コード例 #1
0
  public void readFileAndGenerate(boolean onlyUniquePeptides, ISpectrumDataFilter... filters) {
    @SuppressWarnings("UnusedDeclaration")
    int numberProcessed = 0;
    @SuppressWarnings("UnusedDeclaration")
    double lastRetentionTime = 0;

    @SuppressWarnings("UnusedDeclaration")
    int numberUnProcessed = 0;
    try {
      LineNumberReader rdr = new LineNumberReader(new FileReader(m_File));
      String line = rdr.readLine();
      while (line != null) {
        if (line.contains("<spectrum_query")) {
          String retention_time_sec = XMLUtil.extractAttribute(line, "retention_time_sec");
          scan_id = XMLUtil.extractAttribute(line, "start_scan");
          if (retention_time_sec == null) {
            lastRetentionTime = 0;
          } else {
            try {
              lastRetentionTime = Double.parseDouble(retention_time_sec.trim());
            } catch (NumberFormatException e) {
              lastRetentionTime = 0;
            }
          }
        }

        //noinspection StatementWithEmptyBody,StatementWithEmptyBody
        if (line.contains("<search_result")) {
          String[] searchHitLines = readSearchHitLines(line, rdr);
          //              System.out.println(line);
          boolean processed =
              handleSearchHit(searchHitLines, lastRetentionTime, onlyUniquePeptides, filters);
          if (processed) {
            for (int i = 0; i < searchHitLines.length; i++) {
              @SuppressWarnings("UnusedDeclaration")
              String searchHitLine = searchHitLines[i];
            }
            numberProcessed++;
          } else numberUnProcessed++;
        }
        line = rdr.readLine();
      }

      //noinspection UnnecessaryReturnStatement
      return;
    } catch (IOException e) {
      throw new RuntimeException(e);
    }
  }
コード例 #2
0
  protected String[] readSearchHitLines(
      String line,
      LineNumberReader rdr,
      @SuppressWarnings("UnusedParameters") ISpectrumDataFilter... filters) {
    List<String> holder = new ArrayList<String>();

    try {
      while (line != null) {
        holder.add(line);
        if (line.contains("</search_result")) {
          break; // done
        }
        line = rdr.readLine(); // read next line
      }
    } catch (IOException e) {
      throw new RuntimeException(e);
    }

    String[] ret = new String[holder.size()];
    holder.toArray(ret);
    return ret;
  }