/**
* 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;
}
public String getGelFreeIdentXmlString(String id) {
String result = null;
if (gelFreeAccMap != null && gelFreeAccMap.containsKey(id)) {
result = indexer.getXmlByIndexElement(gelFreeAccMap.get(id));
}
return result;
}
public String getTwoDimIdentXmlString(String id) {
String result = null;
if (twoDimAccMap != null && twoDimAccMap.containsKey(id)) {
result = indexer.getXmlByIndexElement(twoDimAccMap.get(id));
}
return result;
}
public String getSpectrumXmlString(String id) {
String result = null;
if (spectrumIdMap != null && spectrumIdMap.containsKey(id)) {
result = indexer.getXmlByIndexElement(spectrumIdMap.get(id));
}
return result;
}
/**
* 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;
}