/** * Gets the Short Name (or Display Name). * * @param bpe BioPAX element * @return short name field, or null if not available. */ private static String getShortName(BioPAXElement bpe) { String shortName = null; if(bpe instanceof Named) { shortName = ((Named)bpe).getDisplayName(); } return shortName; }
/** * Gets the display name of the node * or URI. * * @param bpe BioPAX Element * @return */ public static String getName(BioPAXElement bpe) { String nodeName = null; if(bpe instanceof Named) nodeName = ((Named)bpe).getDisplayName(); return (nodeName == null || nodeName.isEmpty()) ? bpe.getRDFId() : StringEscapeUtils.unescapeHtml(nodeName); }
/** * 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) + ")"; } }
if (e.getDisplayName() != null && !e.getDisplayName().contains("...")) set.add(e.getDisplayName()); else if (e.getStandardName() != null && !e.getStandardName().contains("...")) set.add(e.getStandardName());
if (e.getDisplayName() != null && !e.getDisplayName().contains("...")) set.add(e.getDisplayName()); else if (e.getStandardName() != null && !e.getStandardName().contains("...")) set.add(e.getStandardName());
if (named.getDisplayName() == null) { if(fix) { String name = named.getDisplayName(); if (name != null) { // if existed or was added above Class<? extends BioPAXElement> cl = ((BioPAXElement)named).getModelInterface();
if (named.getDisplayName() == null) { if(validation.isFix()) { String name = named.getDisplayName(); if (name != null) { // if existed or was added above Integer max = (named instanceof Provenance) ? 50 : MAX_DISPLAYNAME_LEN;
/** * Gets the Short Name (or Display Name). * * @param bpe BioPAX element * @return short name field, or null if not available. */ public static String getShortName(BioPAXElement bpe) { String shortName = null; if(bpe instanceof Named) { shortName = ((Named)bpe).getDisplayName(); } else if(bpe instanceof sequenceFeature) { shortName = ((sequenceFeature)bpe).getSHORT_NAME(); } else if(bpe instanceof physicalEntityParticipant){ // fix PEPs shortName = getShortName(((physicalEntityParticipant)bpe).getPHYSICAL_ENTITY()); } else if(bpe instanceof entity) { shortName = ((entity)bpe).getSHORT_NAME(); } return shortName; }
if (e.getDisplayName() == null) { if (e.getStandardName() != null) { e.setDisplayName(e.getStandardName());
if (e.getDisplayName() == null) { if (e.getStandardName() != null) { e.setDisplayName(e.getStandardName()); if (log.isInfoEnabled()) log.info(e + " displayName auto-fix: " + e.getDisplayName() + ". " + extraInfo()); if(validation != null) validation.setFixed(BiopaxValidatorUtils.getId(e),