/**
ISAcreator is a component of the ISA software suite (http://www.isa-tools.org)
License:
ISAcreator is licensed under the Common Public Attribution License version 1.0 (CPAL)
EXHIBIT A. CPAL version 1.0
The contents of this file are subject to the CPAL version 1.0 (the License);
you may not use this file except in compliance with the License. You may obtain a
copy of the License at http://isa-tools.org/licenses/ISAcreator-license.html.
The License is based on the Mozilla Public License version 1.1 but Sections
14 and 15 have been added to cover use of software over a computer network and
provide for limited attribution for the Original Developer. In addition, Exhibit
A has been modified to be consistent with Exhibit B.
Software distributed under the License is distributed on an AS IS basis,
WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for
the specific language governing rights and limitations under the License.
The Original Code is ISAcreator.
The Original Developer is the Initial Developer. The Initial Developer of the
Original Code is the ISA Team (Eamonn Maguire, eamonnmag@gmail.com;
Philippe Rocca-Serra, proccaserra@gmail.com; Susanna-Assunta Sansone, sa.sanson@gmail.com;
http://www.isa-tools.org). All portions of the code written by the ISA Team are
Copyright (c) 2007-2011 ISA Team. All Rights Reserved.
EXHIBIT B. Attribution Information
Attribution Copyright Notice: Copyright (c) 2008-2011 ISA Team
Attribution Phrase: Developed by the ISA Team
Attribution URL: http://www.isa-tools.org
Graphic Image provided in the Covered Code as file: http://isa-tools.org/licenses/icons/poweredByISAtools.png
Display of Attribution Information is required in Larger Works which are defined in the CPAL as a work which combines Covered Code or portions thereof with code not governed by the terms of the CPAL.
Sponsors:
The ISA Team and the ISA software suite have been funded by the EU Carcinogenomics project (http://www.carcinogenomics.eu), the UK BBSRC (http://www.bbsrc.ac.uk), the UK NERC-NEBC (http://nebc.nerc.ac.uk) and in part by the EU NuGO consortium (http://www.nugo.org/everyone).
*/
package org.isatools.isacreator.visualization.tree;
import prefuse.Constants;
import prefuse.Display;
import prefuse.Visualization;
import prefuse.action.ActionList;
import prefuse.action.ItemAction;
import prefuse.action.RepaintAction;
import prefuse.action.animate.ColorAnimator;
import prefuse.action.animate.LocationAnimator;
import prefuse.action.animate.QualityControlAnimator;
import prefuse.action.animate.VisibilityAnimator;
import prefuse.action.assignment.ColorAction;
import prefuse.action.assignment.DataColorAction;
import prefuse.action.assignment.FontAction;
import prefuse.action.filter.FisheyeTreeFilter;
import prefuse.action.layout.CollapsedSubtreeLayout;
import prefuse.action.layout.graph.NodeLinkTreeLayout;
import prefuse.activity.SlowInSlowOutPacer;
import prefuse.controls.*;
import prefuse.data.Graph;
import prefuse.data.Table;
import prefuse.data.Tree;
