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

Example 1 with MolecularInteraction

use of org.vcell.pathway.MolecularInteraction 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 MolecularInteraction

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

the class PathwayProducerBiopax3 method addContentMolecularInteraction.

private Element addContentMolecularInteraction(BioPaxObject bpObject, Element element) {
    element = addContentInteraction(bpObject, element);
    MolecularInteraction ob = (MolecularInteraction) bpObject;
    Element tmpElement = null;
    return element;
}

Example 3 with MolecularInteraction

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

the class PathwayReader method addObjectMolecularInteraction.

private MolecularInteraction addObjectMolecularInteraction(Element element) {
    MolecularInteraction molecularInteraction = new MolecularInteraction();
    addAttributes(molecularInteraction, element);
    for (Object child : element.getChildren()) {
        if (!addContentMolecularInteraction(molecularInteraction, element, (Element) child)) {
            showUnexpected((Element) child, molecularInteraction);
        }
    }
    pathwayModel.add(molecularInteraction);
    return molecularInteraction;
}

Example 4 with MolecularInteraction

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

the class PathwayGraphModel method refreshAll.

@Override
public void refreshAll() {
    if (pathwayModel == null) {
        clearAllShapes();
        fireGraphChanged();
        return;
    }
    unwantedShapes = new HashSet<Shape>();
    unwantedShapes.addAll(getShapes());
    pathwayContainerShape = (PathwayContainerShape) getShapeFromModelObject(pathwayModel);
    if (pathwayContainerShape == null) {
        pathwayContainerShape = new PathwayContainerShape(this, pathwayModel);
        pathwayContainerShape.getSpaceManager().setSize(400, 300);
        addShape(pathwayContainerShape);
    }
    unwantedShapes.remove(pathwayContainerShape);
    Set<BioPaxObject> bioPaxObjects = new HashSet<BioPaxObject>(pathwayModel.getDisplayableBioPaxObjectList());
    for (BioPaxObject bpObject : bioPaxObjects) {
        BioPaxShape bpObjectShape = (BioPaxShape) getShapeFromModelObject(bpObject);
        if (bpObjectShape == null) {
            if (bpObject instanceof Conversion) {
                bpObjectShape = new BioPaxConversionShape((Conversion) bpObject, this);
            } else if (bpObject instanceof MolecularInteraction) {
                bpObjectShape = new BioPaxMolecularInteractionShape((MolecularInteraction) bpObject, this);
            } else if (bpObject instanceof Protein) {
                bpObjectShape = new BioPaxProteinShape((Protein) bpObject, this);
            } else if (bpObject instanceof Complex) {
                bpObjectShape = new BioPaxComplexShape((Complex) bpObject, this);
            } else if (bpObject instanceof SmallMolecule) {
                bpObjectShape = new BioPaxSmallMoleculeShape((SmallMolecule) bpObject, this);
            } else if (bpObject instanceof Dna) {
                bpObjectShape = new BioPaxDnaShape((Dna) bpObject, this);
            } else if (bpObject instanceof Rna) {
                bpObjectShape = new BioPaxRnaShape((Rna) bpObject, this);
            } else if (bpObject instanceof PhysicalEntity) {
                bpObjectShape = new BioPaxPhysicalEntityShape((PhysicalEntity) bpObject, this);
            } else if (bpObject instanceof GroupObject) {
                bpObjectShape = new BioPaxGroupShape((GroupObject) bpObject, this);
            } else {
                bpObjectShape = new BioPaxObjectShape(bpObject, this);
            }
            if (!(bpObject instanceof Control)) {
                // the Control objects will not be displayed on the diagram
                pathwayContainerShape.addChildShape(bpObjectShape);
                addShape(bpObjectShape);
            }
            Dimension shapeSize = bpObjectShape.getSpaceManager().getSize();
            Rectangle boundary = getContainerLayout().getBoundaryForAutomaticLayout(pathwayContainerShape);
            int xPos = boundary.x + random.nextInt(boundary.width - shapeSize.width);
            int yPos = boundary.y + random.nextInt(boundary.height - shapeSize.height);
            bpObjectShape.setAbsPos(xPos, yPos);
        }
        unwantedShapes.remove(bpObjectShape);
    }
    for (BioPaxObject bpObject : bioPaxObjects) {
        if (bpObject instanceof Conversion) {
            refreshInteraction((Conversion) bpObject);
        } else if (bpObject instanceof MolecularInteraction) {
            refreshInteraction((MolecularInteraction) bpObject);
        } else if (bpObject instanceof Control) {
            refreshControl((Control) bpObject);
        } else if (bpObject instanceof GroupObject) {
            refreshGroupObject((GroupObject) bpObject);
        }
    }
    for (Shape unwantedShape : unwantedShapes) {
        removeShape(unwantedShape);
    }
    refreshRelationshipInfo();
    fireGraphChanged();
}

Example 5 with MolecularInteraction

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

the class PathwayGraphModel method refreshGroupObject.

private void refreshGroupObject(GroupObject groupObject) {
    for (BioPaxObject bpObject : groupObject.getGroupedObjects()) {
        if (bpObject instanceof Conversion) {
            // Conversions inside groupObject
            Conversion conversion = (Conversion) bpObject;
            refreshInteraction(conversion);
        } else if (bpObject instanceof MolecularInteraction) {
            // molecularInteraction inside  groupObject
            MolecularInteraction molecularInteraction = (MolecularInteraction) bpObject;
            refreshInteraction(molecularInteraction);
        } else if (bpObject instanceof GroupObject) {
            // groupObject inside another groupObject
            refreshGroupObject((GroupObject) bpObject);
        }
    }
}