use of cbit.vcell.graph.ReactionRuleDiagramShape in project vcell by virtualcell.
the class SimpleElipticalLayouter method layout.
//
//
//
// protected static JungNode getOrAddInternalNode(ContainerContext cc, Node node) {
// JungNode glgNode = cc.getIntNodeMap().get(node);
// if(glgNode == null) {
// glgNode = new JungNode(node, false); // internal
// cc.jungGraph.addVertex(glgNode);
// cc.intNodeMap.put(node, glgNode);
// double posX = node.getCenterX();
// double posY = node.getCenterY();
// cc.jungLayout.setLocation(glgNode, posX, posY); // TODO: here
// }
// return glgNode;
// }
//
// // inode - internal, already dealt with
// // enode - our external candidate
// protected static JungNode getOrAddExternalNode(ContainerContext cc, Node enode, Node inode) {
// JungNode glgNode = cc.getExtNodeMap().get(enode);
// if(glgNode == null) {
// glgNode = new JungNode(enode, true); // external
// cc.jungGraph.addVertex(glgNode);
// cc.extNodeMap.put(enode, glgNode);
// double posX = enode.getCenterX() - inode.getCenterX();
// double posY = enode.getCenterY() - inode.getCenterY();
// cc.jungLayout.setLocation(glgNode, posX, posY); // TODO: here
// cc.jungLayout.lock(glgNode, true);
// }
// return glgNode;
// }
//
// protected static void getOrAddEdge(ContainerContext cc, Edge edge) {
// Node node1 = edge.getNode1();
// Node node2 = edge.getNode2();
// Container container = cc.getContainer();
// if(container.equals(node1.getContainer()) && container.equals(node2.getContainer())) {
// JungEdge jungEdge = cc.getEdgeMap().get(edge);
// if(jungEdge == null) {
// JungNode glgNode1 = getOrAddInternalNode(cc, node1);
// JungNode glgNode2 = getOrAddInternalNode(cc, node2);
// jungEdge = new JungEdge(edge);
// cc.jungGraph.addEdge(jungEdge, glgNode1, glgNode2);
// cc.edgeMap.put(edge, jungEdge);
// }
// } else if(container.equals(node1.getContainer())) {
// JungEdge jungEdge = cc.getEdgeMap().get(edge);
// if(jungEdge == null) {
// JungNode glgNode1 = getOrAddInternalNode(cc, node1);
// JungNode glgNodeExternal2 = getOrAddExternalNode(cc, node2, node1);
// jungEdge = new JungEdge(edge);
// cc.jungGraph.addEdge(jungEdge, glgNode1, glgNodeExternal2);
// cc.edgeMap.put(edge, jungEdge);
// }
// } else if(container.equals(node2.getContainer())) {
// JungEdge jungEdge = cc.getEdgeMap().get(edge);
// if(jungEdge == null) {
// JungNode glgNodeExternal1 = getOrAddExternalNode(cc, node1, node2);
// JungNode glgNode2 = getOrAddInternalNode(cc, node2);
// jungEdge = new JungEdge(edge);
// cc.jungGraph.addEdge(jungEdge, glgNode2, glgNodeExternal1);
// cc.edgeMap.put(edge, jungEdge);
// }
// }
// }
@Override
public void layout(ContainedGraph graph) {
for (Container container : graph.getContainers()) {
// ContainerContext containerContext = new ContainerContext(container);
// int edgeCount = 0;
// ContainerContext containerContext = new ContainerContext(container);
// DirectedSparseMultigraph<String, Number> dag = new DirectedSparseMultigraph<>();
// Collection<? extends Node> containerNodes = graph.getContainerNodes(container);
// Map<String, Node> speciesNodesMap = new HashMap<>();
// ReactionContainerShape rcs = (ReactionContainerShape)container.getObject();
// Structure structure = rcs.getStructure();
// for(Node node : containerNodes) {
// if(node.object instanceof SpeciesContextShape) {
// SpeciesContextShape scs = (SpeciesContextShape)node.object;
// SpeciesContext sc = (SpeciesContext)(scs.getModelObject());
// dag.addVertex(sc.getName());
// speciesNodesMap.put(sc.getName(), node);
// }
// }
// for(Node node : containerNodes) {
// if(node.object instanceof ReactionStepShape) {
// ReactionStepShape rss = (ReactionStepShape)node.object;
// ReactionStep rs = (ReactionStep)(rss.getModelObject());
