/** * Remove sites from any protein match locations (make sites NULL so they don't appear at all in the XML output) * @param proteins The proteins * @param all Remove all site data (not just empty sites)? */ private void removeSites(List<Protein> proteins, boolean all) { for (Protein protein : proteins) { Set<Match> matches = protein.getMatches(); if (matches != null && matches.size() > 0) { for (Match match : matches) { Set<Location> locations = match.getLocations(); if (locations != null && locations.size() > 0) { for (Location location : locations) { if (location instanceof LocationWithSites) { LocationWithSites l = (LocationWithSites) location; Set<Site> sites = l.getSites(); if (sites != null) { if (all || sites.size() < 1) { l.setSites(null); } } } } } } } } } }
Set<Location> locations = match.getLocations(); if (locations != null) { locationCount += locations.size();
final String description = signature.getDescription(); Set<Location> locations = match.getLocations(); if (locations != null) { locationCount += locations.size();
final String description = signature.getDescription(); Set<Location> locations = match.getLocations(); if (locations != null) { locationCount += locations.size();
Set<Location> locations = match.getLocations(); if (locations != null) { locationCount += locations.size();
Set<LocationWithSites> locations = match.getLocations(); if (locations != null) { locationCount += locations.size();
Set<Location> locations = match.getLocations(); if (locations != null) { locationCount += locations.size();
final String matchId = MATCH_STRING + getMatchCounter(); final Set<Location> locations = match.getLocations(); if (locations != null) { for (Location location : locations) {
final String matchId = MATCH_STRING + getMatchCounter(); final Set<Location> locations = match.getLocations(); if (locations != null) { for (Location location : locations) {