コード例 #1
0
 /**
  * Get all peptide xml strings within an identifiation.
  *
  * @param identId identificatio id
  * @return List<String> a list of peptide xml strings
  */
 public List<String> getPeptideXmlStrings(String identId) {
   List<String> peptides = new ArrayList<String>();
   List<IndexElement> elements = identToPeptideMap.get(identId);
   for (IndexElement element : elements) {
     peptides.add(indexer.getXmlByIndexElement(element));
   }
   return peptides;
 }
コード例 #2
0
  public String getGelFreeIdentXmlString(String id) {
    String result = null;

    if (gelFreeAccMap != null && gelFreeAccMap.containsKey(id)) {
      result = indexer.getXmlByIndexElement(gelFreeAccMap.get(id));
    }

    return result;
  }
コード例 #3
0
  public String getTwoDimIdentXmlString(String id) {
    String result = null;

    if (twoDimAccMap != null && twoDimAccMap.containsKey(id)) {
      result = indexer.getXmlByIndexElement(twoDimAccMap.get(id));
    }

    return result;
  }
コード例 #4
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  public String getSpectrumXmlString(String id) {
    String result = null;

    if (spectrumIdMap != null && spectrumIdMap.containsKey(id)) {
      result = indexer.getXmlByIndexElement(spectrumIdMap.get(id));
    }

    return result;
  }
コード例 #5
0
  /**
   * Get the corresponding xml string for a peptide.
   *
   * @param identId identification id.
   * @param index peptide index within the identification
   * @return String xml string
   */
  public String getPeptideXmlString(String identId, int index) {
    String xml = null;

    List<IndexElement> elements = identToPeptideMap.get(identId);
    if (elements != null && index >= 0 && index < elements.size()) {
      xml = indexer.getXmlByIndexElement(elements.get(index));
    }

    return xml;
  }