/** * Gets the direction of the Control, if exists. * @param cont Control to get its direction * @return the direction of the Control */ protected ConversionDirectionType getCatalysisDirection(Control cont) { if (cont instanceof Catalysis) { CatalysisDirectionType catDir = ((Catalysis) cont).getCatalysisDirection(); if (catDir == CatalysisDirectionType.LEFT_TO_RIGHT) { return ConversionDirectionType.LEFT_TO_RIGHT; } else if (catDir == CatalysisDirectionType.RIGHT_TO_LEFT) { return ConversionDirectionType.RIGHT_TO_LEFT; } } return null; }
private org.opencb.bionetdb.core.models.Catalysis createCatalysis(BioPAXElement bioPAXElement) { org.opencb.bionetdb.core.models.Catalysis catalysis = new org.opencb.bionetdb.core.models.Catalysis(); Catalysis catalysisBP = (Catalysis) bioPAXElement; // Common Interaction properties setInteractionCommonProperties(catalysisBP, catalysis); // Catalysis properties // controllers Set<Controller> controllers = catalysisBP.getController(); for (Controller controller: controllers) { catalysis.getControllers().add(controller.getRDFId().split("#")[1]); } // controlled Set<Process> controlledProcesses = catalysisBP.getControlled(); for (Process controlledProcess: controlledProcesses) { catalysis.getControlledProcesses().add(controlledProcess.getRDFId().split("#")[1]); } // controlType catalysis.setControlType(catalysisBP.getControlType().toString()); // cofactor Set<PhysicalEntity> cofactors = catalysisBP.getCofactor(); for (PhysicalEntity cofactor: cofactors) { catalysis.getCofactors().add(cofactor.getRDFId().split("#")[1]); } return catalysis; }
private void fix(BiochemicalPathwayStep t, Object... values) { if(values[0] instanceof Catalysis) { ((Catalysis)values[0]).setCatalysisDirection((CatalysisDirectionType) values[1]); } else if (values[0] instanceof Conversion){ ((Conversion)values[0]).setConversionDirection((ConversionDirectionType) values[1]); } }
/** * Continues the inference from the Catalysis of seed element. * @param interactionSet inferred interactions * @param aCatalysis the catalysis to follow * @param bpe source of the interaction */ private void processCatalysis(InteractionSetL3 interactionSet, Catalysis aCatalysis, BioPAXElement bpe) { //We have to consider two direction statements //Catalysis.direction and Conversion.spontaneous //This method maps the former to the compatible latter //null means reversible or unknown, both are treated in the same way. ConversionDirectionType catalysisDirection = mapDirectionToConversion(aCatalysis.getCatalysisDirection()); //get the conversions and process them. Set<Process> controlled = aCatalysis.getControlled(); for (Process process : controlled) { assert process instanceof Conversion; Conversion aConversion = (Conversion) process; //let's find the direction that is compatible with catalysis direction ConversionDirectionType dirA = findConsensusDirection(catalysisDirection, aConversion.getConversionDirection()); assert dirA != null; //and let's get the interacting physical entities createInteractions(aConversion, dirA, aCatalysis, interactionSet, bpe); } }
mapDirectionToConversion(consequentCatalysis.getCatalysisDirection()); ConversionDirectionType dirB = findConsensusDirection(nextConversion.getConversionDirection(), direction2); for (Controller controller : consequentCatalysis.getController()) { if (controller instanceof PhysicalEntity) { createAndAdd(bpe, interactionSet.getGroupMap().getEntityReferenceOrGroup(controller),
if(cat.getControlType() != ControlType.ACTIVATION) { error(thing, "range.violated", fix, "controlType", cat.getControlType().name(), "", ControlType.ACTIVATION.name() + " (or empty)");
Set<PhysicalEntity> cofs = ((Catalysis) ctrl).getCofactor(); Glyph g = handlePEGroup(cofs, convertID(ctrl.getUri())); if (g != null)
private void fix(Control t, Object... values) { if(t instanceof Catalysis) { ((Catalysis)t).setControlType(ControlType.ACTIVATION); } else if (t instanceof TemplateReactionRegulation){ if(values.length >0 && values[0] instanceof ControlType) { ControlType ct = (ControlType) values[0]; ((TemplateReactionRegulation)t).setControlType(ct); } else { ((TemplateReactionRegulation)t).setControlType(null); if(logger.isInfoEnabled()) logger.info(t.getRDFId() + " - invalid controlType value deleted"); } } else { logger.error("This does not auto-fix " + " controlType property of " + t.getModelInterface().getSimpleName()); } }
if(cat.getControlType() != ControlType.ACTIVATION) { error(validation, thing, "range.violated", validation.isFix(), "controlType", cat.getControlType().name(), "", ControlType.ACTIVATION.name() + " (or empty)"); if(validation.isFix()) {
/** * Adds a BioPAX Control Interaction. */ private void addControlInteraction(CyNetwork network, Control control) { Collection<Process> controlledList = control.getControlled(); for (Process process : controlledList) { // Determine the BioPAX Edge Type String typeStr = "controlled"; //default ControlType cType = control.getControlType(); typeStr = (cType == null) ? typeStr : cType.toString(); //edge direction (trick) - from control to process (like for 'right', 'cofactor', 'participant') linkNodes(network, process, control, typeStr); } Collection<Controller> controllerList = control.getController(); for (Controller controller : controllerList) { // directed edge - from Controller to Control (like 'left') linkNodes(network, control, controller, "controller"); } // cofactor relationships if(control instanceof Catalysis) { Collection<PhysicalEntity> coFactorList = ((Catalysis) control).getCofactor(); for(PhysicalEntity cofactor : coFactorList) { // direction - from control to cofactor (like 'right', 'participant', 'controlled') linkNodes(network, control, cofactor, "cofactor"); } } }
private void fix(Control t, Object... values) { if(t instanceof Catalysis) { ((Catalysis)t).setControlType(ControlType.ACTIVATION); } else if (t instanceof TemplateReactionRegulation){ if(values.length >0 && values[0] instanceof ControlType) { ControlType ct = (ControlType) values[0]; ((TemplateReactionRegulation)t).setControlType(ct); } else { ((TemplateReactionRegulation)t).setControlType(null); if(logger.isInfoEnabled()) logger.info(t.getUri() + " - invalid controlType value deleted"); } } else { logger.error("This does not auto-fix " + " controlType property of " + t.getModelInterface().getSimpleName()); } }
if(proc instanceof Catalysis) CatalysisDirectionType cdir = ((Catalysis) proc).getCatalysisDirection(); if(cdir != null && cdir != correctDir) { error(step, "direction.conflict", fix,
private void fix(BiochemicalPathwayStep t, Object... values) { if(values[0] instanceof Catalysis) { ((Catalysis)values[0]).setCatalysisDirection((CatalysisDirectionType) values[1]); } else if (values[0] instanceof Conversion){ ((Conversion)values[0]).setConversionDirection((ConversionDirectionType) values[1]); } }
if(proc instanceof Catalysis) CatalysisDirectionType cdir = ((Catalysis) proc).getCatalysisDirection(); if(cdir != null && cdir != correctDir) { error(validation, step, "direction.conflict", validation.isFix(),