/** * 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; }