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

Example 11 with GroupObject

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

the class PathwayGraphModel method refreshControl.

private void refreshControl(Control control) {
    Interaction controlledInteraction = control.getControlledInteraction();
    if (controlledInteraction instanceof Conversion) {
        List<InteractionParticipant> physicalControllers = control.getParticipants();
        if (physicalControllers != null) {
            Conversion conversion = (Conversion) controlledInteraction;
            BioPaxObject ancestorObject = pathwayModel.findTopLevelGroupAncestor(conversion);
            if (ancestorObject == conversion) {
                // conversion was not grouped
                BioPaxConversionShape conversionShape = (BioPaxConversionShape) getShapeFromModelObject(conversion);
                if (conversionShape != null) {
                    for (InteractionParticipant participant : physicalControllers) {
                        refreshParticipant(conversionShape, participant);
                    }
                }
            } else {
                if (ancestorObject instanceof GroupObject) {
                    // conversion has been grouped
                    GroupObject groupObject = (GroupObject) ancestorObject;
                    for (InteractionParticipant participant : physicalControllers) {
                        refreshGroupInteraction(groupObject, participant);
                    }
                }
            }
        }
    }
}

Example 12 with GroupObject

use of org.vcell.pathway.GroupObject 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 13 with GroupObject

use of org.vcell.pathway.GroupObject 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);
        }
    }
}

Example 14 with GroupObject

use of org.vcell.pathway.GroupObject 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 15 with GroupObject

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

the class BioModelEditorPathwayDiagramPanel method deleteSelectedBioPaxObjects.

public static void deleteSelectedBioPaxObjects(Component guiRequester, BioModel bioModel, GraphModel graphModel) {
    StringBuilder warning = new StringBuilder("You can NOT delete the following pathway objects:\n\n");
    StringBuilder text = new StringBuilder("You are going to DELETE the following pathway objects:\n\n");
    // all objects required by user
    List<BioPaxObject> selected = getSelectedBioPaxObjects(graphModel);
    // the user required objects that can be deleted
    List<BioPaxObject> selectedBioPaxObjects = new ArrayList<BioPaxObject>();
    // all objects that will be deleted from the pathway model
    List<BioPaxObject> completeSelectedBioPaxObjects = new ArrayList<BioPaxObject>();
    // used for recover group objects
    HashSet<GroupObject> undeletedGroupObjects = new HashSet<GroupObject>();
    // all objects required by user + grouped elements contained in selected group objects
    List<BioPaxObject> allSelectedBioPaxObjects = new ArrayList<BioPaxObject>();
    // build a list of selected objects with selected grouped elements
    for (BioPaxObject bpObject : selected) {
        if (bpObject instanceof GroupObject) {
            // all elements of the groupObject will be deleted
            allSelectedBioPaxObjects.add(bpObject);
            // check all elements
            allSelectedBioPaxObjects.addAll(getAllGroupedObjects((GroupObject) bpObject));
        } else {
            allSelectedBioPaxObjects.add(bpObject);
        }
    }
    // if so, whether participants and catalysts of a selected reaction can be deleted
    for (BioPaxObject bpObject : allSelectedBioPaxObjects) {
        if (canDelete(bioModel, allSelectedBioPaxObjects, bpObject)) {
            selectedBioPaxObjects.add(bpObject);
            text.append("    " + bpObject.getTypeLabel() + ": \'" + PhysiologyRelationshipTableModel.getLabel(bpObject) + "\'\n");
            completeSelectedBioPaxObjects.add(bpObject);
            if (bpObject instanceof Conversion) {
                // check each participant
                for (InteractionParticipant ip : ((Conversion) bpObject).getParticipants()) {
                    if (canDelete(bioModel, allSelectedBioPaxObjects, ip.getPhysicalEntity())) {
                        completeSelectedBioPaxObjects.add(ip.getPhysicalEntity());
                        // the complex of the pysicalEntity will be removed
                        for (Complex complex : getComplex(bioModel, ip.getPhysicalEntity())) {
                            if (canDelete(bioModel, allSelectedBioPaxObjects, complex))
                                completeSelectedBioPaxObjects.add(complex);
                        }
                    }
                }
                // check catalysts
                for (BioPaxObject bp : bioModel.getPathwayModel().getBiopaxObjects()) {
                    if (bp instanceof Control) {
                        Control control = (Control) bp;
                        if (control.getControlledInteraction() == bpObject) {
                            completeSelectedBioPaxObjects.add(bp);
                            for (PhysicalEntity pe : control.getPhysicalControllers()) {
                                if (canDelete(bioModel, allSelectedBioPaxObjects, pe))
                                    completeSelectedBioPaxObjects.add(pe);
                            }
                        }
                    }
                }
            } else if (bpObject instanceof GroupObject) {
                // all elements of the groupObject will be deleted
                completeSelectedBioPaxObjects.add(bpObject);
                // check all elements
                completeSelectedBioPaxObjects.addAll(getAllGroupedObjects((GroupObject) bpObject));
            }
        } else {
            warning.append("    " + bpObject.getTypeLabel() + ": \'" + PhysiologyRelationshipTableModel.getLabel(bpObject) + "\'\n");
            if (bpObject instanceof GroupObject) {
                undeletedGroupObjects.add((GroupObject) bpObject);
            }
        }
    }
    warning.append("\nThey are either required by other reactions or linked with other physiological objects.\n\n");
    // for(GroupObject gObject : undeletedGroupObjects){
    // for (BioPaxObject bpo : gObject.getGroupedObjects()){
    // completeSelectedBioPaxObjects.remove(bpo);
    // }
    // }
    StringBuilder finalWarningMessage = new StringBuilder();
    if (allSelectedBioPaxObjects.size() > selectedBioPaxObjects.size()) {
        finalWarningMessage.append(warning.toString() + "\n\n");
    }
    if (selectedBioPaxObjects.size() > 0) {
        text.append("\nContinue?");
        finalWarningMessage.append(text.toString());
    }
    if (finalWarningMessage.length() == 0) {
        return;
    }
    String confirm = DialogUtils.showOKCancelWarningDialog(guiRequester, "Deleting pathway objects", finalWarningMessage.toString());
    if (confirm.equals(UserMessage.OPTION_CANCEL)) {
        return;
    }
    if (completeSelectedBioPaxObjects.size() > 0) {
        bioModel.getPathwayModel().remove(completeSelectedBioPaxObjects);
        bioModel.getPathwayModel().cleanGroupObjects();
        bioModel.getRelationshipModel().removeRelationshipObjects(completeSelectedBioPaxObjects);
    }
}