@Override protected Set<ONDEXConcept> retrieveConceptAllConceptClass( ConceptClass conceptClass) { return parent.getConceptsOfConceptClass(conceptClass); }
/** * @param cc * @return * @see net.sourceforge.ondex.core.ONDEXGraph#getConceptsOfConceptClass(net.sourceforge.ondex.core.ConceptClass) */ public Set<ONDEXConcept> getConceptsOfConceptClass(ConceptClass cc) { return og.getConceptsOfConceptClass(cc); }
int counting(ConceptClass cc) { return graph.getConceptsOfConceptClass(cc).size(); } }.count();
public static final void filterKeggPathway(Set<ONDEXConcept> cs, final OVTK2PropertiesAggregator viewer) { ONDEXGraph graph = viewer.getONDEXJUNGGraph(); Set<ONDEXConcept> pathways = graph.getConceptsOfConceptClass(createCC(graph, "Path")); Set<ONDEXConcept> pathwaysToRetain = new HashSet<ONDEXConcept>(); for (ONDEXConcept path : pathways) { Set<ONDEXConcept> reactions = new HashSet<ONDEXConcept>(); } }
@Override public void start() { for (ConceptClass conceptClass : graph.getMetaData().getConceptClasses()) { Set<ONDEXConcept> concepts = graph.getConceptsOfConceptClass(conceptClass); System.out.println("ConceptClassId\tNumber of instances"); if (concepts.size() > 0) { System.out.println(conceptClass.getId() + "\t" + concepts.size()); } } }
/** * Return all of the concept of concept classes with provided ids in the graph * @param graph - Ondex graph * @param strIds - id of concept classes * * @return view */ public static final Set<ONDEXConcept> getConceptsOfTypes(ONDEXGraph graph,Collection<String> strIds){ Set<ONDEXConcept> result = BitSetFunctions.create(graph, ONDEXConcept.class, new BitSet()); ConceptClass [] ccs = ControledVocabularyHelper.convertConceptClasses(graph, strIds); for(ConceptClass cc :ccs){ result.addAll(graph.getConceptsOfConceptClass(cc)); } return result; }
/** * Construct a view of the concepts that have concept class with on of the * supplied ids. * * @param ids * - string concept class ids * @return ondex view of concepts */ public static Set<ONDEXConcept> getConceptsByClassId(ONDEXGraph graph, String... ids) { Set<ONDEXConcept> result = BitSetFunctions.create(graph, ONDEXConcept.class, new BitSet()); if (ids == null) return result; for (int i = 0; i < ids.length; i++) { result.addAll(graph.getConceptsOfConceptClass(createCC(graph, ids[i]))); } return result; }
public static void createContextId(ONDEXGraph graph, String conceptClass, String prefix) throws Exception { ConceptClass cc = graph.getMetaData().getConceptClass(conceptClass); if (cc == null) { throw new Exception("Incorrect concept class specified: " + conceptClass); } Integer i = 0; for (ONDEXConcept c : graph.getConceptsOfConceptClass(cc)) { c.createConceptName(prefix + "_" + i.toString(), true); i++; } } /*
public void run() { if (supportConceptClass != null && supportConceptClass.isInstalled()) supportConceptClass.uninstall(); conceptClasses.removeAllItems(); list.add(Config.language.getProperty("ToolBar.Search.ConceptClass")); conceptClasses.addItem(Config.language.getProperty("ToolBar.Search.ConceptClass")); boolean hasCCs = false; for (ConceptClass conceptClass : graph.getMetaData().getConceptClasses()) { Set<ONDEXConcept> view = graph.getConceptsOfConceptClass(conceptClass); if (view.size() > 0) { hasCCs = true; MetaDataWrapper wrapper = new MetaDataWrapper(conceptClass); conceptClasses.addItem(wrapper); list.add(wrapper); } } conceptClasses.setEnabled(hasCCs); if (hasCCs) addAutoCompleteSupport(list, conceptClasses); } };
@Override public void start() throws Exception { Set<ONDEXConcept> hideConcepts = new HashSet<ONDEXConcept>(); Set<ONDEXRelation> hideRelations = new HashSet<ONDEXRelation>(); List<Integer> ecTerms = (List<Integer>) args.getObjectValueList(EC_LEVEL_ARG); ConceptClass ccEC = graph.getMetaData().getConceptClass(CC_EC); DataSource dataSourceEC = graph.getMetaData().getDataSource(CC_EC); for (ONDEXConcept ecConcept : graph.getConceptsOfConceptClass(ccEC)) { for (ConceptAccession accession : ecConcept.getConceptAccessions()) { if (accession.getElementOf().equals(dataSourceEC)) { int intLevel = getLevel(accession.getAccession()); if (intLevel == 0 || intLevel > 4) { System.err.println("EC accession of " + intLevel + " levels is invalid :" + accession.getAccession()); } if (ecTerms.contains(Integer.valueOf(intLevel))) { hideConcepts.add(ecConcept); for (ONDEXRelation relation : graph.getRelationsOfConcept(ecConcept)) { hideRelations.add(relation); } } } } } System.out.println("finished found " + hideConcepts.size() + " concepts and " + hideRelations.size() + "relations"); visibleConcepts = new HashSet<ONDEXConcept>(graph.getConcepts()); visibleConcepts.removeAll(hideConcepts); visibleRelations = new HashSet<ONDEXRelation>(graph.getRelations()); visibleRelations.removeAll(hideRelations); }
public void start() { ONDEXGraphMetaData metadata = graph.getMetaData(); for (ConceptClass cc : metadata.getConceptClasses()) { System.out.println("ConceptClass " + cc.getId() + " " + cc.getFullname()); System.out.println("\tConcepts = " + graph.getConceptsOfConceptClass(cc).size()); } for (DataSource dataSource : metadata.getDataSources()) { System.out.println("DataSource " + dataSource.getId() + " " + dataSource.getFullname()); System.out.println("\tConcepts = " + graph.getConceptsOfDataSource(dataSource).size()); } for (AttributeName att : metadata.getAttributeNames()) { System.out.println("AttributeName " + att.getId() + " " + att.getFullname()); System.out.println("\tConcepts = " + graph.getConceptsOfAttributeName(att).size()); System.out.println("\tRelations = " + graph.getRelationsOfAttributeName(att).size()); } for (RelationType rt : metadata.getRelationTypes()) { System.out.println("RelationType " + rt.getId() + " " + rt.getFullname()); System.out.println("\tRelations = " + graph.getRelationsOfRelationType(rt).size()); } }
private Set<ONDEXConcept> getBaseConcepts() throws InvalidPluginArgumentException { Set<ONDEXConcept> itConcepts = null; Set<ConceptClass> validCCs = getExclusiveConceptClasses(); if (validCCs.size() > 0) { for (ConceptClass cc : validCCs) { fireEventOccurred(new GeneralOutputEvent("Filtering on cc " + cc.getId(), getCurrentMethodName())); if (itConcepts == null) { itConcepts = BitSetFunctions.copy(graph .getConceptsOfConceptClass(cc)); } else { itConcepts.addAll(graph.getConceptsOfConceptClass(cc)); } } } else { itConcepts = BitSetFunctions.copy(graph.getConcepts()); // map to everything } return itConcepts; }
public static void filterByClassHasRt(OVTK2PropertiesAggregator viewer, String cls, String rt) { ONDEXGraph graph = viewer.getONDEXJUNGGraph(); ONDEXJUNGGraph jung = viewer.getONDEXJUNGGraph(); Set<ONDEXConcept> del = new HashSet<ONDEXConcept>(); for (ONDEXConcept c : graph.getConceptsOfConceptClass(createCC(graph, cls))) { boolean keep = false; for (ONDEXRelation r : graph.getRelationsOfConcept(c)) { if (r.getOfType().getId().equals(rt)) { keep = true; break; } } if (!keep) { del.add(c); } } for (ONDEXConcept c : del) { // graph.deleteConcept(c.getId()); jung.setVisibility(c, false); } }
public static void correctUniprotAccession(OVTK2PropertiesAggregator viewer) { ONDEXGraph graph = viewer.getONDEXJUNGGraph(); ConceptClass prot = graph.getMetaData().getConceptClass("Protein"); DataSource nc_np = graph.getMetaData().getDataSource("NC_NP"); for (ONDEXConcept p : graph.getConceptsOfConceptClass(prot)) { List<String> newAcc = new ArrayList<String>(); for (ConceptAccession ca : p.getConceptAccessions()) { if (ca.getElementOf().equals(nc_np)) { if (ca.getAccession().contains(".")) { newAcc.add(ca.getAccession().split("\\.")[0]); } } } for (String str : newAcc) { p.createConceptAccession(str, nc_np, true); } } }
public void start() { FileFilter filter = setupFilters(graph.getConceptsOfConceptClass(graph .getMetaData().getConceptClass(MetaData.CC_ProtFam)), graph .getMetaData().getDataSource(MetaData.CV_PDB)); try { transformer = new ProteinTransformer(graph); ReadFiles(filter); } catch (Exception e) { e.printStackTrace(); } } }
public static void countMembers(OVTK2PropertiesAggregator viewer, String clsOfConctext, String clsOfMemeber) { ONDEXGraph graph = viewer.getONDEXJUNGGraph(); AttributeName an = createAttName(graph, clsOfMemeber + "_members", Double.class); ConceptClass cls = createCC(graph, clsOfMemeber); for (ONDEXConcept c : graph.getConceptsOfConceptClass(createCC(graph, clsOfConctext))) { Double count = 0d; for (ONDEXConcept oc : graph.getConceptsOfTag(c)) { if (oc.getOfType().equals(cls)) { count++; } } c.createAttribute(an, count, false); } }
