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

Example 16 with GroupObject

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

the class BioModelEditorPathwayDiagramPanel method groupBioPaxObjects.

private void groupBioPaxObjects() {
    HashSet<BioPaxObject> selected = new HashSet<BioPaxObject>();
    selected.addAll(getSelectedBioPaxObjects());
    if (selected.size() == 0)
        return;
    if (bioModel == null || bioModel.getPathwayModel() == null)
        return;
    PathwayGrouping pathwayGrouping = new PathwayGrouping();
    ArrayList<String> names = new ArrayList<String>();
    String id = pathwayGrouping.groupIdGenerator(bioModel.getPathwayModel());
    String newName = null;
    try {
        newName = DialogUtils.showInputDialog0(this, "Name of the GroupObject", id);
    } catch (UtilCancelException ex) {
    // user canceled; it's ok
    }
    if (newName != null) {
        if (newName.length() == 0) {
            PopupGenerator.showErrorDialog(this, "The Name of the GroupObject should be provided.");
        } else {
            names.add(newName);
            GroupObject groupObject = pathwayGrouping.createGroupObject(bioModel.getPathwayModel(), names, id, selected, GroupObject.Type.GROUPEDBIOPAXOBJECTS);
            if (groupObject == null) {
                // error message
                DialogUtils.showErrorDialog(this, "The set of selected objects is a subset of one group object in the model. They will not be grouped together again.");
            } else {
                bioModel.getPathwayModel().add(groupObject);
                bioModel.getPathwayModel().refreshGroupMap();
                // set the grouped object to be selected
                graphCartoonTool.getGraphModel().setSelectedObjects(new GroupObject[] { groupObject });
            }
        }
    }
    pathwayGraphModel.refreshAll();
}

Example 17 with GroupObject

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

the class PathwayReaderBiopax3 method addObjectGroupObject.

private GroupObject addObjectGroupObject(Element element) {
    GroupObject gObject = new GroupObject();
    addAttributes(gObject, element);
    for (Object child : element.getChildren()) {
        if (child instanceof Element) {
            Element childElement = (Element) child;
            if (!addContentGroupObject(gObject, element, childElement)) {
                showUnexpected(childElement);
            }
        }
    }
    pathwayModel.add(gObject);
    return gObject;
}

Example 18 with GroupObject

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

the class PathwayGrouping method updateGroupObjectList.

// get a list of group objects in a pathway model
public Set<BioPaxObject> updateGroupObjectList(PathwayModel pathwayModel) {
    Set<BioPaxObject> groupList = new HashSet<BioPaxObject>();
    Set<BioPaxObject> originalList = pathwayModel.getBiopaxObjects();
    for (BioPaxObject bpObject : originalList) {
        if (bpObject instanceof GroupObject) {
            groupList.add(bpObject);
        }
    }
    return groupList;
}

Example 19 with GroupObject

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

the class PathwayGrouping method createGroupObject.

// create a group object in pathway model
public GroupObject createGroupObject(PathwayModel pathwayModel, ArrayList<String> names, String id, HashSet<BioPaxObject> bpObjects, GroupObject.Type newType) {
    HashSet<BioPaxObject> groupable = updateGroupableList(pathwayModel, bpObjects);
    if (groupable.size() <= 1)
        return null;
    GroupObject gObject = new GroupObject();
    gObject.setName(names);
    gObject.setID(id);
    gObject.setGroupedeObjects(groupable);
    gObject.setType(newType);
    return gObject;
}

Example 20 with GroupObject

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

the class PathwayGrouping method updateBioPaxObjectList.

// get a list of independent biopax Objects including groupObjects
public Set<BioPaxObject> updateBioPaxObjectList(PathwayModel pathwayModel) {
    Set<BioPaxObject> clonedOriginalList = new HashSet<BioPaxObject>(pathwayModel.getBiopaxObjects());
    Set<BioPaxObject> removedList = new HashSet<BioPaxObject>();
    for (BioPaxObject bpObject : clonedOriginalList) {
        if (bpObject instanceof GroupObject) {
            GroupObject gObject = (GroupObject) bpObject;
            for (BioPaxObject bpo : gObject.getGroupedObjects()) {
                removedList.add(bpo);
            }
        }
    }
    clonedOriginalList.removeAll(removedList);
    return clonedOriginalList;
}