Examples with Complex org.vcell.pathway.Complex used on opensource projects

Example 1 with Complex

use of org.vcell.pathway.Complex 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;
    }
}

Example 2 with Complex

use of org.vcell.pathway.Complex 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 3 with Complex

use of org.vcell.pathway.Complex in project vcell by virtualcell.

the class PathwayReader method addObjectComplex.

private Complex addObjectComplex(Element element) {
    Complex complex = new Complex();
    addAttributes(complex, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentComplex(complex, element, childElement)) {
                showUnexpected(childElement, complex);
            }
        }
    }
    pathwayModel.add(complex);
    return complex;
}

Example 4 with Complex

use of org.vcell.pathway.Complex in project vcell by virtualcell.

the class BioModelEditorPathwayDiagramPanel method collapse2Complex.

private GroupObject collapse2Complex(BioPaxObject bpObject) {
    PathwayGrouping pathwayGrouping = new PathwayGrouping();
    GroupObject groupObject = null;
    HashSet<BioPaxObject> hiddenobjects = new HashSet<BioPaxObject>();
    if (bpObject instanceof Complex) {
        // collapse components
        Complex complex = (Complex) bpObject;
        Set<BioPaxObject> bioPaxObjects = new HashSet<BioPaxObject>(bioModel.getPathwayModel().getBiopaxObjects());
        for (PhysicalEntity pe : complex.getComponents()) {
            if (bioPaxObjects.contains(pe)) {
                hiddenobjects.add(pe);
            }
        }
        if (hiddenobjects.size() > 0) {
            hiddenobjects.add(bpObject);
            String id = pathwayGrouping.groupIdGenerator(bioModel.getPathwayModel());
            groupObject = pathwayGrouping.createGroupObject(bioModel.getPathwayModel(), ((Entity) bpObject).getName(), id, hiddenobjects, GroupObject.Type.GROUPEDCOMPLEX);
        } else {
            // error message
            DialogUtils.showErrorDialog(this, "No Collapse action happened because the components of the complex, " + getEntityName(complex) + ", haven't been imported to pathway model.");
        }
    } else if (bpObject instanceof Protein || bpObject instanceof SmallMolecule) {
        Set<BioPaxObject> bioPaxObjects = new HashSet<BioPaxObject>(bioModel.getPathwayModel().getBiopaxObjects());
        ArrayList<String> name = new ArrayList<String>();
        List<BioPaxObject> parents = bioModel.getPathwayModel().getParents(bpObject);
        if (parents.isEmpty()) {
            DialogUtils.showErrorDialog(this, "No Collapse action happened because protein, " + getEntityName((Entity) bpObject) + ", doesn't involve in any complexes in the pathway data.");
            return null;
        }
        for (BioPaxObject bpo : bioModel.getPathwayModel().getParents(bpObject)) {
            if (bpo instanceof Complex && bioPaxObjects.contains(bpo)) {
                hiddenobjects.add(bpo);
                name.addAll(((Complex) bpo).getName());
                for (PhysicalEntity pe : ((Complex) bpo).getComponents()) {
                    if (bioPaxObjects.contains(pe)) {
                        hiddenobjects.add(pe);
                    }
                }
            }
        }
        if (hiddenobjects.size() > 0) {
            hiddenobjects.add(bpObject);
            String id = pathwayGrouping.groupIdGenerator(bioModel.getPathwayModel());
            if (name.size() == 0) {
                name.add(id);
            }
            groupObject = pathwayGrouping.createGroupObject(bioModel.getPathwayModel(), name, id, hiddenobjects, GroupObject.Type.GROUPEDCOMPLEX);
        } else {
            // error message
            DialogUtils.showErrorDialog(this, "No Collapse action happened because complexes that relate to protein, " + getEntityName((Entity) bpObject) + ", haven't been imported to pathway model.");
        }
    }
    return groupObject;
}

Example 5 with Complex

use of org.vcell.pathway.Complex in project vcell by virtualcell.

the class BioModelEditorPathwayPanel method importPathway.

public void importPathway(boolean addComplexes, boolean addComponents, boolean addInteractions) {
    ArrayList<BioPaxObject> selectedBioPaxObjects = new ArrayList<BioPaxObject>();
    int[] rows = table.getSelectedRows();
    if (rows == null || rows.length == 0) {
        return;
    }
    for (int row : rows) {
        BioPaxObject bioPaxObject = tableModel.getValueAt(row);
        selectedBioPaxObjects.add(bioPaxObject);
    }
    PathwaySelectionExpander selectionExpander = new PathwaySelectionExpander();
    PathwayModel rawPathwayModel = pathwayData.getPathwayModel();
    if (addComplexes) {
        selectionExpander.forPhysicalEntitiesAddComplexes(rawPathwayModel, selectedBioPaxObjects);
    }
    if (addComponents) {
        selectionExpander.forComplexesAddComponents(rawPathwayModel, selectedBioPaxObjects);
    }
    if (addInteractions) {
        selectionExpander.forPhysicalEntitiesAddInteractions(rawPathwayModel, selectedBioPaxObjects);
    }
    selectionExpander.forInteractionsAddControls(rawPathwayModel, selectedBioPaxObjects);
    selectionExpander.forInteractionsAddParticipants(rawPathwayModel, selectedBioPaxObjects);
    PathwayModel selectedPathwayModel = new PathwayModel();
    HashSet<BioPaxObject> objectsToDelete = new HashSet<BioPaxObject>();
    for (BioPaxObject candidateObject : selectedBioPaxObjects) {
        // is the object in the current pathwayModel already?
        BioPaxObject keeperObject = bioModel.getPathwayModel().find(candidateObject);
        if (keeperObject == null) {
            // not found in the current pathwayModel, add it
            selectedPathwayModel.add(candidateObject);
        } else {
            // make a list with the objects we don't bring in because of duplication
            objectsToDelete.add(candidateObject);
        }
    }
    // we replace references to those objects within selectedPathwayModel with the real thing
    for (BioPaxObject bpObject : selectedPathwayModel.getBiopaxObjects()) {
        if (bpObject == null) {
            System.out.println("PathwayModel: null BioPaxObject.");
            continue;
        }
        for (BioPaxObject objectToDelete : objectsToDelete) {
            BioPaxObject keeperObject = bioModel.getPathwayModel().find(objectToDelete);
            // for now we only implemented this for InteractionParticipant entities of Conversions
            bpObject.replace(keeperObject);
        }
    }
    // we bring proteins, small molecules, etc that are components of a Complex
    ArrayList<PhysicalEntity> addList = new ArrayList<>();
    for (BioPaxObject bpo : selectedPathwayModel.getBiopaxObjects()) {
        if (bpo instanceof Complex) {
            Complex complex = (Complex) bpo;
            addComplexComponents(complex, addList, 0);
        }
    }
    for (PhysicalEntity pe : addList) {
        if (selectedPathwayModel.find(pe) == null) {
            selectedPathwayModel.add(pe);
        }
    }
    bioModel.getPathwayModel().merge(selectedPathwayModel);
    // jump the view to pathway diagram panel
    if (selectionManager != null) {
        selectionManager.followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.PATHWAY_DIAGRAM_NODE, ActiveViewID.pathway_diagram), selectedPathwayModel.getBiopaxObjects().toArray());
    }
}