Examples with CSGObject cbit.vcell.geometry.CSGObject used on opensource projects

Example 1 with CSGObject

use of cbit.vcell.geometry.CSGObject in project vcell by virtualcell.

the class BioModelEditor method setRightBottomPanelOnSelection.

@Override
protected void setRightBottomPanelOnSelection(Object[] selections) {
    if (selections == null) {
        return;
    }
    // TODO: here
    JComponent bottomComponent = rightBottomEmptyPanel;
    JComponent annotationComponent = rightBottomEmptyAnnotationsPanel;
    // properties panel
    int destComponentIndex = DocumentEditorTabID.object_properties.ordinal();
    // annotations panel
    int annComponentIndex = DocumentEditorTabID.annotations.ordinal();
    boolean bShowInDatabaseProperties = false;
    boolean bShowPathway = false;
    if (selections.length == 1) {
        annotationComponent = getAnnotationsPanel();
        Object singleSelection = selections[0];
        if (singleSelection instanceof ReactionStep) {
            bottomComponent = getReactionPropertiesPanel();
        } else if (singleSelection instanceof ReactionRule) {
            bottomComponent = getReactionRulePropertiesPanel();
        } else if (singleSelection instanceof SpeciesContext) {
            bottomComponent = getSpeciesPropertiesPanel();
        } else if (singleSelection instanceof MolecularType) {
            bottomComponent = getMolecularTypePropertiesPanel();
        } else if (singleSelection instanceof RbmObservable) {
            bottomComponent = getObservablePropertiesPanel();
        } else if (singleSelection instanceof Structure) {
            bottomComponent = getStructurePropertiesPanel();
            getStructurePropertiesPanel().setModel(bioModel.getModel());
        } else if (singleSelection instanceof Parameter) {
            bottomComponent = getParameterPropertiesPanel();
        } else if (singleSelection instanceof SimulationContext) {
            bottomComponent = getApplicationPropertiesPanel();
        } else if (singleSelection instanceof ParameterEstimationTask) {
            bottomComponent = parameterEstimationTaskPropertiesPanel;
        } else if (singleSelection instanceof Product || singleSelection instanceof Reactant) {
            bottomComponent = getReactionParticipantPropertiesPanel();
        } else if (singleSelection instanceof BioModelNode.PublicationInfoNode) {
            bShowInDatabaseProperties = true;
            bottomComponent = bioModelMetaDataPanel;
        } else if (singleSelection instanceof BioModelInfo) {
            bShowInDatabaseProperties = true;
            bottomComponent = bioModelMetaDataPanel;
        } else if (singleSelection instanceof MathModelInfo) {
            bShowInDatabaseProperties = true;
            bottomComponent = mathModelMetaDataPanel;
        } else if (singleSelection instanceof GeometryInfo) {
            bShowInDatabaseProperties = true;
            bottomComponent = geometryMetaDataPanel;
        } else if (singleSelection instanceof SpeciesContextSpec) {
            bottomComponent = getSpeciesContextSpecPanel();
        } else if (singleSelection instanceof ReactionSpec) {
            bottomComponent = getKineticsTypeTemplatePanel();
        } else if (singleSelection instanceof ReactionRuleSpec) {
            // 
            bottomComponent = getReactionRuleSpecPropertiesPanel();
        } else if (singleSelection instanceof BioModelsNetModelInfo) {
            bShowInDatabaseProperties = true;
            bottomComponent = getBioModelsNetPropertiesPanel();
        } else if (singleSelection instanceof Simulation) {
            bottomComponent = getSimulationSummaryPanel();
        } else if (singleSelection instanceof DataSymbol) {
            bottomComponent = getDataSymbolsSpecPanel();
        } else if (singleSelection instanceof BioEvent) {
            bottomComponent = getEventPanel();
        } else if (singleSelection instanceof SpatialObject) {
            bottomComponent = getSpatialObjectPropertyPanel();
        } else if (singleSelection instanceof SpatialProcess) {
            bottomComponent = getSpatialProcessPropertyPanel();
        } else if (singleSelection instanceof BioPaxObject) {
            bottomComponent = bioPaxObjectPropertiesPanel;
        } else if (singleSelection instanceof BioModel) {
            // only contains Notes, is displayed in the Object Properties Panel
            bottomComponent = bioModelEditorAnnotationPanel;
        } else if (singleSelection instanceof VCMetaData) {
            bottomComponent = bioModelEditorAnnotationPanel;
        } else if (singleSelection instanceof PathwayData) {
            bShowPathway = true;
            bottomComponent = getBioModelEditorPathwayPanel();
        } else if (singleSelection instanceof Model) {
        } else if (singleSelection instanceof RuleParticipantSignature) {
            bottomComponent = getReactionRuleParticipantSignaturePropertiesPanel();
        } else if (singleSelection instanceof CSGObject) {
            bottomComponent = csgObjectPropertiesPanel;
            csgObjectPropertiesPanel.setSimulationContext(getSelectedSimulationContext());
        } else if (singleSelection instanceof DocumentEditorTreeFolderNode) {
