public boolean canCheck(Object thing) { if(thing instanceof BioPAXElement) { return notAllowed((BioPAXElement) thing); } else { return false; } }
public boolean canCheck(Object thing) { return notAllowed(thing); }
@Override protected void visit(Object range, BioPAXElement domain, Model model, PropertyEditor editor) { assert range instanceof PhysicalEntity; // - because of filter and mul.cardinality if (thing.equals(range)) { error(thing, "cyclic.inclusion", false, getVisited().toString()); } else if(range instanceof Complex) { traverse((Complex) range, model); } } };
@Override protected void visit(Object range, BioPAXElement domain, Model model, PropertyEditor editor) { if (thing.equals(range)) { error(validation, thing, "cyclic.inclusion", false, "is a component of itself or its componets... : " + domain.getUri()); } else if(range instanceof Complex) { traverse((Complex) range, model); } } };
@Override protected void visit(Object range, BioPAXElement domain, Model model, PropertyEditor editor) { if (thing.equals(range)) { error(thing, "cyclic.inclusion", false, getVisited().toString()); } else { traverse((BioPAXElement) range, model); } } };
public void check(BioPAXElement thing, boolean fix) { String rdfid = thing.getRDFId(); if(rdfid != null && rdfid.length() > URI_MAX_LENGTH) error(thing, "too.long.id", false, rdfid.length(), URI_MAX_LENGTH); }
public void check(BioPAXElement thing, boolean fix) { String rdfid = thing.getRDFId(); if(rdfid != null) { try { URI.create(rdfid); } catch (IllegalArgumentException e) { error(thing, "invalid.rdf.id", false, "not a valid URI: " + rdfid); } } else error(thing, "invalid.rdf.id", false, "null value"); }
public void check(final Validation validation, ProteinReference er) { if(!er.getMemberEntityReference().isEmpty()) { // is generic if (er.getOrganism() == null) { error(validation, er, "min.cardinality.violated", false, "organism", 1); } } }
@Override public void check(Conversion thing, boolean fix) { float lsto = getStoichiometry(thing.getParticipantStoichiometry(), thing.getLeft()), rsto = getStoichiometry(thing.getParticipantStoichiometry(), thing.getRight()), diff = Math.abs(lsto - rsto); if(diff > 0) error(thing, "stoichiometry.mismatch", false, lsto, rsto); }
@Override public void check(Protein p, boolean fix) { if(p.getEntityReference() == null) { if(p.getMemberPhysicalEntity().isEmpty()) { error(p, "null.entity.reference", false, "ProteinReference"); } } } }
@Override public void check(DnaRegion sm, boolean fix) { if(sm.getEntityReference() == null) { if(sm.getMemberPhysicalEntity().isEmpty()) { error(sm, "null.entity.reference", false, "DnaRegionReference"); } } } }
public void check(final Validation validation, RnaRegion sm) { if(sm.getEntityReference() == null) { if(sm.getMemberPhysicalEntity().isEmpty()) { error(validation, sm, "null.entity.reference", false, "RnaRegionReference"); } } } }
public void check(ProteinReference er, boolean fix) { if(er.getMemberEntityReference().isEmpty()) { // is not generic if (er.getOrganism() == null) { error(er, "cardinality.violated", false, "organism", 1); } } }
@Override public void check(Rna sm, boolean fix) { if(sm.getEntityReference() == null) { if(sm.getMemberPhysicalEntity().isEmpty()) { error(sm, "null.entity.reference", false, "RnaReference"); } } } }
public void check(BiochemicalPathwayStep step, boolean fix) { if (step.getStepProcess() != null) { for (Process process : step.getStepProcess()) { if (process instanceof Conversion) { error(step, "misplaced.step.conversion", false, process); } } } } }
public boolean canCheck(Object thing) { if(thing instanceof BioPAXElement) { return notAllowed((BioPAXElement) thing); } else { return false; } }
public boolean canCheck(Object thing) { return notAllowed(thing); }
public void check(final Validation validation, BioPAXElement thing) { String rdfid = thing.getUri(); if(rdfid != null && rdfid.length() > URI_MAX_LENGTH) error(validation, thing, "too.long.id", false, rdfid.length(), URI_MAX_LENGTH); }
public void check(final Validation validation, BioPAXElement thing) { String rdfid = thing.getUri(); if(rdfid != null) { try { URI.create(rdfid); } catch (IllegalArgumentException e) { error(validation, thing, "invalid.rdf.id", false, "not a valid URI: " + rdfid); } } else error(validation, thing, "invalid.rdf.id", false, "null value"); }
public void check(ProteinReference er, boolean fix) { if(!er.getMemberEntityReference().isEmpty()) { // is generic if (er.getOrganism() == null) { error(er, "min.cardinality.violated", false, "organism", 1); } } }