/** * Copies a context list from on concept to another concept * @param acFrom * @param acTo */ public void copyContext(ONDEXConcept acTo, Set<ONDEXConcept> acFrom){ for (ONDEXConcept concept : acFrom) { if (!acTo.getTags().contains(concept)) { acTo.addTag(concept); } } } /**
/** * Copies a context list from on concept to another concept * @param acFrom * @param acTo */ public void copyContext(ONDEXConcept acTo, Set<ONDEXConcept> acFrom){ for (ONDEXConcept concept : acFrom) { if (acTo.getTags().contains(concept) == false) { acTo.addTag(concept); } } } /**
/** * Copies a context list from on concept to another concept * @param acFrom * @param acTo */ public void copyContext(ONDEXConcept acTo, Set<ONDEXConcept> acFrom){ Iterator<ONDEXConcept> concepts = acFrom.iterator(); while(concepts.hasNext()){ ONDEXConcept concept = concepts.next(); if ( acTo.getTags().contains(concept) == false ) acTo.addTag(concept); } } /**
/** * Copies a context list from on concept to another concept * @param acFrom * @param acTo */ public void copyContext(ONDEXConcept acTo, Set<ONDEXConcept> acFrom){ Iterator<ONDEXConcept> concepts = acFrom.iterator(); while(concepts.hasNext()){ ONDEXConcept concept = concepts.next(); if ( acTo.getTags().contains(concept) == false ) acTo.addTag(concept); } } /**
/** * Copies all context information from old concept to new concept and * updates context references on other entities. * * @param oldC * old ONDEXConcept * @param newC * new ONDEXConcept */ private void copyContext(ONDEXConcept oldC, ONDEXConcept newC) { // add new concept to same references as old concept for (ONDEXConcept c : graph.getConceptsOfTag(oldC)) { c.addTag(newC); } for (ONDEXRelation r : graph.getRelationsOfTag(oldC)) { r.addTag(newC); } // transfer context from old concept to new concept for (ONDEXConcept c : oldC.getTags()) { newC.addTag(c); } }
prot.addTag(exp); createHormoneContext(data[2], exp, prot);
/** * Called after parser run finished. * * @param aog * ONDEXGraph * @param idOldNew * Map<Integer, Integer> * @param context * Map<Integer, Set<Integer>> * @throws InconsistencyException */ public static void syncContext(ONDEXGraph aog, Map<Integer, Integer> idOldNew, Map<Integer, Set<Integer>> context) throws InconsistencyException { // update the context for previous parsed concepts for (Integer key : context.keySet()) { ONDEXConcept c = aog.getConcept(idOldNew.get(key)); for (Integer id : context.get(key)) { ONDEXConcept co = aog.getConcept(idOldNew.get(id)); if (co != null) c.addTag(co); else throw new InconsistencyException( "A tag concept for concept " + c.getId() + " is missing."); } } }
@Override public void nodeToConcept(AbstractNode node) { Pathway pathway = (Pathway) node; ONDEXConcept concept = graph.getFactory().createConcept(pathway.getUniqueId(), dataSourceMetaC, ccPathway, etIMPD); concept.addTag(concept); pathway.setConcept(concept); }
@Override public void nodeToConcept(AbstractNode node) { Pathway pathway = (Pathway) node; ONDEXConcept concept = graph.getFactory().createConcept(pathway.getUniqueId(), dataSourceMetaC, ccPathway, etIMPD); concept.addTag(concept); pathway.setConcept(concept); }
@Override public void nodeToConcept(AbstractNode node) { Pathway pathway = (Pathway) node; ONDEXConcept concept = graph.getFactory().createConcept(pathway.getUniqueId(), dataSourceBioC, ccPathway, etIMPD); concept.addTag(concept); pathway.setConcept(concept); }
@Override public void nodeToConcept(AbstractNode node) { Pathway pathway = (Pathway) node; ONDEXConcept concept = graph.getFactory().createConcept(pathway.getUniqueId(), dataSourceAraC, ccPathway, etIMPD); concept.addTag(concept); pathway.setConcept(concept); }
pathC.addTag(pathwayC);
System.out.println("Unknown database " + dbLink.getDbName() + " :" + dbLink.getAccession()); concept.addTag(concept);
