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

Example 1 with GroupObject

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

the class BioModelEditorPathwayDiagramPanel method importIntoModel.

public void importIntoModel() {
    if (bioModel == null) {
        return;
    }
    String warningMessage = "";
    String warningMessage2 = "";
    int warningCount = 0;
    int warningCount2 = 0;
    String infoMessage = "";
    ArrayList<BioPaxObject> importedBPObjects = new ArrayList<BioPaxObject>();
    warningMessage = "The following pathway object(s) have been associated with object(s) in the physiology model:\n";
    warningMessage2 = "The following transport reaction(s) will NOT be converted to the physiology model:\n";
    warningCount = 0;
    warningCount2 = 0;
    infoMessage = "The following pathway object(s) have been coverted in the physiology model:\n\n";
    boolean hasMembrane = false;
    if (bioModel.getModel().getMembranes().size() > 0)
        hasMembrane = true;
    HashSet<BioPaxObject> selected = new HashSet<BioPaxObject>();
    // convert group Object to regular biopaxObjects
    for (BioPaxObject bpo : getSelectedBioPaxObjects()) {
        if (bpo instanceof GroupObject) {
            selected.addAll(((GroupObject) bpo).computeGroupedBioPaxObjects());
        } else {
            selected.add(bpo);
        }
    }
    for (BioPaxObject bpo : selected) {
        if (bpo instanceof Conversion) {
            if (bpo instanceof Transport && !hasMembrane) {
                warningCount2++;
                if (((Conversion) bpo).getName().size() > 0)
                    warningMessage2 += "\nTransport: \'" + ((Conversion) bpo).getName().get(0) + "\'\n";
                else
                    warningMessage2 += "\nTransport: \'" + ((Conversion) bpo).getIDShort() + "\'\n";
            } else if (bioModel.getRelationshipModel().getRelationshipObjects(bpo).size() == 0) {
                importedBPObjects.add(bpo);
            } else {
                warningCount++;
                if (((Conversion) bpo).getName().size() > 0)
                    warningMessage += "\nReaction: \'" + ((Conversion) bpo).getName().get(0) + "\' =>\n";
                else
                    warningMessage += "\nReaction: \'" + ((Conversion) bpo).getIDShort() + "\' =>\n";
                for (RelationshipObject r : bioModel.getRelationshipModel().getRelationshipObjects(bpo)) {
                    warningMessage += "\t=> \'" + r.getBioModelEntityObject().getName() + "\'\n";
                }
            }
        } else if (bpo instanceof PhysicalEntity) {
            if (bioModel.getRelationshipModel().getRelationshipObjects(bpo).size() == 0) {
                importedBPObjects.add(bpo);
            } else {
                warningCount++;
                if (((PhysicalEntity) bpo).getName().size() > 0)
                    warningMessage += "\nSpecies: \'" + ((PhysicalEntity) bpo).getName().get(0) + "\' =>\n";
                else
                    warningMessage += "\nSpecies: \'" + ((PhysicalEntity) bpo).getIDShort() + "\' =>\n";
                for (RelationshipObject r : bioModel.getRelationshipModel().getRelationshipObjects(bpo)) {
                    warningMessage += "\t=> \'" + r.getBioModelEntityObject().getName() + "\'\n";
                }
            }
        }
    }
    // create import panel
    conversionPanel = new ConversionPanel();
    conversionPanel.setBioModel(bioModel);
    conversionPanel.setSelectionManager(getSelectionManager());
    // show warning message
    warningMessage2 += "\nNO membrane structures available in the physiology model.\n";
    if (warningCount2 > 0) {
        DialogUtils.showWarningDialog(conversionPanel, warningMessage2);
    }
    warningMessage += "\nThey will NOT be converted to the physiology model.\n";
    if (warningCount > 0) {
        DialogUtils.showWarningDialog(conversionPanel, warningMessage);
    }
    if (importedBPObjects.size() == 0) {
        return;
    }
    // set the selected objects to be the validly imported biopaxObject set
    conversionPanel.setBioPaxObjects(importedBPObjects);
    int returnCode = DialogUtils.showComponentOKCancelDialog(this, conversionPanel, "Import into Physiology");
    if (returnCode == JOptionPane.OK_OPTION) {
        PathwayMapping pathwayMapping = new PathwayMapping();
        try {
            // function I:
            // pass the table rows that contains user edited values to create Vcell object
            pathwayMapping.createBioModelEntitiesFromBioPaxObjects(bioModel, conversionPanel.getTableRows(), conversionPanel.isAddSubunits());
            for (BioPaxObject bpo : importedBPObjects) {
                if (bpo instanceof Conversion) {
                    infoMessage += "Reaction: \t\'";
                    for (RelationshipObject r : bioModel.getRelationshipModel().getRelationshipObjects(bpo)) {
                        infoMessage += r.getBioModelEntityObject().getName() + "\'\n";
                    }
                    infoMessage += "\n";
                } else if (bpo instanceof PhysicalEntity) {
                    infoMessage += "Species: \t\'";
                    for (RelationshipObject r : bioModel.getRelationshipModel().getRelationshipObjects(bpo)) {
                        infoMessage += r.getBioModelEntityObject().getName() + "\'\n";
                    }
                    infoMessage += "\n";
                }
            }
            DialogUtils.showInfoDialog(this, infoMessage);
            // jump the view to reaction diagram panel
            if (selectionManager != null) {
                selectionManager.setActiveView(new ActiveView(null, DocumentEditorTreeFolderClass.REACTION_DIAGRAM_NODE, ActiveViewID.reaction_diagram));
            }
        } catch (Exception e) {
            e.printStackTrace(System.out);
            DialogUtils.showErrorDialog(this, "Errors occur when converting pathway objects to VCell bioModel objects.\n" + e.getMessage());
        }
    }
}