// for(ReactionParticipant rp1 : rs.getReactionParticipants()) {
// for(ReactionParticipant rp2 : rs.getReactionParticipants()) {
// if(structure == rp1.getStructure() && structure == rp2.getStructure()) {
// if(rp1 instanceof Reactant && rp2 instanceof Product) { // edges from reactants to products
// dag.addEdge(edgeCount, rp1.getName(), rp2.getName());
// edgeCount++;
// }
// if(rp1 instanceof Catalyst && rp2 instanceof Reactant) { // edges from catalysts to reactants
// dag.addEdge(edgeCount, rp1.getName(), rp2.getName());
// edgeCount++;
// }
// if(rp1 instanceof Reactant && rp2 instanceof Reactant && rp1 != rp2) { // edges between reactants
// dag.addEdge(edgeCount, rp1.getName(), rp2.getName());
// edgeCount++;
// dag.addEdge(edgeCount, rp2.getName(), rp1.getName());
// edgeCount++;
// }
// if(rp1 instanceof Product && rp2 instanceof Product && rp1 != rp2) { // edges between products
// dag.addEdge(edgeCount, rp1.getName(), rp2.getName());
// edgeCount++;
// dag.addEdge(edgeCount, rp2.getName(), rp1.getName());
// edgeCount++;
// }
// }
// }
// }
// }
// }
// SpringLayout<String, Number> layout = new SpringLayout<String, Number>(dag);
// layout.setSize(new Dimension((int)container.width,(int)container.height));
//
// for(String v : dag.getVertices()) {
// Node node = speciesNodesMap.get(v);
// layout.setLocation(v, node.getCenterX(), node.getCenterY());
// }
//
// int step = 0;
// while (!springIterate(layout) && step < 1000) {
// step++;
// }
//
// // position the nodes on the new locations
// for(String v : dag.getVertices()) {
// Node node = speciesNodesMap.get(v);
// double x = layout.getX(v);
// double y = layout.getY(v);
// node.setCenter(x, y);
// }
//
// // place all the reaction nodes in the center of mass of its reactants
// for(Node node : containerNodes) {
// if(node.object instanceof ReactionStepShape) {
// int count = 0;
// double x = 0;
// double y = 0;
// ReactionStepShape rss = (ReactionStepShape)node.object;
// ReactionStep rs = (ReactionStep)(rss.getModelObject());
// for(ReactionParticipant rp : rs.getReactionParticipants()) {
// if(structure == rp.getStructure()) {
// x += layout.getX(rp.getName());
// y += layout.getY(rp.getName());
// count++;
// } else { // reactant is in another structure
// x += 5; // just shift it a little
// y += 5;
// // TODO: make big correction as if it's far away to the left or to the right
// // depending on the order of structures in the diagram
// count++;
// }
// }
// if(count > 0) {
// node.setCenter(x/count, y/count);
// }
// }
// }
double centerX = container.getX() + container.getWidth() / 2;
double centerY = container.getY() + container.getHeight() / 2;
double quartaxisX = container.getWidth() / 3;
double quartaxisY = container.getHeight() / 3;
double semiaxisX = container.getWidth() / 2;
double semiaxisY = container.getHeight() / 2;
Collection<? extends Node> containerNodes = graph.getContainerNodes(container);
int nNodes = containerNodes.size();
int iNode = 0;
for (Node node : containerNodes) {
if (node.object instanceof SpeciesContextShape || node.object instanceof RuleParticipantSignatureDiagramShape) {
double angle = 2 * Math.PI * (((double) iNode) / ((double) nNodes));
node.setCenter(centerX + quartaxisX * Math.cos(angle), centerY + quartaxisY * Math.sin(angle));
} else if (node.object instanceof ReactionStepShape || node.object instanceof ReactionRuleDiagramShape) {
double angle = 2 * Math.PI * (((double) iNode) / ((double) nNodes));
node.setCenter(centerX + semiaxisX * Math.cos(angle), centerY + semiaxisY * Math.sin(angle));
}
++iNode;
}
}
stretchLayouter.layout(graph);
}
use of cbit.vcell.graph.ReactionRuleDiagramShape in project vcell by virtualcell.
