Examples with PhysicalEntityProxy org.vcell.pathway.persistence.BiopaxProxy.PhysicalEntityProxy used on opensource projects

Example 1 with PhysicalEntityProxy

use of org.vcell.pathway.persistence.BiopaxProxy.PhysicalEntityProxy in project vcell by virtualcell.

the class PathwayReader method addContentConversion.

private boolean addContentConversion(Conversion conversion, Element element, Element childElement) {
    if (addContentInteraction(conversion, element, childElement)) {
        return true;
    }
    /**
     * String getConversionDirection();
     * ArrayList<PhysicalEntity> getLeftSide();
     * ArrayList<Stoichiometry> getParticipantStoichiometry();
     * ArrayList<PhysicalEntity> getRightSide();
     * Boolean getSpontaneous();
     */
    if (childElement.getName().equals("LEFT") || childElement.getName().equals("RIGHT")) {
        Element physicalEntityParticipantElement = childElement.getChild("physicalEntityParticipant", bp);
        if (physicalEntityParticipantElement != null) {
            boolean found = false;
            PhysicalEntity thePhysicalEntity = null;
            Element physicalEntityPropertyElement = physicalEntityParticipantElement.getChild("PHYSICAL-ENTITY", bp);
            // always create a proxy, the real PhysicalEntity (if present) is not ready to be inserted as is because it is incomplete
            // the reason is that PhysicalEntity object is a "species" in v2 but becomes a "species context" in v3
            PhysicalEntityProxy physicalEntityProxy = null;
            if (physicalEntityPropertyElement != null) {
                found = true;
                physicalEntityProxy = new PhysicalEntityProxy();
                addAttributes(physicalEntityProxy, physicalEntityPropertyElement);
                pathwayModel.add(physicalEntityProxy);
                if (childElement.getName().equals("LEFT")) {
                    conversion.addLeft(physicalEntityProxy);
                } else {
                    conversion.addRight(physicalEntityProxy);
                }
                if (physicalEntityPropertyElement.getChildren().size() > 0) {
                    thePhysicalEntity = addObjectPhysicalEntity(physicalEntityPropertyElement);
                }
            }
            Element cellularLocationElement = physicalEntityParticipantElement.getChild("CELLULAR-LOCATION", bp);
            if (cellularLocationElement != null && found == true) {
                Element controlledVocabularyElement = cellularLocationElement.getChild("openControlledVocabulary", bp);
                if (controlledVocabularyElement != null) {
                    CellularLocationVocabularyProxy cellularLocationVocabularyProxy = new CellularLocationVocabularyProxy();
                    addAttributes(cellularLocationVocabularyProxy, controlledVocabularyElement);
                    pathwayModel.add(cellularLocationVocabularyProxy);
                    if (controlledVocabularyElement.getChildren().size() == 0) {
                        physicalEntityProxy.setCellularLocation(cellularLocationVocabularyProxy);
                    } else {
                        physicalEntityProxy.setCellularLocation(addObjectCellularLocationVocabulary(controlledVocabularyElement));
                    }
                // System.out.println(" -          " + controlledVocabularyElement.getName());
                // we'll use the extra info in this proxy during reconciliation phase to reconstruct a complete PhysicalEntity
                }
            }
            Element stoichiometricCoefficientElement = physicalEntityParticipantElement.getChild("STOICHIOMETRIC-COEFFICIENT", bp);
            if (stoichiometricCoefficientElement != null && found == true) {
                // System.out.println(" -          " + stoichiometricCoefficientElement.getTextTrim());
                // Create a Stoichiometry object from the stoichiometricCoefficient and from PhysicalEntity object
                Stoichiometry stoichiometry = new Stoichiometry();
                stoichiometry.setID(generateInstanceID());
                stoichiometry.setStoichiometricCoefficient(Double.valueOf(stoichiometricCoefficientElement.getTextTrim()));
                if (physicalEntityProxy == null) {
                    // reuse the proxy if we created one already
