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ONDEXConcept.setAnnotation
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How to use
setAnnotation
method
in
net.sourceforge.ondex.core.ONDEXConcept

Best Java code snippets using net.sourceforge.ondex.core.ONDEXConcept.setAnnotation (Showing top 14 results out of 315)

origin: net.sourceforge.ondex.apps/ovtk2

concept.setAnnotation(text);
return text;
origin: net.sourceforge.ondex.modules/protein-structure

concept.setAnnotation(concept.getAnnotation() + " URL:" + dbLink.getAccession());
continue;
origin: net.sourceforge.ondex.apps/ovtk2

concept.setAnnotation(annotation.getText());
origin: net.sourceforge.ondex.modules/cyc-pathwaydbs

@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);
}
origin: net.sourceforge.ondex.modules/chemical

c.setAnnotation(value);
origin: net.sourceforge.ondex.apps.qtlnetminer.common/common-server

concept.setAnnotation(newAnno);
concept.setAnnotation(newDesc);
origin: net.sourceforge.ondex.modules/poplar

g.createConceptName(pathwayKegg, true);
if (!pathwayType.equals("\\N"))
  g.setAnnotation(pathwayType);
if (!pathwayClass.equals("\\N"))
  g.setDescription(pathwayClass);
origin: net.sourceforge.ondex.modules/cyc-pathwaydbs

@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);
}
origin: net.sourceforge.ondex.core/tools

c.setAnnotation(molecularFormula);
origin: net.sourceforge.ondex.modules/cyc-pathwaydbs

@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);
}
origin: net.sourceforge.ondex.modules/legacy

@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);
}
origin: net.sourceforge.ondex.core/tools

nc.setAnnotation(c.getAnnotation());
origin: net.sourceforge.ondex.core/tools

/**
 * 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());
}
origin: net.sourceforge.ondex.core/tools

copyTargetConcept.setAnnotation(copySourceConcept.getAnnotation());
net.sourceforge.ondex.coreONDEXConceptsetAnnotation

Javadoc

Sets the annotation of this instance of AbstractConcept.

Popular methods of ONDEXConcept

  • getId
  • createAttribute
  • createConceptAccession
    Creates a new ConceptAccession with the given accession, the information which DataSource it belongs
  • createConceptName
    Creates a new ConceptName with the given name and the information if this name is preferred. Then ad
  • getOfType
  • getConceptAccessions
  • getElementOf
    Returns the DataSource, which this AbstractConcept belongs to.
  • getPID
    Returns the parser id of this instance of AbstractConcept.
  • getConceptNames
    Returns all ConceptNames contained in the list of ConceptNames.
  • getAttribute
  • getConceptName
    Returns a ConceptName or null if unsuccessful for a given name or null if unsuccessful.
  • getAnnotation
    Returns the annotation of this instance of AbstractConcept.
  • getConceptName,
  • getAnnotation,
  • addTag,
  • getDescription,
  • getAttributes,
  • getTags,
  • getEvidence,
  • getConceptAccession,
  • setDescription

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