the class GraphContainerLayoutReactions method getPreferedSizeReactionContainerShape.
public Dimension getPreferedSizeReactionContainerShape(ReactionContainerShape shape, Graphics2D g) {
// get size when empty
Font origFont = g.getFont();
g.setFont(shape.getLabelFont(g));
try {
Dimension preferredSize = shape.getPreferedSizeSelf(g);
// make larger than empty size so that children fit
for (Shape child : shape.getChildren()) {
if (child instanceof ReactionStepShape || child instanceof SpeciesContextShape || child instanceof RuleParticipantSignatureFullDiagramShape || child instanceof RuleParticipantSignatureShortDiagramShape || child instanceof ReactionRuleDiagramShape) {
preferredSize.width = Math.max(preferredSize.width, child.getSpaceManager().getRelPos().x + child.getSpaceManager().getSize().width);
preferredSize.height = Math.max(preferredSize.height, child.getSpaceManager().getRelPos().y + child.getSpaceManager().getSize().height);
}
}
preferredSize.width = preferredSize.width + WIDTH_PADDING;
preferredSize.height = preferredSize.height + HEIGHT_PADDING;
Structure structure = shape.getStructure();
int minWidthSum = 0;
for (Structure structure2 : shape.getStructureSuite().getStructures()) {
if (structure2 instanceof Feature) {
minWidthSum += FEATURE_MIN_WIDTH;
} else {
minWidthSum += MEMBRANE_MIN_WIDTH;
}
}
int compartmentMinWidth = 0;
if (structure instanceof Feature) {
compartmentMinWidth = FEATURE_MIN_WIDTH;
} else {
compartmentMinWidth = MEMBRANE_MIN_WIDTH;
}
int apportionedWidth = compartmentMinWidth * TOTAL_MIN_WIDTH / minWidthSum;
if (preferredSize.width < compartmentMinWidth) {
preferredSize.width = compartmentMinWidth;
}
if (preferredSize.width < apportionedWidth) {
preferredSize.width = apportionedWidth;
}
if (preferredSize.height < MIN_HEIGHT) {
preferredSize.height = MIN_HEIGHT;
}
return preferredSize;
} finally {
g.setFont(origFont);
}
}
use of cbit.vcell.graph.ReactionRuleDiagramShape in project vcell by virtualcell.
the class ReactionCartoonTool method menuAction.
@Override
protected void menuAction(Shape shape, String menuAction) {
if (shape == null) {
return;
}
if (menuAction.equals(CartoonToolMiscActions.Properties.MENU_ACTION)) {
if (shape instanceof FluxReactionShape) {
// showFluxReactionPropertiesDialog((FluxReactionShape) shape);
} else if (shape instanceof SimpleReactionShape) {
// showSimpleReactionPropertiesDialog((SimpleReactionShape) shape);
} else if (shape instanceof ReactantShape) {
// Point locationOnScreen = shape.getSpaceManager().getAbsLoc();
// Point graphPaneLocation = getGraphPane().getLocationOnScreen();
// locationOnScreen.translate(graphPaneLocation.x,
// graphPaneLocation.y);
// showReactantPropertiesDialog((ReactantShape) shape,
// locationOnScreen);
} else if (shape instanceof ProductShape) {
// Point locationOnScreen = shape.getSpaceManager().getAbsLoc();
// Point graphPaneLocation = getGraphPane().getLocationOnScreen();
// locationOnScreen.translate(graphPaneLocation.x,
// graphPaneLocation.y);
// showProductPropertiesDialog((ProductShape) shape,
// locationOnScreen);
} else if (shape instanceof SpeciesContextShape) {
// showEditSpeciesDialog(getGraphPane(), getReactionCartoon()
// .getModel(), ((SpeciesContextShape) shape)
// .getSpeciesContext());
} else if (shape instanceof ReactionContainerShape) {
// ReactionContainerShape rcs = (ReactionContainerShape) shape;
// if (rcs.getStructure() instanceof Feature) {
// //
// // showFeaturePropertyDialog is invoked in two modes:
// //
// // 1) parent!=null and child==null
// // upon ok, it adds a new feature to the supplied parent.