                    physicalEntityProxy = new PhysicalEntityProxy();
                    String uri = context.unRelativizeURI(physicalEntityPropertyElement, generateResourceID(physicalEntityPropertyElement));
                    physicalEntityProxy.setID(uri);
                    pathwayModel.add(physicalEntityProxy);
                }
                stoichiometry.setPhysicalEntity(physicalEntityProxy);
                // Add the Stoichiometry object to the participantStoichiometry property of the conversion
                conversion.getParticipantStoichiometry().add(stoichiometry);
                // add the Stoichiometry object to the pathway model
                pathwayModel.add(stoichiometry);
                found = true;
            }
            return found;
        }
        Element sequenceParticipantElement = childElement.getChild("sequenceParticipant", bp);
        if (sequenceParticipantElement != null) {
            boolean found = false;
            PhysicalEntity thePhysicalEntity = null;
            Element physicalEntityPropertyElement = sequenceParticipantElement.getChild("PHYSICAL-ENTITY", bp);
            PhysicalEntityProxy physicalEntityProxy = null;
            if (physicalEntityPropertyElement != null) {
                found = true;
                if (physicalEntityPropertyElement.getChildren().size() == 0) {
                    physicalEntityProxy = new PhysicalEntityProxy();
                    addAttributes(physicalEntityProxy, physicalEntityPropertyElement);
                    pathwayModel.add(physicalEntityProxy);
                    if (childElement.getName().equals("LEFT")) {
                        conversion.addLeft(physicalEntityProxy);
                    } else {
                        conversion.addRight(physicalEntityProxy);
                    }
                // return true;
                } else {
                    thePhysicalEntity = addObjectPhysicalEntity(physicalEntityPropertyElement);
                }
                Element cellularLocationElement = sequenceParticipantElement.getChild("CELLULAR-LOCATION", bp);
                if (cellularLocationElement != null && found == true) {
                    Element controlledVocabularyElement = cellularLocationElement.getChild("openControlledVocabulary", bp);
                    if (controlledVocabularyElement != null) {
                        CellularLocationVocabularyProxy cellularLocationVocabularyProxy = new CellularLocationVocabularyProxy();
                        addAttributes(cellularLocationVocabularyProxy, controlledVocabularyElement);
                        pathwayModel.add(cellularLocationVocabularyProxy);
                        if (controlledVocabularyElement.getChildren().size() == 0) {
                            physicalEntityProxy.setCellularLocation(cellularLocationVocabularyProxy);
                        } else {
                            physicalEntityProxy.setCellularLocation(addObjectCellularLocationVocabulary(controlledVocabularyElement));
                        }
                    // System.out.println(" -          " + controlledVocabularyElement.getName());
                    // we'll use the extra info in this proxy during reconciliation phase to reconstruct a complete PhysicalEntity
                    }
                }
            }
            return found;
        }
        if (childElement.getChildren().size() == 0) {
            // PhysicalEntityProxy physicalEntityProxy = new PhysicalEntityProxy();
            // addAttributes(physicalEntityProxy, childElement);
            // pathwayModel.add(physicalEntityProxy);
            // if (childElement.getName().equals("LEFT")){
            // conversion.getLeftSide().add(physicalEntityProxy);
            // }else{
            // conversion.getRightSide().add(physicalEntityProxy);
            // }
            showIgnored(childElement, "conversion/LEFT or conversion/RIGHT assuming redundant sequenceParticipant or physicalEntityParticipant", conversion);
            return true;
        }
        return false;
    // }else if(childElement.getName().equals("participantStoichiometry")) {
    // conversion.getParticipantStoichiometry().add(addObjectStoichiometry(childElement));
    // return true;
    } else {
        return false;
    }
}