import prefuse.data.tuple.TupleSet;
import prefuse.render.AbstractShapeRenderer;
import prefuse.render.DefaultRendererFactory;
import prefuse.render.EdgeRenderer;
import prefuse.render.LabelRenderer;
import prefuse.util.ColorLib;
import prefuse.util.FontLib;
import prefuse.visual.VisualItem;
import prefuse.visual.expression.InGroupPredicate;
import prefuse.visual.sort.TreeDepthItemSorter;
import java.awt.*;
import java.awt.geom.Point2D;
public class TreeView extends Display {
public static String NAME_STRING = "name";
protected static final String tree = "tree";
protected static final String treeNodes = "tree.nodes";
protected static final String treeEdges = "tree.edges";
protected LabelRenderer m_nodeRenderer;
protected EdgeRenderer m_edgeRenderer;
protected int m_orientation;
public TreeView(Tree t, Dimension size) {
this(t, size, NAME_STRING, Constants.ORIENT_LEFT_RIGHT);
}
public TreeView(Tree t, Dimension size, String label, int orientation) {
super(new Visualization());
initialiseTreeView(t, size, label, orientation);
}
public void initialiseTreeView(Tree t, Dimension size, String label, int orientation) {
this.m_orientation = orientation;
m_vis.add(tree, t);
m_nodeRenderer = new LabelRenderer(label);
m_nodeRenderer.setRenderType(AbstractShapeRenderer.RENDER_TYPE_FILL);
m_nodeRenderer.setHorizontalAlignment(Constants.LEFT);
m_nodeRenderer.setRoundedCorner(8, 8);
m_edgeRenderer = new EdgeRenderer(Constants.EDGE_TYPE_CURVE);
DefaultRendererFactory rf = new DefaultRendererFactory(m_nodeRenderer);
rf.add(new InGroupPredicate(treeEdges), m_edgeRenderer);
m_vis.setRendererFactory(rf);
int[] colorPalette = new int[]{ColorLib.rgb(51, 51, 51), ColorLib.rgb(51, 51, 51), ColorLib.rgb(51, 51, 51)};
DataColorAction dca = new DataColorAction("tree.nodes", "type", Constants.NOMINAL, VisualItem.TEXTCOLOR, colorPalette);
// colors
ItemAction nodeColor = new NodeColorAction(treeNodes);
m_vis.putAction("textColor", dca);
ItemAction edgeColor = new ColorAction(treeEdges,
VisualItem.STROKECOLOR, ColorLib.rgba(153, 153, 153, 100));
// quick repaint
ActionList repaint = new ActionList();
repaint.add(nodeColor);
repaint.add(new RepaintAction());
m_vis.putAction("repaint", repaint);
// full paint
ActionList fullPaint = new ActionList();
fullPaint.add(nodeColor);
m_vis.putAction("fullPaint", fullPaint);
// animate paint change
ActionList animatePaint = new ActionList(400);
animatePaint.add(new ColorAnimator(treeNodes));
animatePaint.add(new RepaintAction());
m_vis.putAction("animatePaint", animatePaint);
// create the tree layout action
NodeLinkTreeLayout treeLayout = new NodeLinkTreeLayout(tree,
m_orientation, 50, 0, 8);
treeLayout.setLayoutAnchor(new Point2D.Double(size.width / 2, 15));
m_vis.putAction("treeLayout", treeLayout);
CollapsedSubtreeLayout subLayout = new CollapsedSubtreeLayout(tree,
m_orientation);
m_vis.putAction("subLayout", subLayout);
createAndAddFilter(dca, nodeColor, edgeColor, treeLayout, subLayout);
// animated transition
createAnimation();
// ensure size is reasonable!
