/**
* Get the number of peptides.
*
* @return int the count of entries
*/
public int getNumberOfPeptides() {
int cnt = 0;
// gel free
Collection<IndexElement> gelFreePeptides =
indexer.getIndexElements(PrideXmlXpath.GELFREE_PEPTIDE.getXpath());
cnt += gelFreePeptides == null ? 0 : gelFreePeptides.size();
// two dim
Collection<IndexElement> twoDimPeptides =
indexer.getIndexElements(PrideXmlXpath.TWOD_PEPTIDE.getXpath());
cnt += twoDimPeptides == null ? 0 : twoDimPeptides.size();
return cnt;
}
private Map<String, List<IndexElement>> initPeptideCacheMap() {
// 1. create a empty identification to peptide mapping map
Map<String, List<IndexElement>> identPeptideMap =
new LinkedHashMap<String, List<IndexElement>>();
// 2. get all gel free peptide index element
Collection<IndexElement> gelFreePeptideElements =
indexer.getIndexElements(PrideXmlXpath.GELFREE_PEPTIDE.getXpath());
// 3. iterate over each gel free peptide index element
for (IndexElement gelFreePeptideElement : gelFreePeptideElements) {
String identId = searchForId(gelFreePeptideElement, gelFreeAccMap);
addIdentPeptide(identId, gelFreePeptideElement, identPeptideMap);
}
// 4. get all two dimensional peptide index element
Collection<IndexElement> twoDimPeptideElements =
indexer.getIndexElements(PrideXmlXpath.TWOD_PEPTIDE.getXpath());
// 5. iterate over each peptide index element
for (IndexElement twoDimPeptideElement : twoDimPeptideElements) {
String identId = searchForId(twoDimPeptideElement, twoDimAccMap);
addIdentPeptide(identId, twoDimPeptideElement, identPeptideMap);
}
return identPeptideMap;
}