Examples with PathwayGrouping org.vcell.pathway.group.PathwayGrouping used on opensource projects

Example 1 with PathwayGrouping

use of org.vcell.pathway.group.PathwayGrouping in project vcell by virtualcell.

the class BioModelEditorPathwayDiagramPanel method collapse2Complex.

private GroupObject collapse2Complex(BioPaxObject bpObject) {
    PathwayGrouping pathwayGrouping = new PathwayGrouping();
    GroupObject groupObject = null;
    HashSet<BioPaxObject> hiddenobjects = new HashSet<BioPaxObject>();
    if (bpObject instanceof Complex) {
        // collapse components
        Complex complex = (Complex) bpObject;
        Set<BioPaxObject> bioPaxObjects = new HashSet<BioPaxObject>(bioModel.getPathwayModel().getBiopaxObjects());
        for (PhysicalEntity pe : complex.getComponents()) {
            if (bioPaxObjects.contains(pe)) {
                hiddenobjects.add(pe);
            }
        }
        if (hiddenobjects.size() > 0) {
            hiddenobjects.add(bpObject);
            String id = pathwayGrouping.groupIdGenerator(bioModel.getPathwayModel());
            groupObject = pathwayGrouping.createGroupObject(bioModel.getPathwayModel(), ((Entity) bpObject).getName(), id, hiddenobjects, GroupObject.Type.GROUPEDCOMPLEX);
        } else {
            // error message
            DialogUtils.showErrorDialog(this, "No Collapse action happened because the components of the complex, " + getEntityName(complex) + ", haven't been imported to pathway model.");
        }
    } else if (bpObject instanceof Protein || bpObject instanceof SmallMolecule) {
        Set<BioPaxObject> bioPaxObjects = new HashSet<BioPaxObject>(bioModel.getPathwayModel().getBiopaxObjects());
        ArrayList<String> name = new ArrayList<String>();
        List<BioPaxObject> parents = bioModel.getPathwayModel().getParents(bpObject);
        if (parents.isEmpty()) {
            DialogUtils.showErrorDialog(this, "No Collapse action happened because protein, " + getEntityName((Entity) bpObject) + ", doesn't involve in any complexes in the pathway data.");
            return null;
        }
        for (BioPaxObject bpo : bioModel.getPathwayModel().getParents(bpObject)) {
            if (bpo instanceof Complex && bioPaxObjects.contains(bpo)) {
                hiddenobjects.add(bpo);
                name.addAll(((Complex) bpo).getName());
                for (PhysicalEntity pe : ((Complex) bpo).getComponents()) {
                    if (bioPaxObjects.contains(pe)) {
                        hiddenobjects.add(pe);
                    }
                }
            }
        }
        if (hiddenobjects.size() > 0) {
            hiddenobjects.add(bpObject);
            String id = pathwayGrouping.groupIdGenerator(bioModel.getPathwayModel());
            if (name.size() == 0) {
                name.add(id);
            }
            groupObject = pathwayGrouping.createGroupObject(bioModel.getPathwayModel(), name, id, hiddenobjects, GroupObject.Type.GROUPEDCOMPLEX);
        } else {
            // error message
            DialogUtils.showErrorDialog(this, "No Collapse action happened because complexes that relate to protein, " + getEntityName((Entity) bpObject) + ", haven't been imported to pathway model.");
        }
    }
    return groupObject;
}

Example 2 with PathwayGrouping

use of org.vcell.pathway.group.PathwayGrouping 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 3 with PathwayGrouping

use of org.vcell.pathway.group.PathwayGrouping 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 4 with PathwayGrouping

use of org.vcell.pathway.group.PathwayGrouping in project vcell by virtualcell.

the class PathwayModel method findTopLevelGroupAncestor.

public BioPaxObject findTopLevelGroupAncestor(BioPaxObject bpObject) {
    Map<BioPaxObject, BioPaxObject> groupMap = getGroupMap();
    PathwayGrouping pathwayGrouping = new PathwayGrouping();
    return pathwayGrouping.findGroupAncestor(groupMap, bpObject);
}