Example 2 with PhysicalEntityProxy

use of org.vcell.pathway.persistence.BiopaxProxy.PhysicalEntityProxy in project vcell by virtualcell.

the class PathwayReader method addContentInteraction.

private boolean addContentInteraction(Interaction interaction, Element element, Element childElement) {
    if (addContentEntity(interaction, element, childElement)) {
        return true;
    }
    if (childElement.getName().equals("PARTICIPANTS")) {
        Element physicalEntityParticipantElement = childElement.getChild("physicalEntityParticipant", bp);
        if (physicalEntityParticipantElement != null) {
            Element physicalEntityPropertyElement = physicalEntityParticipantElement.getChild("PHYSICAL-ENTITY", bp);
            if (physicalEntityPropertyElement != null) {
                if (physicalEntityPropertyElement.getChildren().size() == 0) {
                    PhysicalEntityProxy physicalEntityProxy = new PhysicalEntityProxy();
                    addAttributes(physicalEntityProxy, physicalEntityPropertyElement);
                    pathwayModel.add(physicalEntityProxy);
                    interaction.addPhysicalEntityAsParticipant(physicalEntityProxy, InteractionParticipant.Type.PARTICIPANT);
                    return true;
                }
            }
        }
        Element sequenceParticipantElement = childElement.getChild("sequenceParticipant", bp);
        if (sequenceParticipantElement != null) {
            Element physicalEntityPropertyElement = sequenceParticipantElement.getChild("PHYSICAL-ENTITY", bp);
            if (physicalEntityPropertyElement != null) {
                if (physicalEntityPropertyElement.getChildren().size() == 0) {
                    PhysicalEntityProxy physicalEntityProxy = new PhysicalEntityProxy();
                    addAttributes(physicalEntityProxy, physicalEntityPropertyElement);
                    pathwayModel.add(physicalEntityProxy);
                    interaction.addPhysicalEntityAsParticipant(physicalEntityProxy, InteractionParticipant.Type.PARTICIPANT);
                    return true;
                }
            }
        }
        return false;
    } else if (childElement.getName().equals("INTERACTION-TYPE")) {
        interaction.getInteractionTypes().add(addObjectInteractionVocabulary(childElement));
        return true;
    // showIgnored(childElement, "Can't convert openControlledVocabulary (v2) to InteractionVocabulary (v3).", interaction);
    // return false;
    } else {
        return false;
    }
}

Example 3 with PhysicalEntityProxy

use of org.vcell.pathway.persistence.BiopaxProxy.PhysicalEntityProxy in project vcell by virtualcell.

the class PathwayReader method addContentComplex.

private boolean addContentComplex(Complex complex, Element element, Element childElement) {
    if (addContentPhysicalEntity(complex, element, childElement)) {
        return true;
    }
    /**
     * ArrayList<PhysicalEntity> component
     * ArrayList<Stoichiometry> componentStoichiometry
     */
    if (childElement.getName().equals("COMPONENTS")) {
        Element physicalEntityParticipantElement = childElement.getChild("physicalEntityParticipant", bp);
        if (physicalEntityParticipantElement != null) {
            Element physicalEntityPropertyElement = physicalEntityParticipantElement.getChild("PHYSICAL-ENTITY", bp);
            if (physicalEntityPropertyElement != null) {
                if (physicalEntityPropertyElement.getChildren().size() == 0) {
                    PhysicalEntityProxy physicalEntityProxy = new PhysicalEntityProxy();
                    addAttributes(physicalEntityProxy, physicalEntityPropertyElement);
                    pathwayModel.add(physicalEntityProxy);
                    complex.getComponents().add(physicalEntityProxy);
                    return true;
                }
            }
        }
        Element sequenceParticipantElement = childElement.getChild("sequenceParticipant", bp);
        if (sequenceParticipantElement != null) {
            Element physicalEntityPropertyElement = sequenceParticipantElement.getChild("PHYSICAL-ENTITY", bp);
            if (physicalEntityPropertyElement != null) {
                if (physicalEntityPropertyElement.getChildren().size() == 0) {
                    PhysicalEntityProxy physicalEntityProxy = new PhysicalEntityProxy();
                    addAttributes(physicalEntityProxy, physicalEntityPropertyElement);
                    pathwayModel.add(physicalEntityProxy);
                    complex.getComponents().add(physicalEntityProxy);
                    return true;
                }
            }
        }
        if (childElement.getChildren().size() == 0) {
            // PhysicalEntityProxy physicalEntityProxy = new PhysicalEntityProxy();
            // addAttributes(physicalEntityProxy, childElement);
            // pathwayModel.add(physicalEntityProxy);
            // if (childElement.getName().equals("LEFT")){
            // conversion.getLeftSide().add(physicalEntityProxy);
            // }else{
            // conversion.getRightSide().add(physicalEntityProxy);
            // }
            showIgnored(childElement, "complex/COMPONENTS assuming redundant sequenceParticipant or physicalEntityParticipant", complex);
            return true;
        }
        return false;
    } else {
        // no match
        return false;
    }
}

Example 4 with PhysicalEntityProxy

use of org.vcell.pathway.persistence.BiopaxProxy.PhysicalEntityProxy in project vcell by virtualcell.

the class PathwayReaderBiopax3 method addObjectPhysicalEntity.

