Package versusSNP.blast.util

Examples of versusSNP.blast.util.SNPList

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  @Override
  public void update(Observable o, Object arg) {
    Document document = (Document)o;
    if (document.getQueryGenome() != null && document.getSubjectGenome() != null) {
      SNPList snpList = document.getQueryGenome().getNsSNPList(document.getSubjectGenome());
      if (snpList != null) {
        this.snpList = snpList;
        tableControl.setSnpList(snpList);
        accept(snpList);
      }
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  @Override
  public void update(Observable o, Object arg) {
    Document document = (Document)o;
    if (document.getQueryGenome() != null && document.getSubjectGenome() != null) {
      if (this.type == SNP.INSERTION) {
        SNPList inSnpList = document.getQueryGenome().getInSNPList(document.getSubjectGenome());
        if (inSnpList != null) {
          this.snpList = inSnpList;
          tableControl.setSnpList(snpList);
          accept(inSnpList);
        }
      } else {
        SNPList delSnpList = document.getQueryGenome().getDelSNPList(document.getSubjectGenome());
        if (delSnpList != null) {
          this.snpList = delSnpList;
          tableControl.setSnpList(snpList);
          accept(delSnpList);
        }
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  public BlastSet() {
    super();
    qSeq = new StringBuffer();
    sSeq = new StringBuffer();
    annotation = new StringBuffer();
    snpList = new SNPList();
    alignmentStore = new AlignmentStore();
    isQuerySubjectOrfSet = false;
  }
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    return orfList;
  }

  public SNPList getSSNPList(Genome subjectGenome) {
    for (Iterator<SNPList> iter = sSNPList.iterator(); iter.hasNext();) {
      SNPList snpList = iter.next();
      if (snpList.getSubjectGenome() == subjectGenome)
        return snpList;
    }
    return null;
  }
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    return null;
  }

  public SNPList getNsSNPList(Genome subjectGenome) {
    for (Iterator<SNPList> iter = nsSNPList.iterator(); iter.hasNext();) {
      SNPList snpList = iter.next();
      if (snpList.getSubjectGenome() == subjectGenome)
        return snpList;
    }
    return null;
  }
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    return null;
  }

  public SNPList getInSNPList(Genome subjectGenome) {
    for (Iterator<SNPList> iter = inSNPList.iterator(); iter.hasNext();) {
      SNPList snpList = iter.next();
      if (snpList.getSubjectGenome() == subjectGenome)
        return snpList;
    }
    return null;
  }
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    return null;
  }

  public SNPList getDelSNPList(Genome subjectGenome) {
    for (Iterator<SNPList> iter = delSNPList.iterator(); iter.hasNext();) {
      SNPList snpList = iter.next();
      if (snpList.getSubjectGenome() == subjectGenome)
        return snpList;
    }
    return null;
  }
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  }
  public void attachBlastSets(BlastList blastList, Genome subjectGenome) {
    attachBlastSets(blastList, subjectGenome, false);
  }
  public void attachBlastSets(BlastList blastList, Genome subjectGenome, boolean no_gui) {
    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);
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  @Override
  public void update(Observable o, Object arg) {
    Document document = (Document)o;
    if (document.getQueryGenome() != null && document.getSubjectGenome() != null) {
      SNPList snpList = document.getQueryGenome().getSSNPList(document.getSubjectGenome());
      if (snpList != null) {
        this.snpList = snpList;
        tableControl.setSnpList(snpList);
        accept(snpList);
      }
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Related Classes of versusSNP.blast.util.SNPList

  • versusSNP.blast.BlastSet
  • versusSNP.genome.Genome
  • versusSNP.genome.SNP
  • versusSNP.gui.InDelPanel
  • versusSNP.gui.NSPanel
  • versusSNP.gui.SPanel
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