Examples of ORF

Examples of versusSNP.genome.ORF

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    Document document = (Document)o;
    tableModel.setRowCount(0);  // clear previous table things
    if (document.getQueryGenome() == null)
      return;
    for (Iterator<ORF> iter = document.getQueryGenome().getOrfList().iterator(); iter.hasNext();) {
      ORF orf = iter.next();
      tableModel.insertRow(tableModel.getRowCount(), new ORF[]{orf});
    }
  }
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Examples of versusSNP.genome.ORF

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  public static boolean writeFile(String path, Genome genome) {
    try {
      PrintWriter out = new PrintWriter(new BufferedWriter(
          new OutputStreamWriter(new FileOutputStream(new File(path)))));
      for (Iterator<ORF> iter = genome.getOrfList().iterator(); iter.hasNext();) {
        ORF orf = iter.next();
        if (orf.getSequence() == null) continue;
        out.println(">" + orf.getName());
        intoLines(orf.getSequence().getSequence(), out);
      }
      out.close();
      return true;
    } catch (Exception e) {
      JOptionPane.showMessageDialog(null, UICaption.dialog_error_file_not_writable, UICaption.dialog_caption_error, JOptionPane.ERROR_MESSAGE);
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Examples of versusSNP.genome.ORF

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      else
        v = line.split("\\s+");
      // remove "###,###" format
      if (v[1].indexOf('"') != -1 && v[1].indexOf(',') != -1 &&
        v[2].indexOf('"') != -1 && v[2].indexOf('"') != -1)
        genome.addORF(new ORF(v[0], Utils.toIntegar(v[1]), Utils.toIntegar(v[2]), Utils.toStrand(v[3])));
      else
        genome.addORF(new ORF(v[0], Integer.parseInt(v[1]), Integer.parseInt(v[2]), Utils.toStrand(v[3])));
    }
  }
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Examples of versusSNP.genome.ORF

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    String line = null;
    while ((line = br.readLine())!=null) {
      if (!checkLine(line))
        continue;
      String[] v = line.split(",");
      genome.addORF(new ORF(v[0], Integer.parseInt(v[1]), Integer.parseInt(v[2]), Utils.toStrand(v[3])));
    }
  }
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Examples of versusSNP.genome.ORF

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    this.referenceGenome = referenceGenome;
  }
  public void addORF(final ArrayList<ORF> orfList) {
    for (CopiedIterator<ORF> iter = new CopiedIterator<ORF>(referenceGenome
        .getOrfList().iterator()); iter.hasNext();) {
      ORF orf = iter.next();
      addItem(orf);
    }
  }
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