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

Example 16 with PhysicalEntity

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

the class PathwayTableModel method refreshData.

private void refreshData() {
    if (pathwayModel == null) {
        setData(null);
        return;
    }
    List<BioPaxObject> allPathwayObjectList = new ArrayList<BioPaxObject>();
    for (BioPaxObject bpObject1 : pathwayModel.getBiopaxObjects()) {
        if (bpObject1 instanceof PhysicalEntity || (bpObject1 instanceof Interaction && !(bpObject1 instanceof Control))) {
            allPathwayObjectList.add(bpObject1);
        }
    }
    ArrayList<BioPaxObject> pathwayObjectList = new ArrayList<BioPaxObject>();
    for (BioPaxObject bpObject : allPathwayObjectList) {
        if (searchText == null || searchText.length() == 0 || getLabel(bpObject).toLowerCase().contains(searchText.toLowerCase()) || getType(bpObject).toLowerCase().contains(searchText.toLowerCase())) {
            pathwayObjectList.add(bpObject);
            bioPaxObjectImportedMap.put(bpObject, bioModel != null && bioModel.getPathwayModel().find(bpObject) != null);
        }
    }
    setData(pathwayObjectList);
}

Example 17 with PhysicalEntity

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

the class PathwayGraphModel method refreshParticipant.

private void refreshParticipant(BioPaxInteractionShape interactionShape, InteractionParticipant participant) {
    BioPaxInteractionParticipantShape edgeShape = (BioPaxInteractionParticipantShape) getShapeFromModelObject(participant);
    PhysicalEntity physicalEntity = participant.getPhysicalEntity();
    BioPaxObject ancestorObject = pathwayModel.findTopLevelGroupAncestor(physicalEntity);
    if (edgeShape == null) {
        Shape shape = getShapeFromModelObject(physicalEntity);
        if (shape instanceof BioPaxPhysicalEntityShape) {
            BioPaxPhysicalEntityShape physicalEntityShape = (BioPaxPhysicalEntityShape) shape;
            edgeShape = new BioPaxInteractionParticipantShape(participant, interactionShape, physicalEntityShape, this);
            pathwayContainerShape.addChildShape(edgeShape);
            addShape(edgeShape);
        }
    } else {
        // edges without end objects will be removed
        if (ancestorObject != physicalEntity) {
            removeEdgeShape(edgeShape);
        }
    }
    unwantedShapes.remove(refreshGroup(pathwayContainerShape, ancestorObject, interactionShape, participant));
    unwantedShapes.remove(edgeShape);
}

Example 18 with PhysicalEntity

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

the class PathwayGraphModel method refreshGroupInteraction.

private void refreshGroupInteraction(GroupObject groupObject, InteractionParticipant participant) {
    BioPaxGroupShape groupShape = (BioPaxGroupShape) getShapeFromModelObject(groupObject);
    PhysicalEntity physicalEntity = participant.getPhysicalEntity();
    GroupNeighbor groupNeighbor = new GroupNeighbor(groupObject, physicalEntity, participant.getType());
    BioPaxGroupNeighborShape edgeShape = (BioPaxGroupNeighborShape) getShapeFromModelObject(groupNeighbor);
    BioPaxObject ancestorObject = pathwayModel.findTopLevelGroupAncestor(physicalEntity);
    if (edgeShape == null) {
        Shape shape = getShapeFromModelObject(physicalEntity);
        if (shape instanceof BioPaxPhysicalEntityShape) {
            BioPaxPhysicalEntityShape physicalEntityShape = (BioPaxPhysicalEntityShape) shape;
            edgeShape = new BioPaxGroupNeighborShape(groupNeighbor, groupShape, physicalEntityShape, this);
            pathwayContainerShape.addChildShape(edgeShape);
            addShape(edgeShape);
        }
    } else {
        // edges without end objects will be removed
        if (ancestorObject != physicalEntity) {
            // for grouped objects
            removeEdgeShape(edgeShape);
        }
    }
    unwantedShapes.remove(refreshGroup(pathwayContainerShape, ancestorObject, groupShape, participant));
    unwantedShapes.remove(edgeShape);
}

Example 19 with PhysicalEntity

use of org.vcell.pathway.PhysicalEntity 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 20 with PhysicalEntity

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

the class PathwayProducerBiopax3 method addContentConversion.

// right 						PhysicalEntity 	multiple
// participantStoichiometry 	Stoichiometry 	multiple
// left 						PhysicalEntity 	multiple
// spontaneous 				Boolean 		single
// conversionDirection 		String 			single
private Element addContentConversion(BioPaxObject bpObject, Element element) {
    element = addContentInteraction(bpObject, element);
    Conversion ob = (Conversion) bpObject;
    Element tmpElement = null;
    if (ob.getLeft() != null && ob.getLeft().size() > 0) {
        List<PhysicalEntity> list = ob.getLeft();
        for (PhysicalEntity item : list) {
            tmpElement = new Element("left", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getRight() != null && ob.getRight().size() > 0) {
        List<PhysicalEntity> list = ob.getRight();
        for (PhysicalEntity item : list) {
            tmpElement = new Element("right", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getParticipantStoichiometry() != null && ob.getParticipantStoichiometry().size() > 0) {
        List<Stoichiometry> list = ob.getParticipantStoichiometry();
        for (Stoichiometry item : list) {
            tmpElement = new Element("participantStoichiometry", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getSpontaneous() != null) {
        tmpElement = new Element("spontaneous", bp);
        tmpElement.setAttribute("datatype", schemaBoolean, rdf);
        tmpElement.setText(ob.getSpontaneous().toString());
        element.addContent(tmpElement);
    }
    if (ob.getConversionDirection() != null && ob.getConversionDirection().length() > 0) {
        tmpElement = new Element("conversionDirection", bp);
        tmpElement.setAttribute("datatype", schemaString, rdf);
        tmpElement.setText(ob.getConversionDirection());
        element.addContent(tmpElement);
    }
    return element;
}