Examples of Protein

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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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> 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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Examples of net.sf.mzmine.modules.peaklistmethods.identification.mascot.data.Protein

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   */
  public static String peptideToString(Peptide peptide) {
    StringBuffer buf = new StringBuffer();
    Format mzFormat = MZmineCore.getConfiguration().getMZFormat();

    Protein protein = peptide.getProtein();
    ProteinSection section;
    section = protein.getSection(peptide);
    buf.append(protein.getSysname() + ":" + section.getName() + "; "
        + protein.getHits() + " hits");

    buf.append("\n" + peptide.getSequence());
    buf.append("\nPeptideMz ");
    buf.append(mzFormat.format(peptide.getMass()));
    buf.append(" ;CalculatedMz ");
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Examples of net.sf.mzmine.modules.peaklistmethods.identification.mascot.data.Protein

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      // Protein info
      ProteinSection section;
      tokens = proteinInfos[pepIndex].split(":");
      String sysname = tokens[0].replace("\"", "");

      Protein protein = pepDataFile.getProtein(sysname);
      if (protein == null)
        protein = new Protein(sysname);

      int startRegion = Integer.parseInt(tokens[2]);
      int stopRegion = Integer.parseInt(tokens[3]);
      int multiplicity = Integer.parseInt(tokens[4]);
      section = new ProteinSection(startRegion, stopRegion, multiplicity);

      // Link peptide and protein
      peptide.setProtein(protein);
      protein.addPeptide(peptide, section, isTopScore);

      peptides.add(peptide);

    }
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