            DocumentEditorTreeFolderClass folderClass = ((DocumentEditorTreeFolderNode) singleSelection).getFolderClass();
            if ((folderClass == DocumentEditorTreeFolderClass.REACTIONS_NODE) && !(singleSelection instanceof ReactionRule)) {
                bottomComponent = getReactionPropertiesPanel();
            } else if ((folderClass == DocumentEditorTreeFolderClass.REACTIONS_NODE) && (singleSelection instanceof ReactionRule)) {
                bottomComponent = getReactionRulePropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.STRUCTURES_NODE) {
                bottomComponent = getStructurePropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.SPECIES_NODE) {
                bottomComponent = getSpeciesPropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.MOLECULAR_TYPES_NODE) {
                bottomComponent = getMolecularTypePropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.OBSERVABLES_NODE) {
                bottomComponent = getObservablePropertiesPanel();
            } else if (folderClass == DocumentEditorTreeFolderClass.APPLICATIONS_NODE) {
                bottomComponent = getApplicationsPropertiesPanel();
                getApplicationsPropertiesPanel().setBioModel(bioModel);
            } else if (folderClass == DocumentEditorTreeFolderClass.PARAMETER_ESTIMATION_NODE) {
                bottomComponent = parameterEstimationTaskPropertiesPanel;
            }
        } else if (singleSelection instanceof SelectionManager.AnnotationNavigator) {
            Object entity = ((SelectionManager.AnnotationNavigator) singleSelection).getEntity();
            if (entity instanceof ReactionStep) {
                bottomComponent = getReactionPropertiesPanel();
            } else if (entity instanceof SpeciesContext) {
                bottomComponent = getSpeciesPropertiesPanel();
            } else if (entity instanceof Structure) {
                // Observables. MolecularType, Structures
                bottomComponent = getStructurePropertiesPanel();
            } else if (entity instanceof MolecularType) {
                bottomComponent = getMolecularTypePropertiesPanel();
            } else if (entity instanceof RbmObservable) {
                bottomComponent = getObservablePropertiesPanel();
            } else {
                bottomComponent = bioModelEditorAnnotationPanel;
            }
        }
    }
    if (bShowPathway) {
        int numTabs = rightBottomTabbedPane.getTabCount();
        for (destComponentIndex = 0; destComponentIndex < numTabs; destComponentIndex++) {
            Component current = rightBottomTabbedPane.getComponentAt(destComponentIndex);
            if (current == bottomComponent) {
                break;
            }
        }
        String tabTitle = "Pathway Preview";
        if (rightBottomTabbedPane.getTabCount() == destComponentIndex) {
            rightBottomTabbedPane.addTab(tabTitle, new TabCloseIcon(), bottomComponent);
        }
    } else if (bShowInDatabaseProperties) {
        for (destComponentIndex = 0; destComponentIndex < rightBottomTabbedPane.getTabCount(); destComponentIndex++) {
            Component c = rightBottomTabbedPane.getComponentAt(destComponentIndex);
            if (c == bioModelMetaDataPanel || c == mathModelMetaDataPanel || c == geometryMetaDataPanel || c == getBioModelsNetPropertiesPanel()) {
                break;
            }
        }
        if (rightBottomTabbedPane.getTabCount() == destComponentIndex) {
            rightBottomTabbedPane.addTab(DATABASE_PROPERTIES_TAB_TITLE, new TabCloseIcon(), bottomComponent);
        }
    }
    if (rightBottomTabbedPane.getComponentAt(destComponentIndex) != bottomComponent) {
        bottomComponent.setBorder(GuiConstants.TAB_PANEL_BORDER);
        annotationComponent.setBorder(GuiConstants.TAB_PANEL_BORDER);
        rightBottomTabbedPane.setComponentAt(destComponentIndex, bottomComponent);
        rightBottomTabbedPane.setComponentAt(annComponentIndex, annotationComponent);
        rightSplitPane.repaint();
    }
    Component selectedComponent = rightBottomTabbedPane.getSelectedComponent();
    if (selections.length == 1 && selections[0] instanceof BioModel && bottomComponent instanceof BioModelEditorAnnotationPanel) {
        // if the biomodel name is selected in the upper left tree, we select the Annotations tab
        rightBottomTabbedPane.setSelectedComponent(annotationComponent);
    } else if (selections.length == 1 && selections[0] instanceof SelectionManager.AnnotationNavigator && selections[0] instanceof SelectionManager.AnnotationNavigator) {
        // we want to navigate to the AnnotationPanel
        rightBottomTabbedPane.setSelectedComponent(annotationComponent);
    // } else if(selections.length == 1 && selections[0] instanceof SelectionManager.AnnotationNavigator && bottomComponent instanceof BioModelEditorAnnotationPanel) {
    // // we want to navigate to the AnnotationPanel (old way)
    // rightBottomTabbedPane.setSelectedComponent(annotationComponent);
    } else if (selectedComponent != bottomComponent) /* && rightBottomTabbedPane.getSelectedComponent() != annotationComponent */
    {
        rightBottomTabbedPane.setSelectedComponent(bottomComponent);
    }
}