private PhysicalEntity addObjectPhysicalEntity(Element element) {
    if (element.getChildren().size() == 0) {
        // we got lucky: no children, it means a reference -> create a proxy
        PhysicalEntityProxy proxy = new PhysicalEntityProxy();
        addAttributes(proxy, element);
        pathwayModel.add(proxy);
        return proxy;
    }
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            // </bp:component>
            if (childElement.getName().equals("Complex")) {
                Complex thingie = addObjectComplex(childElement);
                pathwayModel.add(thingie);
                return thingie;
            } else if (childElement.getName().equals("Dna")) {
                Dna thingie = addObjectDna(childElement);
                pathwayModel.add(thingie);
                return thingie;
            } else if (childElement.getName().equals("DnaRegion")) {
                DnaRegion thingie = addObjectDnaRegion(childElement);
                pathwayModel.add(thingie);
                return thingie;
            } else if (childElement.getName().equals("Rna")) {
                Rna thingie = addObjectRna(childElement);
                pathwayModel.add(thingie);
                return thingie;
            } else if (childElement.getName().equals("RnaRegion")) {
                RnaRegion thingie = addObjectRnaRegion(childElement);
                pathwayModel.add(thingie);
                return thingie;
            } else if (childElement.getName().equals("Protein")) {
                Protein thingie = addObjectProtein(childElement);
                pathwayModel.add(thingie);
                return thingie;
            } else if (childElement.getName().equals("SmallMolecule")) {
                SmallMolecule thingie = addObjectSmallMolecule(childElement);
                pathwayModel.add(thingie);
                return thingie;
            }
        }
    }
    PhysicalEntity physicalEntity = new PhysicalEntity();
    if (element.getAttributes().size() > 0) {
        // real PhysicalEntity, with ID and everything
        addAttributes(physicalEntity, element);
    }
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentPhysicalEntity(physicalEntity, element, childElement)) {
                showUnexpected(childElement);
            }
        }
    }
    pathwayModel.add(physicalEntity);
    return physicalEntity;
}

Example 5 with PhysicalEntityProxy

use of org.vcell.pathway.persistence.BiopaxProxy.PhysicalEntityProxy in project vcell by virtualcell.

the class PathwayReaderBiopax3 method addContentControl.

