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

Example 6 with SmallMolecule

use of org.vcell.pathway.SmallMolecule 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 7 with SmallMolecule

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

the class BioModelEditorPathwayDiagramPanel method collapseBioPaxObject.

private void collapseBioPaxObject() {
    HashSet<BioPaxObject> selected = new HashSet<BioPaxObject>(getSelectedBioPaxObjects());
    if (selected.size() == 0)
        return;
    if (bioModel == null || bioModel.getPathwayModel() == null)
        return;
    PathwayGrouping pathwayGrouping = new PathwayGrouping();
    GroupObject groupObject = null;
    HashSet<BioPaxObject> hiddenobjects = new HashSet<BioPaxObject>();
    for (BioPaxObject bpObject : selected) {
        hiddenobjects.clear();
        if (bpObject instanceof Complex || bpObject instanceof Protein || bpObject instanceof SmallMolecule) {
            // collapse complex with physicalEntities
            groupObject = collapse2Complex(bpObject);
        } else if (bpObject instanceof Interaction) {
            for (InteractionParticipant itp : ((Interaction) bpObject).getParticipants()) {
                hiddenobjects.add(itp.getPhysicalEntity());
            }
            hiddenobjects.add(bpObject);
            String id = pathwayGrouping.groupIdGenerator(bioModel.getPathwayModel());
            groupObject = pathwayGrouping.createGroupObject(bioModel.getPathwayModel(), ((Entity) bpObject).getName(), id, hiddenobjects, GroupObject.Type.GROUPEDINTERACTION);
        }
    }
    if (groupObject != null) {
        bioModel.getPathwayModel().add(groupObject);
        bioModel.getPathwayModel().refreshGroupMap();
        // set the grouped object to be selected
        graphCartoonTool.getGraphModel().setSelectedObjects(new GroupObject[] { groupObject });
        pathwayGraphModel.refreshAll();
    }
}

Example 8 with SmallMolecule

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

the class PathwayReaderBiopax3 method addObjectSmallMolecule.

private SmallMolecule addObjectSmallMolecule(Element element) {
    SmallMolecule smallMolecule = new SmallMolecule();
    addAttributes(smallMolecule, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentSmallMolecule(smallMolecule, element, childElement)) {
                showUnexpected(childElement);
            }
        }
    }
    pathwayModel.add(smallMolecule);
    return smallMolecule;
}

Example 9 with SmallMolecule

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

the class AnnotationMapping method createPhysicalEntity.

private PhysicalEntity createPhysicalEntity(ArrayList<Xref> xRef, ArrayList<String> refName, String name) {
    PhysicalEntity physicalEntity = null;
    if (isSmallMolecule(xRef)) {
        physicalEntity = new SmallMolecule();
    } else {
        physicalEntity = new PhysicalEntity();
    }
    physicalEntity.setName(refName);
    physicalEntity.setID("BIOMODEL_" + name);
    // physicalEntity.setxRef(xRef);
    for (Xref ref : xRef) {
        physicalEntity.getxRef().add(ref);
    }
    return physicalEntity;
}

Example 10 with SmallMolecule

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

the class PathwayReader method addObjectSmallMolecule.

private SmallMolecule addObjectSmallMolecule(Element element) {
    SmallMolecule smallMolecule = new SmallMolecule();
    addAttributes(smallMolecule, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentSmallMolecule(smallMolecule, element, childElement)) {
                showUnexpected(childElement, smallMolecule);
            }
        }
    }
    pathwayModel.add(smallMolecule);
    return smallMolecule;
}