Examples with GeometryContextGeometryShape cbit.vcell.graph.GeometryContextGeometryShape used on opensource projects

Example 1 with GeometryContextGeometryShape

use of cbit.vcell.graph.GeometryContextGeometryShape in project vcell by virtualcell.

the class GraphContainerLayoutVCellClassical method getPreferedSizeGeometryContextGeometryShape.

public Dimension getPreferedSizeGeometryContextGeometryShape(GeometryContextGeometryShape shape, Graphics2D g) throws GraphModel.NotReadyException {
    Dimension d = shape.getPreferedSizeSelf(g);
    int height = 2 * shape.getLabelSize().height + 2;
    Dimension childDim = new Dimension();
    try {
        if (shape.countChildren() > 0) {
            for (Shape child : shape.getChildren()) {
                childDim.height += getPreferedSize(child, g).height;
                childDim.width = Math.max(childDim.width, getPreferedSize(child, g).width);
            }
        } else {
            childDim = new Dimension(100, 100);
        }
    } catch (ConcurrentModificationException exception) {
        throw new GraphModel.NotReadyException(exception);
    }
    Dimension newDim = new Dimension(Math.max(d.width, childDim.width) + 10, height + childDim.height);
    return newDim;
}

Example 2 with GeometryContextGeometryShape

use of cbit.vcell.graph.GeometryContextGeometryShape in project vcell by virtualcell.

the class GraphContainerLayoutVCellClassical method refreshLayoutChildrenGeometryContextGeometryShape.

public void refreshLayoutChildrenGeometryContextGeometryShape(GeometryContextGeometryShape shape) {
    final int PAD_Y = 5;
    int centerX = shape.getSpaceManager().getSize().width / 2;
    int totalPadY = PAD_Y * (shape.countChildren() - 1);
    int totalChildHeight = 0;
    int maxChildWidth = 0;
    for (Shape child : shape.getChildren()) {
        totalChildHeight += child.getSpaceManager().getSize().height;
        maxChildWidth = Math.max(maxChildWidth, child.getSpaceManager().getSize().width);
    }
    int currentY = shape.getSpaceManager().getSize().height / 2 + shape.getLabelSize().height / 2 - totalPadY / 2 - totalChildHeight / 2;
    for (int i = 0; i < shape.countChildren(); ++i) {
        Shape child = shape.getChildren().get(i);
        if (i == shape.countChildren() - 1) {
            child.getSpaceManager().setRelPos(centerX - child.getSpaceManager().getSize().width / 2, currentY);
        } else {
            child.getSpaceManager().setRelPos(centerX - maxChildWidth / 2, currentY);
        }
        int dy = child.getSpaceManager().getSize().height + PAD_Y;
        currentY += dy;
        child.refreshLayoutSelf();
        refreshLayoutChildren(child);
    }
}

Example 3 with GeometryContextGeometryShape

use of cbit.vcell.graph.GeometryContextGeometryShape in project vcell by virtualcell.

the class StructureMappingCartoon method refreshAll.