Example 2 with CSGObject

use of cbit.vcell.geometry.CSGObject in project vcell by virtualcell.

the class GeometryGuiTest method getExampleGeometryCSG.

public static Geometry getExampleGeometryCSG() throws PropertyVetoException, ExpressionException, GeometryException, ImageException {
    // translated rotated cube
    CSGPrimitive cube = new CSGPrimitive("cube", CSGPrimitive.PrimitiveType.CUBE);
    CSGRotation rotatedCube = new CSGRotation("Rotation", new Vect3d(1, 2, 3), Math.PI / 4.0);
    rotatedCube.setChild(cube);
    // translated sphere
    CSGTranslation translatedSphere = new CSGTranslation("translation", new Vect3d(0.5, 0.5, 0.5));
    CSGPrimitive sphere = new CSGPrimitive("sphere", CSGPrimitive.PrimitiveType.SPHERE);
    translatedSphere.setChild(sphere);
    // union
    CSGSetOperator csgSetOperator = new CSGSetOperator("difference", OperatorType.DIFFERENCE);
    csgSetOperator.addChild(rotatedCube);
    csgSetOperator.addChild(translatedSphere);
    // scaled union
    CSGScale csgScale = new CSGScale("scale", new Vect3d(3, 3, 3));
    csgScale.setChild(csgSetOperator);
    CSGTranslation csgTranslatedUnion = new CSGTranslation("translationUnion", new Vect3d(5, 5, 5));
    csgTranslatedUnion.setChild(csgScale);
    Geometry geometry = new Geometry("csg", 3);
    CSGObject csgObject = new CSGObject(null, "obj1", 1);
    csgObject.setRoot(csgTranslatedUnion);
    geometry.getGeometrySpec().addSubVolume(new AnalyticSubVolume("background", new Expression(1.0)));
    geometry.getGeometrySpec().addSubVolume(csgObject, true);
    geometry.refreshDependencies();
    geometry.precomputeAll(new GeometryThumbnailImageFactoryAWT());
    return geometry;
}

Example 3 with CSGObject

use of cbit.vcell.geometry.CSGObject in project vcell by virtualcell.

the class CSGObjectPropertiesPanel method addNode.

private boolean addNode(CSGNode newCsgNode) {
    if (newCsgNode == null) {
        return false;
    }
    Object obj = csgObjectTree.getLastSelectedPathComponent();
    if (obj == null || !(obj instanceof BioModelNode)) {
        return false;
    }
    BioModelNode selectedNode = (BioModelNode) obj;
    Object selectedUserObject = selectedNode.getUserObject();
    if (selectedUserObject == csgObject) {
        csgObject.setRoot(newCsgNode);
        return true;
    }
    if (selectedUserObject instanceof CSGSetOperator) {
        CSGSetOperator csgSetOperator = (CSGSetOperator) selectedUserObject;
        csgSetOperator.addChild(newCsgNode);
        return true;
    }
    if (selectedUserObject instanceof CSGTransformation) {
        CSGTransformation csgTransformation = (CSGTransformation) selectedUserObject;
        csgTransformation.setChild(newCsgNode);
        return true;
    }
    return false;
}

Example 4 with CSGObject

use of cbit.vcell.geometry.CSGObject in project vcell by virtualcell.

the class CSGObjectPropertiesPanel method showPopupMenu.

