Examples of SNP

Examples of versusSNP.genome.SNP

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    }
  }
 
  private void drawSNP(SNPList snpList) {
    for (Iterator<SNP> iter = snpList.iterator(); iter.hasNext();) {
      SNP snp = iter.next();
      dot(adjustDot(snp.getQPosInGenome(), SwingConstants.HORIZONTAL, ratio_x),
        adjustDot(snp.getSPosInGenome(), SwingConstants.VERTICAL, ratio_y), snp.getByteType());
    }
  }
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Examples of versusSNP.genome.SNP

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    this.snpContainer = snpContainer;
    setRowCount(0);  // clear previous table things
    int record = -1;
    for (Iterator<SNP> iter = snpList.iterator(); iter.hasNext();) {
//      if (getRowCount() > SNPTableControl.PAGE_RECORD_LIMIT) return;
      SNP snp = iter.next();
      record++;
      if (record < snpContainer.getRecord())
        continue;
      else if (record >= snpContainer.getRecord() + SNPTableControl.PAGE_RECORD_LIMIT)
        break;
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Examples of versusSNP.genome.SNP

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        qPos += set.biasQStrand();
      if (sBase != '-')
        sPos += set.biasSStrand();
      if (qBase != sBase) {
        if (sBase != '-') {
          set.addSNP(new SNP(qPos, sPos, qBase, sBase));
        } else {
          set.addSNP(new SNP(qPos, set.isSStrand() ? sPos + 1 : sPos, qBase, sBase));
        }
      }
    }
    set.emptyQuerySubjectSeq();
  }
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Examples of versusSNP.genome.SNP

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    this.snpList.addAll(snpList.getSNPs());
  }
 
  public static void add(SNPList snpList, SNPList sSNPList, SNPList nsSNPList, SNPList inSNPList, SNPList delSNPList) {
    for (Iterator<SNP> iter = snpList.iterator(); iter.hasNext();) {
      SNP snp = iter.next();
      switch (snp.getByteType()) {
      case SNP.SYNONYMOUS:
        sSNPList.add(snp);
        break;
      case SNP.NON_SYNONYMOUS:
        nsSNPList.add(snp);
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