// //
// // 2) parent==null and child!=null
// // upon ok, edits the feature name
// //
// showFeaturePropertiesDialog(getGraphPane(),
// (getReactionCartoon().getModel() == null ? null
// : getReactionCartoon().getModel()), null,
// (Feature) rcs.getStructure());
// } else if (rcs.getStructure() instanceof Membrane) {
// showMembranePropertiesDialog(getGraphPane(), (Membrane) rcs
// .getStructure());
// }
}
} else if (menuAction.equals(CartoonToolMiscActions.AddSpecies.MENU_ACTION)) {
if (shape instanceof ReactionContainerShape) {
getGraphModel().deselectShape(shape);
// showCreateSpeciesContextDialog(getGraphPane(),
// getReactionCartoon().getModel(),
// ((ReactionContainerShape) shape).getStructure(), null);
SpeciesContext speciesContext = getReactionCartoon().getModel().createSpeciesContext(((ReactionContainerShape) shape).getStructure());
getGraphModel().select(speciesContext);
}
} else if (menuAction.equals(CartoonToolEditActions.Copy.MENU_ACTION)) {
if (shape instanceof SpeciesContextShape || shape instanceof ReactionStepShape || // rule participants whose rule is not selected won't
shape instanceof RuleParticipantSignatureDiagramShape || // be copied since standalone they are meaningless
shape instanceof ReactionRuleDiagramShape) {
SpeciesContext[] spArray = getSelectedSpeciesContextArray();
ReactionStep[] rsArray = getSelectedReactionStepArray();
ReactionRule[] rrArray = getSelectedReactionRuleArray();
MolecularType[] mtArray = getSelectedMolecularTypeArray(rrArray, rsArray, spArray);
Structure[] structArray = getSelectedStructuresArray(rrArray, rsArray, spArray, mtArray);
Structure fromStruct = null;
ReactionContainerShape rcs = null;
Shape parentShape = shape.getParent();
if (parentShape instanceof ReactionContainerShape) {
rcs = (ReactionContainerShape) parentShape;
fromStruct = rcs.getStructure();
}
ReactionSpeciesCopy reactionSpeciesCopy = new ReactionSpeciesCopy(spArray, rsArray, rrArray, mtArray, fromStruct, structArray);
VCellTransferable.sendToClipboard(reactionSpeciesCopy);
}
} else if (/*menuAction.equals(CartoonToolEditActions.Paste.MENU_ACTION)
|| */
menuAction.equals(CartoonToolEditActions.PasteNew.MENU_ACTION)) {
if (shape instanceof ReactionContainerShape) {
pasteReactionsAndSpecies(((ReactionContainerShape) shape).getStructure());
}
} else if (menuAction.equals(CartoonToolEditActions.Delete.MENU_ACTION)) {
try {
if (getGraphModel().getSelectedShape() instanceof ReactionContainerShape && menuAction.equals(CartoonToolEditActions.Delete.MENU_ACTION)) {
getModel().removeStructure(((ReactionContainerShape) getGraphModel().getSelectedShape()).getStructure());
return;
}
if (getSelectedReactionStepArray() != null || getSelectedSpeciesContextArray() != null) {
deleteReactionsAndSpecies(getGraphPane(), getSelectedReactionStepArray(), getSelectedSpeciesContextArray());
}
if (getSelectedReactionParticipantArray() != null && menuAction.equals(CartoonToolEditActions.Delete.MENU_ACTION)) {
ReactionParticipant[] reactionParticipantArr = getSelectedReactionParticipantArray();
String response = DialogUtils.showWarningDialog(getGraphPane(), "Delete " + reactionParticipantArr.length + " Reaction Stoichiometries", new String[] { RXSPECIES_DELETE, RXSPECIES_CANCEL }, RXSPECIES_CANCEL);
if (response != null && response.equals(RXSPECIES_DELETE)) {
for (int i = 0; i < reactionParticipantArr.length; i++) {
ReactionStep reactionStep = reactionParticipantArr[i].getReactionStep();
