> proteins = dbase.getProteins();
        Iterator<Protein> itr = proteins.iterator();
        while(itr.hasNext()){
            Protein  protein = itr.next();
            ArrayList<Integer> residueSiteIndeces = protein.getResidueIndeces(centerResidue);
            Iterator<Integer> itr2 = residueSiteIndeces.iterator();
            while(itr2.hasNext()){
               int residueSiteIndex = itr2.next();
               if((residueSiteIndex > preNPostSiteLength ) && ((protein.getSequence().length() - residueSiteIndex) > preNPostSiteLength)){
                   AminoAcid[] aArr = new AminoAcid[(preNPostSiteLength * 2) + 1];
                   for(int i = -preNPostSiteLength, j = 0; j < aArr.length; i++,j++){
                      char symb = protein.getSequence().charAt(residueSiteIndex + i);
                      boolean isCenter = false;
                      if( i == 0 ){ isCenter = true; }
                      int pos = i; // relative position to center...
                      aArr[j] = new AminoAcid(symb, isCenter, pos);
                     
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        ArrayList<AroundSiteFPeptideObject> bGFPep = new ArrayList<AroundSiteFPeptideObject>();
        ArrayList<Protein> proteins = dbase.getProteins();
        Iterator<Protein> itr = proteins.iterator();
        while(itr.hasNext()){
            Protein  protein = itr.next();
            ArrayList<Integer> glycosites = protein.getGlycositeIndeces();
            Iterator<Integer> itr2 = glycosites.iterator();
            while(itr2.hasNext()){
               int glyc_loc = itr2.next();
               if((glyc_loc > 6 ) && ((protein.getSequence().length() - glyc_loc) > 6)){
                   AminoAcid[] aArr = new AminoAcid[13];
                   for(int i = -6, j = 0; j < aArr.length; i++,j++){
                      char symb = protein.getSequence().charAt(glyc_loc + i);
                      boolean isGlyc = false;
                      if( i == 0 ){ isGlyc = true; }
                      int pos = i;
                      aArr[j] = new AminoAcid(symb,isGlyc,pos);;
                     
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Related Classes of database.Protein

  • jmotifx.preprocess.JMotifXAroundSitePeptideObjectsMaker
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