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

Example 6 with Control

use of org.vcell.pathway.Control 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 Control

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

Example 8 with Control

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

the class BioPaxObjectPropertiesPanel method getControllersNames.

private Set<String> getControllersNames(Interaction interaction) {
    Set<String> controllersNames = new HashSet<String>();
    if (bioModel == null) {
        return controllersNames;
    }
    Set<Control> controls = BioPAXUtil.getControlsOfInteraction(interaction, bioModel.getPathwayModel());
    for (Control control : controls) {
        if (control.getPhysicalControllers() != null) {
            for (PhysicalEntity ep : control.getPhysicalControllers()) {
                String type = control.getControlType();
                if (type == null) {
                    type = "";
                } else {
                    type = " (" + type + ")";
                }
                if (ep.getName().size() > 0)
                    controllersNames.add(ep.getName().get(0) + type);
                else {
                    controllersNames.add(ep.getIDShort() + type);
                }
            }
        }
    }
    return controllersNames;
}

Example 9 with Control

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

the class BioModelEditorConversionTableModel method refreshData.

private void refreshData() {
    if (bioModel == null || bioModel.getPathwayModel() == null || bioPaxObjects == null) {
        setData(null);
        return;
    }
    // function I :: get selected objects only
    // create ConversionTableRow objects
    allPathwayObjectList = new ArrayList<ConversionTableRow>();
    convertedBPObjects = new HashSet<BioPaxObject>();
    printObjects(bioPaxObjects);
    BioModel.printBpModelObjects(bioModel.getPathwayModel().getBiopaxObjects());
    // BioModel.printBpRelationshipObjects(bioModel.getRelationshipModel().getBioPaxObjects());	// derived; the bpObjects that are part of a relationship
    BioModel.printRelationships(bioModel.getRelationshipModel().getRelationshipObjects());
    System.out.println("----------------------------------------------------------------------");
    for (BioPaxObject bpo : bioPaxObjects) {
        if (bpo instanceof Conversion) {
            if (bioModel.getRelationshipModel().getRelationshipObjects(bpo).size() == 0) {
                Conversion conversion = (Conversion) bpo;
                ArrayList<String> nameList = conversion.getName();
                String interactionId = conversion.getID();
                String interactionLabel = nameList.isEmpty() ? conversion.getIDShort() : nameList.get(0);
                ConversionTableRow newConversionTableRow = createTableRow(conversion, interactionId, interactionLabel, "Conversion", 1.0, null);
                allPathwayObjectList.add(newConversionTableRow);
                convertedBPObjects.add(bpo);
                ArrayList<Stoichiometry> stoichiometryList = conversion.getParticipantStoichiometry();
                // stoichiometryMap problem:
                // how to deal with the case that the same object occurs on both left and right sides
                HashMap<PhysicalEntity, Double> stoichiometryMap = createStoichiometryMap(stoichiometryList);
                // reactant
                for (BioPaxObject bpObject1 : conversion.getLeft()) {
                    Double stoich = 1.0;
                    if (stoichiometryMap.get((PhysicalEntity) bpObject1) != null) {
                        stoich = stoichiometryMap.get((PhysicalEntity) bpObject1);
                    }
                    ConversionTableRow conversionTableRow;
                    if (bioModel.getRelationshipModel().getRelationshipObjects(bpObject1).isEmpty()) {
                        if (conversion instanceof Transport)
                            conversionTableRow = createTableRowForTransportParticipant(bpObject1, interactionId, interactionLabel, "Reactant", stoich, null);
                        else
                            conversionTableRow = createTableRow(bpObject1, interactionId, interactionLabel, "Reactant", stoich, null);
                    } else {
                        if (conversion instanceof Transport)
                            conversionTableRow = createTableRowForTransportParticipant(bpObject1, interactionId, interactionLabel, "Reactant", stoich, bioModel.getRelationshipModel().getRelationshipObjects(bpObject1));