reactionStep.removeReactionParticipant(reactionParticipantArr[i]);
}
}
}
} catch (UserCancelException uce) {
return;
} catch (PropertyVetoException e) {
DialogUtils.showErrorDialog(getGraphPane(), e.getMessage());
} catch (Exception e) {
DialogUtils.showErrorDialog(getGraphPane(), e.getMessage(), e);
}
} else if (menuAction.equals(CartoonToolMiscActions.SearchReactions.MENU_ACTION)) {
try {
if (shape instanceof ReactionContainerShape) {
showReactionBrowserDialog(((ReactionContainerShape) shape).getStructure(), null);
}
} catch (Exception e) {
DialogUtils.showErrorDialog(getGraphPane(), e.getMessage(), e);
}
} else if (menuAction.equals(CartoonToolSaveAsImageActions.MenuAction.MENU_ACTION)) {
try {
String resType = null;
if (shape instanceof ReactionContainerShape) {
showSaveReactionImageDialog();
}
} catch (Exception e) {
e.printStackTrace();
DialogUtils.showErrorDialog(getGraphPane(), e.getMessage(), e);
}
} else if (menuAction.equals(CartoonToolMiscActions.Annotate.MENU_ACTION)) {
if (shape instanceof ReactionStepShape) {
// MIRIAMHelper.showMIRIAMAnnotationDialog(((SimpleReactionShape)shape).getReactionStep());
// System.out.println("Menu action annotate activated...");
ReactionStep rs = ((ReactionStepShape) shape).getReactionStep();
VCMetaData vcMetaData = rs.getModel().getVcMetaData();
try {
String newAnnotation = DialogUtils.showAnnotationDialog(getGraphPane(), vcMetaData.getFreeTextAnnotation(rs));
vcMetaData.setFreeTextAnnotation(rs, newAnnotation);
} catch (UtilCancelException e) {
// Do Nothing
} catch (Throwable exc) {
exc.printStackTrace(System.out);
DialogUtils.showErrorDialog(getGraphPane(), "Failed to edit annotation!\n" + exc.getMessage(), exc);
}
}
} else {
// default action is to ignore
}
}
use of cbit.vcell.graph.ReactionRuleDiagramShape in project vcell by virtualcell.
the class ReactionCartoonTool method mouseDragged.
@Override
public void mouseDragged(MouseEvent event) {
if (getGraphPane().getComponentCount() > 0) {
// we're editing, cancel
stopEditing();
}
if (event.isPopupTrigger()) {
return;
}
boolean bShift = (event.getModifiers() & InputEvent.SHIFT_MASK) == InputEvent.SHIFT_MASK;
boolean bCntrl = (event.getModifiers() & InputEvent.CTRL_MASK) == InputEvent.CTRL_MASK;
if (mode == Mode.SELECT && bStartRxContainerLabel) {
if (dragStructTimer != null) {
dragStructTimer.stop();
}
Point dragPointWorld = getGraphModel().getResizeManager().unzoom(event.getPoint());
RXContainerDropTargetInfo lastTrueRXContainerDropTargetInfo = getSelectedContainerDropTargetInfo();
lastRXContainerDropTargetInfoMap = updateRXContainerDropTargetInfoMap(dragPointWorld);
RXContainerDropTargetInfo currentTrueRXContainerDropTargetInfo = getSelectedContainerDropTargetInfo();
// System.out.println(lastTrueRXContainerDropTargetInfo+" "+currentTrueRXContainerDropTargetInfo);
if (dragStructTimer != null || !Compare.isEqualOrNull(lastTrueRXContainerDropTargetInfo, currentTrueRXContainerDropTargetInfo)) {
activateDropTargetEnable();
getGraphPane().repaint();
}
return;
}
try {
switch(mode) {
case SELECT:
{
Point worldPoint = screenToWorld(event.getX(), event.getY());
if (bMoving) {
if (movingShape instanceof ReactionContainerShape) {
bMoving = false;
return;
}
List<Shape> selectedShapes = getReactionCartoon().getSelectedShapes();
// constrain to stay within the corresponding parent for the
// "movingShape" as well as all other selected (hence
// moving) shapes.
