Package versusSNP.blast

Examples of versusSNP.blast.BlastSet

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      JMenuItem menuItem = new JMenuItem(UICaption.popup_menuitem_orf_sequence);
      menuItem.addActionListener(this);
      popupMenu.add(menuItem);
      popupMenu.addSeparator();
      for (Iterator<BlastSet> iter = currentORF.getBlastList().iterator(); iter.hasNext();) {
        BlastSet set = iter.next();
        JMenuItem orfItem = new JMenuItem(set.getSName());
        orfItem.addActionListener(this);
        popupMenu.add(orfItem);
      }
      popupMenu.show(e.getComponent(), e.getX(), e.getY());
    }
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      if (((JMenuItem)obj).getActionCommand().equals(UICaption.popup_menuitem_orf_sequence)) {
        controller.getSeqPanel().setSequence(currentORF);
        controller.getSeqPanel().setOrfSummary(currentORF);
      } else {
        String subjectName = ((JMenuItem)obj).getActionCommand();
        BlastSet set = currentORF.getBlastSet(subjectName);
//        currentORF.statSNP();
        if (set != null) {
          controller.getSeqPanel().setAlignmentSummary(set);
          controller.getTabbedPane().setSelectedComponent(controller.getTabbedPane().getSnpPanel());
          controller.getTabbedPane().getSnpPanel().accept(set.getSNPList());
        }
      }
    }
  }
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  public void setSequence(Sequence sequence) {
    this.sequence = sequence;
  }
  public BlastSet getBlastSet(String subjectName) {
    for (Iterator<BlastSet> iter = blastList.iterator(); iter.hasNext();) {
      BlastSet set = iter.next();
      if (set.getSName().equals(subjectName)) {
        return set;
      }
    }
    return null;
  }
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    }
  }
 
  public void statSNP() {
    for (Iterator<BlastSet> iter = blastList.iterator(); iter.hasNext();) {
      BlastSet set = iter.next();
      if (!set.isQuerySubjectOrfSet()) return;
      ORF sOrf = set.getSOrf();
      for (Iterator<SNP> iter2 = set.getSNPList().iterator(); iter2.hasNext();) {
        try {
          SNP snp = iter2.next();
          Codon qCodon = new Codon(sequence.subString(
              snp.getQCodonBeginPos(), snp.getQCodonEndPos()));
          Codon sCodon = new Codon(sOrf.getSequence().subString(
              snp.getSCodonBeginPos(), snp.getSCodonEndPos()));
//          System.out.println(sOrf.getName() + ' '+sOrf.getSequence().subString(
//              snp.getSCodonBeginPos()-3, snp.getSCodonEndPos()+3));
          snp.setQPosInCodon(snp.getQCodonBeginPos());
          snp.setSPosInCodon(snp.getSCodonBeginPos());
          snp.setQCodon(qCodon);
          snp.setSCodon(sCodon);
          snp.setQPosInGenome(this);
          snp.setSPosInGenome(set.getSOrf());
          snp.setComplement(set.isComplement());
          snp.setComplementPosInCodon(set.isComplement());
          snp.setType();
          snp.setQOrf(this);
          snp.setSOrf(set.getSOrf());
          snp.setComplete();
        } catch (IndexOutOfBoundsException e) {
          continue;
        }
      }
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    SNPList sSNPList = new SNPList(this, subjectGenome);
    SNPList nsSNPList = new SNPList(this, subjectGenome);
    SNPList inSNPList = new SNPList(this, subjectGenome);
    SNPList delSNPList = new SNPList(this, subjectGenome);
    for (Iterator<BlastSet> iter = blastList.iterator(); iter.hasNext();) {
      BlastSet set = iter.next();
      ORF qOrf, sOrf;
      if ((qOrf = findORF(set.getQName())) != null) {
        qOrf.addBlastSet(set);
        if (no_gui)
          set.getAlignmentStore().transverseCount();
        if ((sOrf = subjectGenome.findORF(set.getSName())) != null) {
          set.setQuerySubjectOrf(qOrf, sOrf);
          qOrf.statSNP();
          SNPList.add(set.getSNPList(), sSNPList, nsSNPList, inSNPList, delSNPList);
        }
      }
    }
    addSSNPList(sSNPList);
    addNsSNPList(nsSNPList);
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Related Classes of versusSNP.blast.BlastSet

  • versusSNP.blast.util.AlignmentStore
  • versusSNP.blast.util.SNPList
  • versusSNP.genome.Genome
  • versusSNP.genome.ORF
  • versusSNP.gui.ChoosePanel
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