                        else
                            conversionTableRow = createTableRow(bpObject1, interactionId, interactionLabel, "Reactant", stoich, bioModel.getRelationshipModel().getRelationshipObjects(bpObject1));
                    }
                    allPathwayObjectList.add(conversionTableRow);
                    convertedBPObjects.add(bpObject1);
                }
                // product
                for (BioPaxObject bpObject1 : conversion.getRight()) {
                    Double stoich = 1.0;
                    if (stoichiometryMap.get((PhysicalEntity) bpObject1) != null) {
                        stoich = stoichiometryMap.get((PhysicalEntity) bpObject1);
                    }
                    ConversionTableRow conversionTableRow;
                    if (bioModel.getRelationshipModel().getRelationshipObjects(bpObject1).isEmpty()) {
                        if (conversion instanceof Transport)
                            conversionTableRow = createTableRowForTransportParticipant(bpObject1, interactionId, interactionLabel, "Product", stoich, null);
                        else
                            conversionTableRow = createTableRow(bpObject1, interactionId, interactionLabel, "Product", stoich, null);
                    } else {
                        if (conversion instanceof Transport)
                            conversionTableRow = createTableRowForTransportParticipant(bpObject1, interactionId, interactionLabel, "Product", stoich, bioModel.getRelationshipModel().getRelationshipObjects(bpObject1));
                        else
                            conversionTableRow = createTableRow(bpObject1, interactionId, interactionLabel, "Product", stoich, bioModel.getRelationshipModel().getRelationshipObjects(bpObject1));
                    }
                    allPathwayObjectList.add(conversionTableRow);
                    convertedBPObjects.add(bpObject1);
                }
                // control
                for (BioPaxObject bpObject : bioModel.getPathwayModel().getBiopaxObjects()) {
                    if (bpObject instanceof Control) {
                        Control control = (Control) bpObject;
                        if (control instanceof Catalysis) {
                            // catalysis
                            if (BioPAXUtil.getControlledNonControlInteraction(control) == conversion) {
                                for (PhysicalEntity pe : ((Catalysis) control).getPhysicalControllers()) {
                                    ConversionTableRow conversionTableRow;
                                    if (bioModel.getRelationshipModel().getRelationshipObjects(pe).isEmpty()) {
                                        conversionTableRow = createTableRow(pe, interactionId, interactionLabel, "Catalyst", 1.0, null);
                                    } else {
                                        conversionTableRow = createTableRow(pe, interactionId, interactionLabel, "Catalyst", 1.0, bioModel.getRelationshipModel().getRelationshipObjects(pe));
                                    }
                                    allPathwayObjectList.add(conversionTableRow);
                                    convertedBPObjects.add(pe);
                                }
                            }
                        } else {
                            // other control types
                            if (BioPAXUtil.getControlledNonControlInteraction(control) == conversion) {
                                for (PhysicalEntity pe : control.getPhysicalControllers()) {
                                    ConversionTableRow conversionTableRow;
                                    if (bioModel.getRelationshipModel().getRelationshipObjects(pe).isEmpty()) {
                                        conversionTableRow = createTableRow(pe, interactionId, interactionLabel, "Control", 1.0, null);
                                    } else {
                                        conversionTableRow = createTableRow(pe, interactionId, interactionLabel, "Control", 1.0, bioModel.getRelationshipModel().getRelationshipObjects(pe));
                                    }
                                    allPathwayObjectList.add(conversionTableRow);
                                    convertedBPObjects.add(pe);
                                }
                            }
                        }
                    }
                }
            }
        } else if (bpo instanceof Catalysis) {