Example 2 with GroupObject

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

the class BioModelEditorPathwayDiagramPanel method ungroupBioPaxObjects.

private void ungroupBioPaxObjects() {
    HashSet<BioPaxObject> selected = new HashSet<BioPaxObject>();
    selected.addAll(getSelectedBioPaxObjects());
    if (selected.size() == 0)
        return;
    if (bioModel == null || bioModel.getPathwayModel() == null)
        return;
    for (BioPaxObject bpObject : selected) {
        if (bpObject instanceof GroupObject) {
            // remove the GroupObject from pathway model
            GroupObject group = (GroupObject) bpObject;
            ArrayList<BioPaxObject> groupElements = new ArrayList<BioPaxObject>();
            for (BioPaxObject bpo : group.getGroupedObjects()) {
                groupElements.add(bpo);
            }
            bioModel.getPathwayModel().remove(bpObject);
            // set the group elements to be selected
            graphCartoonTool.getGraphModel().setSelectedObjects(groupElements.toArray());
        }
    }
    pathwayGraphModel.refreshAll();
}

Example 3 with GroupObject

use of org.vcell.pathway.GroupObject 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 4 with GroupObject

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

the class BioModelEditorPathwayDiagramPanel method refreshButtons.

private void refreshButtons() {
    deleteButton.setEnabled(false);
    physiologyLinkButton.setEnabled(false);
    groupButton.setEnabled(false);
    if (showPhysiologyLinksMenuItem != null) {
        showPhysiologyLinksMenuItem.setEnabled(false);
    }
    if (editPhysiologyLinksMenuItem != null) {
        editPhysiologyLinksMenuItem.setEnabled(false);
    }
    if (importIntoModelMenuItem != null) {
        importIntoModelMenuItem.setEnabled(false);
    }
    if (groupMenuItem != null) {
        groupMenuItem.setEnabled(false);
    }
    if (ungroupMenuItem != null) {
        ungroupMenuItem.setEnabled(false);
    }
    if (expandMenuItem != null) {
        expandMenuItem.setEnabled(false);
    }
    if (collapseMenuItem != null) {
        collapseMenuItem.setEnabled(false);
    }
    if (showPhysiologyLinksMenuItem1 != null) {
        showPhysiologyLinksMenuItem1.setEnabled(false);
    }
    if (editPhysiologyLinksMenuItem1 != null) {
        editPhysiologyLinksMenuItem1.setEnabled(false);
    }
    if (importIntoModelMenuItem1 != null) {
        importIntoModelMenuItem1.setEnabled(false);
    }
    if (groupMenuItem1 != null) {
        groupMenuItem1.setEnabled(false);
    }
    if (ungroupMenuItem1 != null) {
        ungroupMenuItem1.setEnabled(false);
    }
    if (expandMenuItem1 != null) {
        expandMenuItem1.setEnabled(false);
    }
    if (collapseMenuItem1 != null) {
        collapseMenuItem1.setEnabled(false);
    }
    if (deleteMenuItem != null) {
        deleteMenuItem.setEnabled(false);
    }
    if (selectAllMenuItem != null) {
        selectAllMenuItem.setEnabled(false);
    }
    if (selectionManager != null && tabbedPane.getSelectedComponent() != sourceTabPanel) {
        ArrayList<Object> selectedObjects = selectionManager.getSelectedObjects(BioPaxObject.class);
        if (bioModel.getPathwayModel().getBiopaxObjects().size() > 0 && selectAllMenuItem != null) {
            selectAllMenuItem.setEnabled(true);
        }
        if (selectedObjects.size() > 0) {
            deleteButton.setEnabled(true);
            if (deleteMenuItem != null) {
                deleteMenuItem.setEnabled(true);
            }
            physiologyLinkButton.setEnabled(true);
            if (importIntoModelMenuItem != null) {
                importIntoModelMenuItem.setEnabled(true);
            }
            if (importIntoModelMenuItem1 != null) {
                importIntoModelMenuItem1.setEnabled(true);
            }
            if (selectedObjects.size() == 1) {
