/** * Gets the Name Field. * * @param bpe BioPAX element * @return name field, or null if not available. */ private static String getStandardName(BioPAXElement bpe) { if(bpe instanceof Named) { return ((Named)bpe).getStandardName(); } else return null; }
/** * Finds a name for the variable. * @param ele element to check * @return a name */ public String getAName(BioPAXElement ele) { String name = null; if (ele instanceof Named) { Named n = (Named) ele; if (n.getDisplayName() != null && n.getDisplayName().length() > 0) name = n.getDisplayName(); else if (n.getStandardName() != null && n.getStandardName().length() > 0) name = n.getStandardName(); else if (!n.getName().isEmpty() && n.getName().iterator().next().length() > 0) name = n.getName().iterator().next(); } if (name == null ) name = ele.getUri(); return name + " (" + ele.getModelInterface().getName().substring( ele.getModelInterface().getName().lastIndexOf(".") + 1) + ")"; } }
else if (e.getStandardName() != null && !e.getStandardName().contains("...")) set.add(e.getStandardName()); else if (!e.getName().isEmpty()) { Set<String> names = new TreeSet<String>();
if(fix) { if (named.getStandardName() != null) { named.setDisplayName(named.getStandardName()); fixed = true;
else if (e.getStandardName() != null && !e.getStandardName().contains("...")) set.add(e.getStandardName()); else if (!e.getName().isEmpty()) { Set<String> names = new TreeSet<String>();
if(validation.isFix()) { if (named.getStandardName() != null) { named.setDisplayName(named.getStandardName()); fixed = true;
if (e.getStandardName() != null) { e.setDisplayName(e.getStandardName()); } else if (!e.getName().isEmpty()) { String dsp = e.getName().iterator().next();
if (e.getStandardName() != null) { e.setDisplayName(e.getStandardName()); if (log.isInfoEnabled()) log.info(e + " displayName auto-fix: "
/** * Gets the Name Field. * * @param bpe BioPAX element * @return name field, or null if not available. */ public static String getStandardName(BioPAXElement bpe) { String stdName = null; if(bpe instanceof Named) { stdName = ((Named)bpe).getStandardName(); } else if(bpe instanceof sequenceFeature) { stdName = ((sequenceFeature)bpe).getNAME(); } else if(bpe instanceof physicalEntityParticipant){ stdName = getStandardName(((physicalEntityParticipant)bpe).getPHYSICAL_ENTITY()); } else if(bpe instanceof entity) { stdName = ((entity)bpe).getNAME(); } else if(bpe instanceof bioSource) { stdName = ((bioSource)bpe).getNAME(); } else if(bpe instanceof dataSource) { stdName = ((dataSource)bpe).getNAME().toString(); } return stdName; }