Package versusSNP.blast.util

Examples of versusSNP.blast.util.SNPFinder.find()

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          if (isAnother) {
            if (filter.test(set)) {
              blastList.add(set);
            }
            isAnother = isQuery = isSubject = false;
            snpFinder.find(set);
            set = new BlastSet();
          }
          set.setQName(m.group(1));
        } else if ((m=m_Letters.matcher(line)).find()) {
          set.setQLen(m.group(1));
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          if (isAnother) {
            if (filter.test(set)) {
              blastList.add(set);
            }
            isAnother = isQuery = isSubject = false;
            snpFinder.find(set);
            set = new BlastSet(set.getQName());
          }
          set.setSName(m.group(1));
          if ((m=m_Annotation.matcher(line)).find()) {
            set.setAnnotation(m.group(1));
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          if (isAnother) {
            if (filter.test(set)) {
              blastList.add(set);
            }
            isAnother = isQuery = isSubject = false;
            snpFinder.find(set);
            set = new BlastSet(set.getQName(), set.getSName());
          }
          set.setScore(m.group(1));
          set.setExpect(m.group(2));
         
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      if (isAnother) {
        if (filter.test(set)) {
          blastList.add(set);
        }
        isAnother = isQuery = isSubject = false;
        snpFinder.find(set);
        set = new BlastSet(set.getQName(), set.getSName());
      }
      br.close();
      System.gc();
      return true;
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