Point movingParentLoc = movingShape.getParent().getSpaceManager().getAbsLoc();
Dimension movingParentSize = movingShape.getParent().getSpaceManager().getSize();
worldPoint.x = Math.max(movingOffsetWorld.x + movingParentLoc.x, Math.min(movingOffsetWorld.x + movingParentLoc.x + movingParentSize.width - movingShape.getSpaceManager().getSize().width, worldPoint.x));
worldPoint.y = Math.max(movingOffsetWorld.y + movingParentLoc.y, Math.min(movingOffsetWorld.x + movingParentLoc.y + movingParentSize.height - movingShape.getSpaceManager().getSize().height, worldPoint.y));
for (Shape shape : selectedShapes) {
if (shape != movingShape) {
Point selectedParentLoc = shape.getParent().getSpaceManager().getAbsLoc();
Dimension selectedParentSize = shape.getParent().getSpaceManager().getSize();
int selectedMovingOffsetX = movingOffsetWorld.x + (movingShape.getSpaceManager().getAbsLoc().x - shape.getSpaceManager().getAbsLoc().x);
int selectedMovingOffsetY = movingOffsetWorld.y + (movingShape.getSpaceManager().getAbsLoc().y - shape.getSpaceManager().getAbsLoc().y);
worldPoint.x = Math.max(selectedMovingOffsetX + selectedParentLoc.x, Math.min(selectedMovingOffsetX + selectedParentLoc.x + selectedParentSize.width - shape.getSpaceManager().getSize().width, worldPoint.x));
worldPoint.y = Math.max(selectedMovingOffsetY + selectedParentLoc.y, Math.min(selectedMovingOffsetY + selectedParentLoc.y + selectedParentSize.height - shape.getSpaceManager().getSize().height, worldPoint.y));
}
}
getGraphPane().setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
Point newMovingPoint = new Point(worldPoint.x - movingOffsetWorld.x, worldPoint.y - movingOffsetWorld.y);
int deltaX = newMovingPoint.x - movingPointWorld.x;
int deltaY = newMovingPoint.y - movingPointWorld.y;
movingPointWorld = newMovingPoint;
movingShape.getSpaceManager().setRelPos(movingPointWorld.x - movingParentLoc.x, movingPointWorld.y - movingParentLoc.y);
// them also
for (Shape shape : selectedShapes) {
if (shape != movingShape) {
shape.getSpaceManager().move(deltaX, deltaY);
}
}
getGraphPane().invalidate();
((JViewport) getGraphPane().getParent()).revalidate();
getGraphPane().repaint();
} else if (bRectStretch) {
// constain to stay within parent
Point parentLoc = rectShape.getParent().getSpaceManager().getAbsLoc();
Dimension parentSize = rectShape.getParent().getSpaceManager().getSize();
worldPoint.x = Math.max(1, Math.min(parentSize.width - 1, worldPoint.x - parentLoc.x)) + parentLoc.x;
worldPoint.y = Math.max(1, Math.min(parentSize.height - 1, worldPoint.y - parentLoc.y)) + parentLoc.y;
getGraphPane().setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
// getGraphPane().repaint();
Graphics2D g = (Graphics2D) getGraphPane().getGraphics();
AffineTransform oldTransform = g.getTransform();
g.scale(0.01 * getReactionCartoon().getZoomPercent(), 0.01 * getReactionCartoon().getZoomPercent());
g.setXORMode(Color.white);
rectShape.setEnd(endPointWorld);
rectShape.paint(g, 0, 0);
endPointWorld = worldPoint;
rectShape.setEnd(endPointWorld);
rectShape.paint(g, 0, 0);
g.setTransform(oldTransform);
} else {
Shape shape = (getGraphModel().getSelectedShape() != null ? getGraphModel().getSelectedShape() : getReactionCartoon().pickWorld(worldPoint));
if (!bCntrl && !bShift && (shape instanceof SpeciesContextShape || shape instanceof ReactionStepShape || shape instanceof RuleParticipantSignatureDiagramShape || shape instanceof ReactionRuleDiagramShape)) {
bMoving = true;
movingShape = shape;
movingPointWorld = shape.getSpaceManager().getAbsLoc();
movingOffsetWorld = new Point(worldPoint.x - movingPointWorld.x, worldPoint.y - movingPointWorld.y);
} else if (shape instanceof ReactionContainerShape || bShift || bCntrl) {
if (rectShape == null) {
return;
}
if (startPointWorld != null && worldPoint != null && startPointWorld.equals(worldPoint)) {