            for (PhysicalEntity pe : ((Catalysis) bpo).getPhysicalControllers()) {
                if (!convertedBPObjects.contains(pe)) {
                    ConversionTableRow conversionTableRow;
                    if (bioModel.getRelationshipModel().getRelationshipObjects(bpo).isEmpty()) {
                        conversionTableRow = createTableRow(pe, "", "", "Catalyst", 1.0, null);
                    } else {
                        conversionTableRow = createTableRow(pe, "", "", "Catalyst", 1.0, bioModel.getRelationshipModel().getRelationshipObjects(bpo));
                    }
                    allPathwayObjectList.add(conversionTableRow);
                    convertedBPObjects.add(pe);
                }
            }
            for (Pathway pathway : ((Catalysis) bpo).getPathwayControllers()) {
            // TODO
            }
        } else if (bpo instanceof Control) {
            for (PhysicalEntity pe : ((Catalysis) bpo).getPhysicalControllers()) {
                if (!convertedBPObjects.contains(pe)) {
                    ConversionTableRow conversionTableRow;
                    if (bioModel.getRelationshipModel().getRelationshipObjects(bpo).isEmpty()) {
                        conversionTableRow = createTableRow(pe, "", "", "Control", 1.0, null);
                    } else {
                        conversionTableRow = createTableRow(pe, "", "", "Control", 1.0, bioModel.getRelationshipModel().getRelationshipObjects(bpo));
                    }
                    allPathwayObjectList.add(conversionTableRow);
                    convertedBPObjects.add(pe);
                }
            }
            for (Pathway pathway : ((Catalysis) bpo).getPathwayControllers()) {
            // TODO
            }
        }
    }
    // 2nd pass - entities selected as themselves
    for (BioPaxObject bpo : bioPaxObjects) {
        if (bpo instanceof PhysicalEntity) {
            if (bioModel.getRelationshipModel().getRelationshipObjects(bpo).size() == 0) {
                PhysicalEntity physicalEntityObject = (PhysicalEntity) bpo;
                // we add standalone selected entities, only if they were not already added as part of any reaction
                if (!convertedBPObjects.contains(physicalEntityObject)) {
                    ConversionTableRow conversionTableRow = createTableRow(physicalEntityObject, "", "", "", 1.0, null);
                    allPathwayObjectList.add(conversionTableRow);
                    convertedBPObjects.add(physicalEntityObject);
                }
            }
        }
    }
    // apply text search function for particular columns
    ArrayList<ConversionTableRow> pathwayObjectList = new ArrayList<ConversionTableRow>();
    if (searchText == null || searchText.length() == 0) {
        pathwayObjectList.addAll(allPathwayObjectList);
    } else {
        String lowerCaseSearchText = searchText.toLowerCase();
        for (ConversionTableRow rs : allPathwayObjectList) {
            BioPaxObject bpObject = rs.getBioPaxObject();
            if (rs.interactionLabel().toLowerCase().contains(lowerCaseSearchText) || rs.participantType().toLowerCase().contains(lowerCaseSearchText) || getLabel(bpObject).toLowerCase().contains(lowerCaseSearchText) || getType(bpObject).toLowerCase().contains(lowerCaseSearchText)) {
                pathwayObjectList.add(rs);
            }
        }
    }
    setData(pathwayObjectList);
    GuiUtils.flexResizeTableColumns(ownerTable);
}

Example 10 with Control

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

the class PathwayTableModel method refreshData.

private void refreshData() {
    if (pathwayModel == null) {
        setData(null);
        return;
    }
    List<BioPaxObject> allPathwayObjectList = new ArrayList<BioPaxObject>();
    for (BioPaxObject bpObject1 : pathwayModel.getBiopaxObjects()) {
        if (bpObject1 instanceof PhysicalEntity || (bpObject1 instanceof Interaction && !(bpObject1 instanceof Control))) {
            allPathwayObjectList.add(bpObject1);
        }
    }
    ArrayList<BioPaxObject> pathwayObjectList = new ArrayList<BioPaxObject>();
    for (BioPaxObject bpObject : allPathwayObjectList) {
        if (searchText == null || searchText.length() == 0 || getLabel(bpObject).toLowerCase().contains(searchText.toLowerCase()) || getType(bpObject).toLowerCase().contains(searchText.toLowerCase())) {
            pathwayObjectList.add(bpObject);
            bioPaxObjectImportedMap.put(bpObject, bioModel != null && bioModel.getPathwayModel().find(bpObject) != null);
        }
    }
    setData(pathwayObjectList);
}