/**
 * This method was created by a SmartGuide.
 */
@Override
public void refreshAll() {
    clearAllShapes();
    if (getSimulationContext() == null) {
        fireGraphChanged(new GraphEvent(this));
        return;
    }
    GeometryContextGeometryShape geometryShape = new GeometryContextGeometryShape(this, getGeometryContext().getGeometry());
    // GeometryContextStructureShape structureShape = new GeometryContextStructureShape(this,getGeometryContext().getModel());
    // GeometryContextContainerShape containerShape = new GeometryContextContainerShape(this,getGeometryContext(),structureShape,geometryShape);
    // addShape(containerShape);
    addShape(geometryShape);
    // addShape(structureShape);
    getGeometryContext().removePropertyChangeListener(this);
    getGeometryContext().addPropertyChangeListener(this);
    // 
    // create all StructureShapes
    // 
    // Structure structures[] = getGeometryContext().getModel().getStructures();
    // for (int i=0;i<structures.length;i++){
    // if (structures[i] instanceof Feature){
    // //addShape(new FeatureShape((Feature)structures[i],getGeometryContext().getModel(),this));
    // StructureMappingFeatureShape smShape = new StructureMappingFeatureShape((Feature)structures[i],getGeometryContext().getModel(),this);
    // addShape(smShape);
    // containerShape.addChildShape(smShape);
    // structures[i].removePropertyChangeListener(this);
    // structures[i].addPropertyChangeListener(this);
    // }
    // }
    // create all SubvolumeLegendShapes (for legend)
    // 
    GeometrySpec geometrySpec = getGeometryContext().getGeometry().getGeometrySpec();
    SubVolume[] subVolumes = geometrySpec.getSubVolumes();
    for (int i = 0; i < subVolumes.length; i++) {
        cbit.vcell.geometry.SubVolume subvolume = subVolumes[i];
        GeometryClassLegendShape subvolumeLegendShape = new GeometryClassLegendShape(subvolume, getGeometryContext().getGeometry(), this, 10);
        addShape(subvolumeLegendShape);
        geometryShape.addChildShape(subvolumeLegendShape);
    }
    // --------------------------------------------------
    if ((subVolumeContainerShape == null) || (subVolumeContainerShape.getModelObject() != getGeometryContext().getGeometry())) {
        subVolumeContainerShape = new SubVolumeContainerShape(getGeometryContext().getGeometry(), this);
    }
    subVolumeContainerShape.removeAllChildren();
    addShape(subVolumeContainerShape);
    geometryShape.addChildShape(subVolumeContainerShape);
    // --------------------------------------------------
    // // create all SubvolumeShapes (for image)
    // //
    // for (int i=0;i<subVolumes.length;i++){
    // cbit.vcell.geometry.SubVolume subvolume = (cbit.vcell.geometry.SubVolume)subVolumes[i];
    // SubvolumeShape subvolumeShape = new SubvolumeShape(subvolume,getGeometryContext().getGeometry(),this);
    // addShape(subvolumeShape);
    // subVolumeContainerShape.addChildShape(subvolumeShape);
    // }
    // 
    // create all FeatureMappingShapes
    // 
    // StructureMapping structureMappings[] = getGeometryContext().getStructureMappings();
    // for (int i=0;i<structureMappings.length;i++){
    // StructureMapping structureMapping = structureMappings[i];
    // if (structureMapping instanceof FeatureMapping){
    // FeatureMapping featureMapping = (FeatureMapping)structureMapping;
    // if (featureMapping.getSubVolume()!=null){
    // FeatureShape featureShape = (FeatureShape)getShapeFromModelObject(featureMapping.getFeature());
    // SubvolumeLegendShape subvolumeLegendShape = (SubvolumeLegendShape)getShapeFromModelObject(featureMapping.getSubVolume());
    // FeatureMappingShape fmShape = new FeatureMappingShape(featureMapping,featureShape,subvolumeLegendShape,this);
    // //FeatureMappingShape fmShape = new FeatureMappingShape(featureMapping,featureShape,featureMapping.getSubVolume(),imageShape,this);
    // addShape(fmShape);
    // containerShape.addChildShape(fmShape);
    // }
    // }
    // }
    // 
    // assign children to shapes according to heirarchy in Model
    // 
    // int nullParentCount=0;
    // Enumeration enum_shape = getShapes();
    // while (enum_shape.hasMoreElements()){
    // Shape shape = (Shape)enum_shape.nextElement();
    // //
    // // for each featureShape, find corresponding featureShape
    // //
    // if (shape instanceof FeatureShape){
    // FeatureShape fs = (FeatureShape)shape;
    // Membrane membrane = fs.getFeature().getMembrane();
    // if (membrane!=null){
    // //
    // // add this feature as child to parent feature
    // //
    // Feature parentFeature = membrane.getOutsideFeature();
    // FeatureShape parentFeatureShape = (FeatureShape)getShapeFromModelObject(parentFeature);
    // if (!parentFeatureShape.contains(fs)){
    // parentFeatureShape.addChildShape(fs);
    // }
    // }else{
    // if (!structureShape.contains(fs)){
    // structureShape.addChildShape(fs);
    // }
    // nullParentCount++;
    // }
    // }
    // }
    fireGraphChanged(new GraphEvent(this));
}