// Don't start stretching until mouse moves at least 1 from startpoint
return;
}
bRectStretch = true;
endPointWorld = new Point((startPointWorld != null ? startPointWorld.x : worldPoint.x), (startPointWorld != null ? startPointWorld.y : worldPoint.y));
rectShape.setEnd(endPointWorld);
if (!(shape instanceof ReactionContainerShape)) {
shape.getParent().addChildShape(rectShape);
} else {
shape.addChildShape(rectShape);
}
Graphics2D g = (Graphics2D) getGraphPane().getGraphics();
AffineTransform oldTransform = g.getTransform();
g.scale(0.01 * getReactionCartoon().getZoomPercent(), 0.01 * getReactionCartoon().getZoomPercent());
g.setXORMode(Color.white);
rectShape.paint(g, 0, 0);
g.setTransform(oldTransform);
}
}
break;
}
case LINE:
case LINEDIRECTED:
case LINECATALYST:
{
int x = event.getX();
int y = event.getY();
Point worldPoint = new Point((int) (x * 100.0 / getReactionCartoon().getZoomPercent()), (int) (y * 100.0 / getReactionCartoon().getZoomPercent()));
if (bLineStretch) {
// repaint last location with XOR
Graphics2D g = (Graphics2D) getGraphPane().getGraphics();
g.setXORMode(Color.white);
edgeShape.setEnd(endPointWorld);
AffineTransform oldTransform = g.getTransform();
g.scale(getReactionCartoon().getZoomPercent() * 0.01, getReactionCartoon().getZoomPercent() * 0.01);
edgeShape.paint_NoAntiAlias(g, 0, 0);
g.setTransform(oldTransform);
// set label and color for line depending on attachment area on ReactionStepShape
LineType lineType;
if (Mode.LINE.equals(mode)) {
SpeciesContext speciesContext = (SpeciesContext) edgeShape.getStartShape().getModelObject();
lineType = getLineTypeFromAttachment(speciesContext, worldPoint);
} else if (Mode.LINECATALYST.equals(mode)) {
lineType = LineType.CATALYST;
} else if (edgeShape.getStartShape() instanceof SpeciesContextShape) {
lineType = LineType.REACTANT;
} else {
lineType = LineType.PRODUCT;
}
edgeShape.setLabel(lineType.getLabel());
edgeShape.setForgroundColor(lineType.getColor());
getGraphPane().setCursor(lineType.getCursor());
// move line and paint with XOR
endPointWorld = worldPoint;
edgeShape.setEnd(worldPoint);
oldTransform = g.getTransform();
g.scale(getReactionCartoon().getZoomPercent() * 0.01, getReactionCartoon().getZoomPercent() * 0.01);
edgeShape.paint_NoAntiAlias(g, 0, 0);
g.setTransform(oldTransform);
} else {
if (edgeShape != null) {
return;
}
if (startShape instanceof SpeciesContextShape || ((Mode.LINEDIRECTED.equals(mode) || Mode.LINECATALYST.equals(mode)) && startShape instanceof ElipseShape)) {
ElipseShape startElipseShape = (ElipseShape) startShape;
bLineStretch = true;
endPointWorld = worldPoint;
edgeShape = new RubberBandEdgeShape(startElipseShape, null, getReactionCartoon());
edgeShape.setEnd(worldPoint);
Graphics2D g = (Graphics2D) getGraphPane().getGraphics();
g.setXORMode(Color.white);
AffineTransform oldTransform = g.getTransform();
g.scale(getReactionCartoon().getZoomPercent() * 0.01, getReactionCartoon().getZoomPercent() * 0.01);
edgeShape.paint(g, 0, 0);
g.setTransform(oldTransform);
} else if ((Mode.LINEDIRECTED.equals(mode) || Mode.LINECATALYST.equals(mode)) && startShape instanceof ContainerShape) {
bLineStretch = true;
endPointWorld = worldPoint;
edgeShape = new RubberBandEdgeShape((ElipseShape) null, null, getReactionCartoon());
edgeShape.setStart(startPointWorld);
edgeShape.setEnd(worldPoint);
Graphics2D g = (Graphics2D) getGraphPane().getGraphics();
g.setXORMode(Color.white);
AffineTransform oldTransform = g.getTransform();
g.scale(getReactionCartoon().getZoomPercent() * 0.01, getReactionCartoon().getZoomPercent() * 0.01);
edgeShape.paint(g, 0, 0);
g.setTransform(oldTransform);
}
}
break;
}
default:
{
break;
}
}
} catch (Exception e) {
System.out.println("CartoonTool.mouseDragged: uncaught exception");
e.printStackTrace(System.out);
}
}
use of cbit.vcell.graph.ReactionRuleDiagramShape in project vcell by virtualcell.