private void showPopupMenu(MouseEvent e) {
    if (!e.isPopupTrigger()) {
        return;
    }
    if (popupMenu == null) {
        popupMenu = new JPopupMenu();
    }
    if (popupMenu.isShowing()) {
        return;
    }
    selectClickPath(e);
    TreePath[] selectedPaths = csgObjectTree.getSelectionPaths();
    boolean bShowPopup = true;
    boolean bTransform = false;
    boolean bApplySetOperator = false;
    boolean bAddPrimitive = false;
    boolean bAddTransformation = false;
    boolean bAddOperator = false;
    boolean bEdit = false;
    boolean bDelete = true;
    if (selectedPaths == null) {
        return;
    }
    for (TreePath tp : selectedPaths) {
        Object obj = tp.getLastPathComponent();
        if (obj == null || !(obj instanceof BioModelNode)) {
            continue;
        }
        BioModelNode selectedNode = (BioModelNode) obj;
        Object userObject = selectedNode.getUserObject();
        if (userObject == csgObject) {
            bDelete = false;
            if (csgObject.getRoot() == null) {
                bAddPrimitive = true;
                bAddOperator = true;
                bAddTransformation = true;
            }
        } else if (userObject instanceof CSGPrimitive) {
            bApplySetOperator = true;
            bTransform = true;
            bAddPrimitive = false;
            bAddOperator = false;
            bAddTransformation = false;
        } else if (userObject instanceof CSGSetOperator) {
            bApplySetOperator = true;
            bTransform = true;
            bAddPrimitive = true;
            bAddOperator = true;
            bAddTransformation = true;
        } else if (userObject instanceof CSGTransformation) {
            bApplySetOperator = true;
            bTransform = true;
            bEdit = true;
            if (((CSGTransformation) userObject).getChild() == null) {
                bAddPrimitive = true;
                bAddOperator = true;
                bAddTransformation = true;
            }
        }
    }
    if (bShowPopup) {
        popupMenu.removeAll();
        if (bAddPrimitive || bAddTransformation || bAddOperator) {
            getAddPrimitiveMenu().setEnabled(bAddPrimitive);
            getAddTransformationMenu().setEnabled(bAddTransformation);
            getAddSetOperatorMenu().setEnabled(bAddOperator);
            popupMenu.add(getAddMenu());
        }
        if (popupMenu.getComponents().length > 0) {
            popupMenu.add(new JSeparator());
        }
        // everything can be renamed
        popupMenu.add(getRenameMenuItem());
        if (bEdit) {
            popupMenu.add(getEditMenuItem());
        }
        if (bDelete) {
            popupMenu.add(getDeleteMenuItem());
        }
        if (bTransform) {
            if (popupMenu.getComponents().length > 0) {
                popupMenu.add(new JSeparator());
            }
            popupMenu.add(getTransformMenu());
        }
        if (bApplySetOperator) {
            if (popupMenu.getComponents().length > 0 && !bTransform) {
                popupMenu.add(new JSeparator());
            }
            popupMenu.add(getApplySetOperatorMenu());
        }
        Point mousePoint = e.getPoint();
        popupMenu.show(csgObjectTree, mousePoint.x, mousePoint.y);
    }
}

Example 5 with CSGObject

use of cbit.vcell.geometry.CSGObject in project vcell by virtualcell.

the class CSGObjectPropertiesPanel method transformOrApplySetOperator.

private boolean transformOrApplySetOperator(CSGNode newCsgNode) {
    if (newCsgNode == null) {
        return false;
    }
    Object obj = csgObjectTree.getLastSelectedPathComponent();
    if (obj == null || !(obj instanceof BioModelNode)) {
        return false;
    }
    BioModelNode selectedNode = (BioModelNode) obj;
    Object selectedUserObject = selectedNode.getUserObject();
    if (!(selectedUserObject instanceof CSGNode)) {
        return false;
    }
    CSGNode selectedCSGNode = (CSGNode) selectedUserObject;
    TreeNode parentNode = selectedNode.getParent();
    if (parentNode == null || !(parentNode instanceof BioModelNode)) {
        return false;
    }
    Object parentObject = ((BioModelNode) parentNode).getUserObject();
    if (newCsgNode instanceof CSGTransformation) {
        CSGTransformation csgTransformation = (CSGTransformation) newCsgNode;
        csgTransformation.setChild(selectedCSGNode);
    } else if (newCsgNode instanceof CSGSetOperator) {
        CSGSetOperator csgSetOperator = (CSGSetOperator) newCsgNode;
        csgSetOperator.addChild(selectedCSGNode);
    }
    if (parentObject == csgObject) {
        csgObject.setRoot(newCsgNode);
    } else if (parentObject instanceof CSGSetOperator) {
        CSGSetOperator parentCSGSetOperator = (CSGSetOperator) parentObject;
        int index = parentCSGSetOperator.indexOf(selectedCSGNode);
        if (index >= 0) {
            parentCSGSetOperator.setChild(index, newCsgNode);
            return true;
        }
    } else if (parentObject instanceof CSGTransformation) {
        CSGTransformation parentCSGTransformation = (CSGTransformation) parentObject;
        parentCSGTransformation.setChild(newCsgNode);
        return true;
    }
    return false;
}