concept.setAnnotation(text); return text;
concept.setAnnotation(concept.getAnnotation() + " URL:" + dbLink.getAccession()); continue;
concept.setAnnotation(annotation.getText());
@Override public void nodeToConcept(AbstractNode node) { Reaction reaction = (Reaction) node; ONDEXConcept concept = graph.getFactory().createConcept( reaction.getUniqueId(), dataSourceMetaC, ccReaction, etIMPD); if (reaction.getBalancedState() != null) concept.setAnnotation(reaction.getBalancedState()); concept.createConceptName(constructFormula(reaction), false); if (reaction.getDeltaGo() != null) { concept.createAttribute(deltaGo, reaction.getDeltaGo(), false); } if (reaction.getDirection() != null) { concept.setAnnotation(reaction.getDirection()); } reaction.setConcept(concept); }
concept.setAnnotation(newAnno); concept.setAnnotation(newDesc);
g.createConceptName(pathwayKegg, true); if (!pathwayType.equals("\\N")) g.setAnnotation(pathwayType); if (!pathwayClass.equals("\\N")) g.setDescription(pathwayClass);
@Override public void nodeToConcept(AbstractNode node) { Reaction reaction = (Reaction) node; ONDEXConcept concept = graph.getFactory().createConcept( reaction.getUniqueId(), dataSourceAraC, ccReaction, etIMPD); if (reaction.getBalancedState() != null) concept.setAnnotation(reaction.getBalancedState()); concept.createConceptName(constructFormula(reaction), false); if (reaction.getDeltaGo() != null) { concept.createAttribute(deltaGo, reaction.getDeltaGo(), false); } reaction.setConcept(concept); }
c.setAnnotation(molecularFormula);
@Override public void nodeToConcept(AbstractNode node) { Reaction reaction = (Reaction) node; ONDEXConcept concept = graph.getFactory().createConcept( reaction.getUniqueId(), dataSourceMetaC, ccReaction, etIMPD); if (reaction.getBalancedState() != null) concept.setAnnotation(reaction.getBalancedState()); concept.createConceptName(constructFormula(reaction), false); if (reaction.getDeltaGo() != null) { concept.createAttribute(deltaGo, reaction.getDeltaGo(), false); } reaction.setConcept(concept); }
@Override public void nodeToConcept(AbstractNode node) { Reaction reaction = (Reaction) node; ONDEXConcept concept = graph.getFactory().createConcept( reaction.getUniqueId(), dataSourceBioC, ccReaction, etIMPD); if (reaction.getBalancedState() != null) concept.setAnnotation(reaction.getBalancedState()); concept.createConceptName(constructFormula(reaction), false); if (reaction.getDeltaGo() != null) { concept.createAttribute(deltaGo, reaction.getDeltaGo(), false); } reaction.setConcept(concept); }
nc.setAnnotation(c.getAnnotation());
/** * Copies all of the attributes from one concept to another (only if they do * not already exist at target) * * @param from * - concept to copy from * @param to * - concept to copy to * @throws AccessDeniedException * @throws NullValueException * @throws EmptyStringException */ public static void copyConceptAttributes(ONDEXConcept from, ONDEXConcept to) throws NullValueException, AccessDeniedException, EmptyStringException { for (EvidenceType et : from.getEvidence()) addNewEvidence(to, et); for (ConceptAccession ca : from.getConceptAccessions()) addNewAccession(to, ca); for (ConceptName cn : from.getConceptNames()) addNewName(to, cn); for (Attribute attribute : from.getAttributes()) addNewAttribute(to, attribute); if (from.getAnnotation() != null && to.getDescription() == null) to.setAnnotation(from.getAnnotation()); if (from.getDescription() != null && to.getDescription() == null) to.setDescription(from.getDescription()); }
copyTargetConcept.setAnnotation(copySourceConcept.getAnnotation());