finaliseVisualizationSteps(size);
}
protected void finaliseVisualizationSteps(Dimension size) {
size.width = (size.width < 100) ? 200 : size.width;
size.height = (size.height < 100) ? 200 : size.height;
setSize(size);
setItemSorter(new TreeDepthItemSorter());
addControlListeners();
setOrientation(m_orientation);
m_vis.run("filter");
}
protected void createAnimation() {
ActionList animate = new ActionList(1000);
animate.setPacingFunction(new SlowInSlowOutPacer());
animate.add(new QualityControlAnimator());
animate.add(new VisibilityAnimator(tree));
animate.add(new LocationAnimator(treeNodes));
animate.add(new ColorAnimator(treeNodes));
animate.add(new RepaintAction());
m_vis.putAction("animate", animate);
m_vis.alwaysRunAfter("filter", "animate");
}
protected void createAndAddFilter(DataColorAction dca, ItemAction nodeColor, ItemAction edgeColor, NodeLinkTreeLayout treeLayout, CollapsedSubtreeLayout subLayout) {
// create the filtering and layout
ActionList filter = new ActionList();
if (m_orientation == Constants.ORIENT_LEFT_RIGHT) {
filter.add(new FisheyeTreeFilter(tree, 2));
}
filter.add(new FontAction(treeNodes, FontLib.getFont("Verdana", 14)));
filter.add(treeLayout);
filter.add(subLayout);
filter.add(dca);
filter.add(nodeColor);
filter.add(edgeColor);
m_vis.putAction("filter", filter);
}
private void addControlListeners() {
addControlListener(new ZoomToFitControl());
addControlListener(new ZoomControl());
addControlListener(new WheelZoomControl());
addControlListener(new PanControl());
addControlListener(new FocusControl(1, "filter"));
}
public int getOrientation() {
return m_orientation;
}
// ------------------------------------------------------------------------
public void setOrientation(int orientation) {
NodeLinkTreeLayout rtl = (NodeLinkTreeLayout) m_vis.getAction(
"treeLayout");
CollapsedSubtreeLayout stl = (CollapsedSubtreeLayout) m_vis.getAction(
"subLayout");
switch (orientation) {
case Constants.ORIENT_LEFT_RIGHT:
m_nodeRenderer.setHorizontalAlignment(Constants.LEFT);
m_edgeRenderer.setHorizontalAlignment1(Constants.RIGHT);
m_edgeRenderer.setHorizontalAlignment2(Constants.LEFT);
m_edgeRenderer.setVerticalAlignment1(Constants.CENTER);
m_edgeRenderer.setVerticalAlignment2(Constants.CENTER);
break;
case Constants.ORIENT_RIGHT_LEFT:
m_nodeRenderer.setHorizontalAlignment(Constants.RIGHT);
m_edgeRenderer.setHorizontalAlignment1(Constants.LEFT);
m_edgeRenderer.setHorizontalAlignment2(Constants.RIGHT);
m_edgeRenderer.setVerticalAlignment1(Constants.CENTER);
m_edgeRenderer.setVerticalAlignment2(Constants.CENTER);
break;
case Constants.ORIENT_TOP_BOTTOM:
m_nodeRenderer.setHorizontalAlignment(Constants.CENTER);
m_edgeRenderer.setHorizontalAlignment1(Constants.CENTER);
m_edgeRenderer.setHorizontalAlignment2(Constants.CENTER);
m_edgeRenderer.setVerticalAlignment1(Constants.BOTTOM);
m_edgeRenderer.setVerticalAlignment2(Constants.TOP);
break;
case Constants.ORIENT_BOTTOM_TOP:
m_nodeRenderer.setHorizontalAlignment(Constants.CENTER);
m_edgeRenderer.setHorizontalAlignment1(Constants.CENTER);
m_edgeRenderer.setHorizontalAlignment2(Constants.CENTER);
m_edgeRenderer.setVerticalAlignment1(Constants.TOP);
m_edgeRenderer.setVerticalAlignment2(Constants.BOTTOM);
break;
default:
throw new IllegalArgumentException(
"Unrecognized orientation value: " + orientation);
}
m_orientation = orientation;
rtl.setOrientation(orientation);
stl.setOrientation(orientation);
}
public static class NodeColorAction extends ColorAction {
public NodeColorAction(String group) {
super(group, VisualItem.FILLCOLOR);
}
public int getColor(VisualItem item) {
if (m_vis.isInGroup(item, Visualization.SEARCH_ITEMS)) {
return ColorLib.rgba(153, 153, 153, 100);
} else if (m_vis.isInGroup(item, Visualization.FOCUS_ITEMS)) {
return ColorLib.rgba(153, 153, 153, 100);
} else if (item.getDOI() > -1) {
return ColorLib.rgb(164, 193, 193);
} else {
return ColorLib.rgba(255, 255, 255, 0);
}
}
}
}