public static void createContext(OVTK2PropertiesAggregator viewer, String name) { ONDEXGraph graph = viewer.getONDEXJUNGGraph(); ONDEXConcept context = graph.getFactory().createConcept(name, createDataSource(graph, "unknown"), createCC(graph, "Thing"), createEvidence(graph, "manual")); context.createConceptName(name, true); for (ONDEXConcept c : graph.getConcepts()) { c.addTag(context); } }
/** * Will add a specified tag concept to all members of this subgraph * * @param tag - a tag concept */ public void addTag(ONDEXConcept tag) { int conceptCounter = 0; for(ONDEXConcept c : concepts) { if (graph.getConcept(c.getId()) != null) { graph.getConcept(c.getId()).addTag(tag); conceptCounter++; } } int relationCounter = 0; for(ONDEXRelation r : relations) { if (graph.getRelation(r.getId()) != null) { graph.getRelation(r.getId()).addTag(tag); relationCounter++; } } System.err.println("Assigned tag to " + conceptCounter + " concepts and " + relationCounter + " relations."); }
if ( pathway.isSuperPathWay()) pathwayNode.setBelongsToSuperPathway(true); pathwayNode.getConcept().addTag(node.getConcept()); graph.getFactory().createRelation(pathway.getConcept(),pathwayNode.getConcept(), rtPrecededBy, etIMPD).addTag(node.getConcept()); pathwayNode.setBelongsToSuperPathway(true); if ( !pathwayNode.getConcept().getTags().contains(node.getConcept())) pathwayNode.getConcept().addTag(node.getConcept()); graph.getFactory().createRelation(pathwayNode.getConcept(),pathway.getConcept(), rtMemberIsPart, etIMPD).addTag(node.getConcept());
if ( pathway.isSuperPathWay()) pathwayNode.setBelongsToSuperPathway(true); pathwayNode.getConcept().addTag(node.getConcept()); graph.getFactory().createRelation(pathway.getConcept(),pathwayNode.getConcept(), rtPrecededBy, etIMPD).addTag(node.getConcept()); pathwayNode.setBelongsToSuperPathway(true); if ( !pathwayNode.getConcept().getTags().contains(node.getConcept())) pathwayNode.getConcept().addTag(node.getConcept()); graph.getFactory().createRelation(pathwayNode.getConcept(),pathway.getConcept(), rtMemberIsPart, etIMPD).addTag(node.getConcept());
pathwayNode.setBelongsToSuperPathway(true); if ( !pathwayNode.getConcept().getTags().contains(node.getConcept())) pathwayNode.getConcept().addTag(node.getConcept()); graph.getFactory().createRelation(pathwayNode.getConcept(),pathway.getConcept(), rtMemberIsPart, etIMPD).addTag(node.getConcept());
@Override public void start() throws Exception { String conceptClass = (String) args.getUniqueValue(CC); String name = (String) args.getUniqueValue(NAME); Set<ONDEXConcept> cs = graph.getConcepts(); Set<ONDEXRelation> rs = graph.getRelations(); ONDEXConcept c = graph.getFactory().createConcept(name, createDataSource(graph, "UC"), createCC(graph, conceptClass), createEvidence(graph, "M")); c.createConceptName(name, true); for (ONDEXConcept co : cs) { co.addTag(c); } for (ONDEXRelation re : rs) { re.addTag(c); } }
/** * This function will create a context from a set of concepts and relations * currently selected in the graph * * @param viewer * - viewer * @param name * - name that the new context will have */ public static void createContextFromSelection(OVTK2PropertiesAggregator viewer, String name) { ONDEXGraph graph = viewer.getONDEXJUNGGraph(); ONDEXConcept context = graph.getFactory().createConcept(name, createDataSource(graph, "unknown"), createCC(graph, "Thing"), createEvidence(graph, "manual")); context.createConceptName(name, true); PickedState<ONDEXRelation> stateE = viewer.getVisualizationViewer().getPickedEdgeState(); Set<ONDEXRelation> setE = stateE.getPicked(); for (ONDEXRelation e : setE) { graph.getRelation(e.getId()).addTag(context); } PickedState<ONDEXConcept> stateN = viewer.getVisualizationViewer().getPickedVertexState(); Set<ONDEXConcept> setN = stateN.getPicked(); for (ONDEXConcept n : setN) { graph.getConcept(n.getId()).addTag(context); } } }