                if (bioModel.getRelationshipModel().getRelationshipObjects((BioPaxObject) selectedObjects.get(0)).size() > 0) {
                    if (showPhysiologyLinksMenuItem != null) {
                        showPhysiologyLinksMenuItem.setEnabled(true);
                    }
                    if (showPhysiologyLinksMenuItem1 != null) {
                        showPhysiologyLinksMenuItem1.setEnabled(true);
                    }
                }
                if (editPhysiologyLinksMenuItem != null) {
                    editPhysiologyLinksMenuItem.setEnabled(true);
                }
                if (editPhysiologyLinksMenuItem1 != null) {
                    editPhysiologyLinksMenuItem1.setEnabled(true);
                }
                if ((selectedObjects.get(0) instanceof GroupObject)) {
                    GroupObject selectedGroup = (GroupObject) selectedObjects.get(0);
                    if (// (selectedGroup.getType().equals(GroupObject.Type.GROUPEDCOMPLEX)) || // expand function for complex
                    (selectedGroup.getType().equals(GroupObject.Type.GROUPEDINTERACTION))) {
                        groupButton.setEnabled(true);
                        if (expandMenuItem != null) {
                            // expand function only available when one grouped complex or interaction is selected
                            expandMenuItem.setEnabled(true);
                        }
                        if (expandMenuItem1 != null) {
                            // expand function only available when one grouped complex or interaction is selected
                            expandMenuItem1.setEnabled(true);
                        }
                    }
                }
                if (// (selectedObjects.get(0) instanceof Protein) ||  // collapse function for Protein
                (selectedObjects.get(0) instanceof Interaction)) {
                    groupButton.setEnabled(true);
                    if (collapseMenuItem != null) {
                        collapseMenuItem.setEnabled(true);
                    }
                    if (collapseMenuItem1 != null) {
                        collapseMenuItem1.setEnabled(true);
                    }
                }
            }
            if (selectedObjects.size() > 1) {
                // only provide the "group" function when users select more than one object
                groupButton.setEnabled(true);
                if (groupMenuItem != null) {
                    groupMenuItem.setEnabled(true);
                }
                if (groupMenuItem1 != null) {
                    groupMenuItem1.setEnabled(true);
                }
            }
            boolean includingGroup = false;
            for (Object object : selectedObjects) {
                if (object instanceof GroupObject) {
                    includingGroup = true;
                    break;
                }
            }
            if (includingGroup) {
                // only provide the "ungroup" function when selected objects contain at least one GroupObject
                groupButton.setEnabled(true);
                if (ungroupMenuItem != null) {
                    ungroupMenuItem.setEnabled(true);
                }
                if (ungroupMenuItem1 != null) {
                    ungroupMenuItem1.setEnabled(true);
                }
            }
        }
    }
}

Example 5 with GroupObject

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

the class BioModelEditorPathwayDiagramPanel method collapseComplex.

private void collapseComplex() {
    HashSet<BioPaxObject> selected = new HashSet<BioPaxObject>(getSelectedBioPaxObjects());
    if (selected.size() != 1)
        return;
    if (bioModel == null || bioModel.getPathwayModel() == null)
        return;
    GroupObject groupObject = null;
    for (BioPaxObject bpObject : selected) {
        groupObject = collapse2Complex(bpObject);
    }
    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();
    }
}