private boolean addContentControl(Control control, Element element, Element childElement) {
    if (addContentInteraction(control, element, childElement)) {
        return true;
    }
    /**
     * InteractionImpl controlledInteraction
     * Pathway controlledPathway
     * String controlType
     * ArrayList<Pathway> pathwayControllers
     * ArrayList<PhysicalEntity> physicalControllers
     */
    if (childElement.getName().equals("controller")) {
        // if (resourceAttribute != null){
        if (childElement.getChildren().size() == 0) {
            // if there are no children it must be a resource inside another object
            // we don't know yet whether it's Interaction or Pathway, we make a proxy for each
            // at the time when we solve the references we'll find out which is fake
            PhysicalEntityProxy proxyE = new PhysicalEntityProxy();
            addAttributes(proxyE, childElement);
            pathwayModel.add(proxyE);
            control.addPhysicalController(proxyE);
            PathwayProxy proxyP = new PathwayProxy();
            addAttributes(proxyP, childElement);
            pathwayModel.add(proxyP);
            control.getPathwayControllers().add(proxyP);
            return true;
        } else {
            for (Object child : element.getChildren()) {
                if (child instanceof Element) {
                    if (((Element) child).getName().equals("Pathway")) {
                        Pathway thingie = addObjectPathway((Element) child);
                        control.getPathwayControllers().add(thingie);
                        return true;
                    } else if (((Element) child).getName().equals("Complex")) {
                        Complex thingie = addObjectComplex((Element) child);
                        control.getPhysicalControllers().add(thingie);
                        return true;
                    } else if (((Element) child).getName().equals("Dna")) {
                        Dna thingie = addObjectDna((Element) child);
                        control.getPhysicalControllers().add(thingie);
                        return true;
                    } else if (((Element) child).getName().equals("DnaRegion")) {
                        DnaRegion thingie = addObjectDnaRegion((Element) child);
                        control.getPhysicalControllers().add(thingie);
                        return true;
                    } else if (((Element) child).getName().equals("Rna")) {
                        Rna thingie = addObjectRna((Element) child);
                        control.getPhysicalControllers().add(thingie);
                        return true;
                    } else if (((Element) child).getName().equals("RnaRegion")) {
                        RnaRegion thingie = addObjectRnaRegion((Element) child);
                        control.getPhysicalControllers().add(thingie);
                        return true;
                    } else if (((Element) child).getName().equals("Protein")) {
                        Protein thingie = addObjectProtein((Element) child);
                        control.getPhysicalControllers().add(thingie);
                        return true;
                    } else if (((Element) child).getName().equals("SmallMolecule")) {
                        SmallMolecule thingie = addObjectSmallMolecule((Element) child);
                        control.getPhysicalControllers().add(thingie);
                        return true;
                    } else {
                        return false;
                    }
                }
            }
        }
        return false;
    } else if (childElement.getName().equals("controlled")) {
        if (childElement.getChildren().size() == 0) {
            InteractionProxy proxyI = new InteractionProxy();
            addAttributes(proxyI, childElement);
            pathwayModel.add(proxyI);
            control.setControlledInteraction(proxyI);
            PathwayProxy proxyP = new PathwayProxy();
            addAttributes(proxyP, childElement);
            pathwayModel.add(proxyP);
            control.setControlledPathway(proxyP);
            return true;
        } else {
            for (Object child : childElement.getChildren()) {
                if (child instanceof Element) {
                    if (((Element) child).getName().equals("Pathway")) {
                        Pathway thingie = addObjectPathway((Element) child);
                        control.setControlledPathway(thingie);
                        return true;
                    } else {
                        Interaction thingie = (Interaction) addObjectBioPaxObjectSubclass((Element) child);
                        if (thingie == null) {
                            return false;
                        } else {
                            control.setControlledInteraction(thingie);
                            return true;
                        }
                    }
                // if(((Element)child).getName().equals("Pathway")) {
                // Pathway thingie = addObjectPathway((Element)child);
                // control.setControlledPathway(thingie);
                // return true;
                // } else if(((Element)child).getName().equals("Interaction")) {
                // Interaction thingie = addObjectInteraction((Element)child);
                // control.setControlledInteraction(thingie);
                // return true;
                // } else if(((Element)child).getName().equals("Control")) {
                // Control thingie = addObjectControl((Element)child);
                // control.setControlledInteraction(thingie);
                // return true;
                // } else if(((Element)child).getName().equals("Modulation")) {
                // Modulation thingie = addObjectModulation((Element)child);
                // control.setControlledInteraction(thingie);
                // return true;
                // } else if(((Element)child).getName().equals("Catalysis")) {
                // Catalysis thingie = addObjectCatalysis((Element)child);
                // control.setControlledInteraction(thingie);
                // return true;
                // } else if(((Element)child).getName().equals("TemplateReactionRegulation")) {
                // TemplateReactionRegulation thingie = addObjectTemplateReactionRegulation((Element)child);
                // control.setControlledInteraction(thingie);
                // return true;
                // } else if(((Element)child).getName().equals("Conversion")) {
                // Conversion thingie = addObjectConversion((Element)child);
                // control.setControlledInteraction(thingie);
                // return true;
                // } else if(((Element)child).getName().equals("BiochemicalReaction")) {
                // BiochemicalReaction thingie = addObjectBiochemicalReaction((Element)child);
                // control.setControlledInteraction(thingie);
                // return true;
                // } else if(((Element)child).getName().equals("TransportWithBiochemicalReaction")) {
                // TransportWithBiochemicalReaction thingie = addObjectTransportWithBiochemicalReaction((Element)child);
                // control.setControlledInteraction(thingie);
                // return true;
                // } else if(((Element)child).getName().equals("ComplexAssembly")) {
                // ComplexAssembly thingie = addObjectComplexAssembly((Element)child);
                // control.setControlledInteraction(thingie);
                // return true;
                // } else if(((Element)child).getName().equals("Degradation")) {
                // Degradation thingie = addObjectDegradation((Element)child);
                // control.setControlledInteraction(thingie);
                // return true;
                // } else if(((Element)child).getName().equals("Transport")) {
                // Transport thingie = addObjectTransport((Element)child);
                // control.setControlledInteraction(thingie);
                // return true;
                // } else if(((Element)child).getName().equals("GeneticInteraction")) {
                // GeneticInteraction thingie = addObjectGeneticInteraction((Element)child);
                // control.setControlledInteraction(thingie);
                // return true;
                // } else if(((Element)child).getName().equals("MolecularInteraction")) {
                // MolecularInteraction thingie = addObjectMolecularInteraction((Element)child);
                // control.setControlledInteraction(thingie);
                // return true;
                // } else if(((Element)child).getName().equals("TemplateReaction")) {
                // TemplateReaction thingie = addObjectTemplateReaction((Element)child);
                // control.setControlledInteraction(thingie);
                // return true;
                // } else {
                // return false;
                // }
                }
            }
        }
        return false;
    } else if (childElement.getName().equals("controlType")) {
        control.setControlType(childElement.getTextTrim());
        return true;
    } else {
        return false;
    }
}