Package database

Examples of database.AminoAcid

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                   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);
                     
                   }
                   bGFPep.add(new AroundSiteFPeptideObject(aArr));
               }
            }
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                   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);;
                     
                   }
                   //bGFPep.add(new AroundSiteFPeptideObject(aArr));
                   AroundSiteFPeptideObject fgbo = new AroundSiteFPeptideObject(aArr);
                   String str = fgbo.getSequence();
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                //randomly assign aminoacid char for positions -6 to -1, +1, and +3 to +6
                if(j <= -1 || j == 1 || j >= 3){
                    char symb = dbAAsArr[random.nextInt(dbAAsArr.length)].getSymbol();
                    boolean isGlyc = false;
                    int pos = j;
                    aArr[k] = new AminoAcid(symb,isGlyc,pos);
                }
                if( j == 0 ){
                    char symb = 'N';
                    boolean isGlyc = true;
                    int pos = j;
                    aArr[k] = new AminoAcid(symb,isGlyc,pos);
                }
                if( j == 2 ){
                    char symb = sT[random.nextInt(sT.length)];
                    boolean isGlyc = false;
                    int pos = j;
                    aArr[k] = new AminoAcid(symb,isGlyc,pos);
                }
             
            }
            rPep.add(new AroundSiteFPeptideObject(aArr));
        }      
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            boolean isCenter = false;
            if(index == centerIndex){
                isCenter = true;
            }
            int rel_pos = index - centerIndex;
            seqArray[index]  = new AminoAcid(symb, isCenter, rel_pos);
            index++;          
        }       
    }
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    private void setSequence() {
        //throw new UnsupportedOperationException("Not yet implemented");
        char[] cArr = new char[seqArray.length];
        for(int i = 0; i < seqArray.length; i++){
            AminoAcid aAcid = seqArray[i];
            cArr[i] = aAcid.getSymbol();
        }
        sequence = new String(cArr);
    }
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Related Classes of database.AminoAcid

  • jmotifx.preprocess.JMotifXAroundSitePeptideObjectsMaker
  • jmotifx.sequenceobjects.AroundSiteFPeptideObject
  • jmotifx.sequenceobjects.AroundSitePeptideObject
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