the class ReactionCartoonTool method editInPlace.
private void editInPlace(final Shape selectedShape, Point worldPoint) {
if (getGraphPane().getComponentCount() > 0) {
// remove any existing editor
getGraphPane().remove(0);
}
Rectangle labelOutline = null;
// What kind of thing is being edited
if (selectedShape instanceof ReactionContainerShape) {
labelOutline = ((ReactionContainerShape) selectedShape).getLabelOutline(selectedShape.getAbsX(), selectedShape.getAbsY());
if (!labelOutline.contains(worldPoint)) {
return;
}
} else if (selectedShape instanceof SpeciesContextShape) {
labelOutline = ((SpeciesContextShape) selectedShape).getLabelOutline(selectedShape.getAbsX(), selectedShape.getAbsY());
} else if (selectedShape instanceof SimpleReactionShape) {
labelOutline = ((SimpleReactionShape) selectedShape).getLabelOutline(selectedShape.getAbsX(), selectedShape.getAbsY());
} else if (selectedShape instanceof FluxReactionShape) {
labelOutline = ((FluxReactionShape) selectedShape).getLabelOutline(selectedShape.getAbsX(), selectedShape.getAbsY());
} else if (selectedShape instanceof ReactionRuleDiagramShape) {
labelOutline = ((ReactionRuleDiagramShape) selectedShape).getLabelOutline(selectedShape.getAbsX(), selectedShape.getAbsY());
} else {
return;
}
// Add press 'Enter' action, 'Escape' action, editor gets focus and mouse 'Exit' parent action
if (true) {
final JTextField jTextField = new JTextField(selectedShape.getLabel());
jTextField.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
try {
// Type specific edit actions
if (selectedShape instanceof ReactionContainerShape) {
((ReactionContainerShape) selectedShape).getStructure().setName(jTextField.getText(), true);
} else if (selectedShape instanceof SpeciesContextShape) {
((SpeciesContextShape) selectedShape).getSpeciesContext().setName(jTextField.getText());
} else if (selectedShape instanceof SimpleReactionShape) {
((SimpleReactionShape) selectedShape).getReactionStep().setName(jTextField.getText());
} else if (selectedShape instanceof FluxReactionShape) {
((FluxReactionShape) selectedShape).getReactionStep().setName(jTextField.getText());
} else if (selectedShape instanceof ReactionRuleDiagramShape) {
((ReactionRuleDiagramShape) selectedShape).getReactionRule().setName(jTextField.getText());
}
} catch (Exception e2) {
e2.printStackTrace();
DialogUtils.showErrorDialog(ReactionCartoonTool.this.getGraphPane(), e2.getMessage());
}
stopEditing();
}
});
// just to be sure
ReactionCartoonTool.this.getGraphPane().removeMouseListener(myStopEditAdapter);
ReactionCartoonTool.this.getGraphPane().addMouseListener(myStopEditAdapter);
getGraphModel().removeGraphListener(myGraphListener);
getGraphModel().addGraphListener(myGraphListener);
InputMap im = jTextField.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
ActionMap am = jTextField.getActionMap();
im.put(KeyStroke.getKeyStroke("ESCAPE"), "cancelChange");
am.put("cancelChange", new AbstractAction() {
@Override
public void actionPerformed(ActionEvent e) {
stopEditing();
}
});
GraphResizeManager grm = getGraphModel().getResizeManager();
jTextField.setBounds((int) grm.zoom(labelOutline.x), (int) grm.zoom(labelOutline.y), Math.max((int) grm.zoom(labelOutline.width + 2), 100), Math.max((int) grm.zoom(labelOutline.height + 2), 20));
getGraphPane().add(jTextField);
getGraphPane().validate();
jTextField.requestFocus();
}
return;
}
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