/** * checks all requirements in the graph. * * @return if everything is ok. */ private boolean checkGraphRequirements() { boolean continueRun = true; if (graph.getConceptsOfConceptClass(cc_protFam).isEmpty()) { continueRun = false; fireEventOccurred(new InconsistencyEvent("Graph does not contain protein families.", getName())); } if (graph.getConceptsOfConceptClass(cc_protein).isEmpty()) { continueRun = false; fireEventOccurred(new InconsistencyEvent("Graph does not contain proteins.", getName())); } if (graph.getRelationsOfRelationType(rts_ortholog).isEmpty()) { continueRun = false; fireEventOccurred(new InconsistencyEvent("Graph does not contain ortholog relations.", getName())); } if (graph.getRelationsOfRelationType(rts_seq2pfam).isEmpty()) { continueRun = false; fireEventOccurred(new InconsistencyEvent("Graph does not contain protein to pfam mappings.", getName())); } return continueRun; }
/** * returns a view of concepts that meet both criteria * * @param graph the currentGraph * @param taxId * @return concept that are of specified cc and have the specified att */ private Set<ONDEXConcept> getSet(ONDEXGraph graph, ConceptClass ccName, AttributeName sequenceTypeName, AttributeName taxId) { Set<ONDEXConcept> concepts = BitSetFunctions.copy(graph.getConceptsOfAttributeName(sequenceTypeName)); fireEventOccurred(new GeneralOutputEvent(concepts.size() + " concepts found with att " + sequenceTypeName.getId(), getCurrentMethodName())); if (taxId != null) { Set<ONDEXConcept> taxConcepts = graph.getConceptsOfAttributeName(taxId); fireEventOccurred(new GeneralOutputEvent(taxConcepts.size() + " concepts found with taxId ", getCurrentMethodName())); concepts.retainAll(taxConcepts); } if (ccName != null) { concepts.retainAll(graph.getConceptsOfConceptClass(ccName)); fireEventOccurred(new GeneralOutputEvent(concepts.size() + " concepts found with att " + sequenceTypeName.getId() + " and taxId and cc " + ccName.getId(), getCurrentMethodName())); } return concepts; }
/** * Counts the number of context members of particular class and stores this * value in a attribute with specified name. * * @param viewer * - Ovtk2 viewer * @param membersClass * - class of members to count * @param arg_name * - name of an argument for storing the count */ public static void annotationByContextCounter(OVTK2PropertiesAggregator viewer, String membersClass, String arg_name) { ONDEXGraph graph = viewer.getONDEXJUNGGraph(); AttributeName an = createAttName(graph, arg_name, Double.class); Set<ONDEXConcept> ccRestriction = graph.getConceptsOfConceptClass(createCC(graph, membersClass)); for (ONDEXConcept context : graph.getConcepts()) { Set<ONDEXConcept> members = graph.getConceptsOfTag(context); int count = BitSetFunctions.and(ccRestriction, members).size(); if (count > 0) { context.createAttribute(an, count, false); } } }
private void validateOndexKB() { System.out.println("Start Validating OndexKB Graph..."); int errors = 0; ConceptClass ccGene = graph.getMetaData().getConceptClass("Gene"); AttributeName attChromosome = graph.getMetaData().getAttributeName( "Chromosome"); AttributeName attScaffold = graph.getMetaData().getAttributeName( "Scaffold"); AttributeName attBegin = graph.getMetaData().getAttributeName("BEGIN"); AttributeName attEnd = graph.getMetaData().getAttributeName("END"); AttributeName attTaxID = graph.getMetaData().getAttributeName("TAXID"); for (ONDEXConcept concept : graph.getConceptsOfConceptClass(ccGene)) { Attribute attT = concept.getAttribute(attTaxID); Attribute attC = concept.getAttribute(attChromosome); Attribute attS = concept.getAttribute(attScaffold); Attribute attB = concept.getAttribute(attBegin); Attribute attE = concept.getAttribute(attEnd); if ((attC == null && attS == null) || (attB == null) || (attE == null)) { errors++; } } System.out.println("Validation completed with " + errors + " errors."); }