Author: scooter
Date: 2012-10-01 15:38:56 -0700 (Mon, 01 Oct 2012)
New Revision: 30567
Added:
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/heatstrip/
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/heatstrip/HeatStripChart.java
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/heatstrip/HeatStripFactory.java
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/heatstrip/HeatStripLayer.java
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/stripe/
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/stripe/StripeChart.java
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/stripe/StripeChartFactory.java
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/stripe/StripeLayer.java
Modified:
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/CyActivator.java
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/bar/BarLayer.java
Log:
Added heatstrip and stripe charts
Modified:
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/CyActivator.java
===================================================================
---
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/CyActivator.java
2012-10-01 22:25:52 UTC (rev 30566)
+++
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/CyActivator.java
2012-10-01 22:38:56 UTC (rev 30567)
@@ -4,6 +4,9 @@
import org.osgi.framework.BundleContext;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.service.util.AbstractCyActivator;
import org.cytoscape.view.presentation.customgraphics.CyCustomGraphicsFactory;
@@ -11,11 +14,14 @@
import
edu.ucsf.rbvi.enhancedcg.internal.gradients.linear.LinearGradientCGFactory;
import
edu.ucsf.rbvi.enhancedcg.internal.gradients.radial.RadialGradientCGFactory;
import edu.ucsf.rbvi.enhancedcg.internal.charts.bar.BarChartFactory;
+import edu.ucsf.rbvi.enhancedcg.internal.charts.heatstrip.HeatStripFactory;
import edu.ucsf.rbvi.enhancedcg.internal.charts.line.LineChartFactory;
import edu.ucsf.rbvi.enhancedcg.internal.charts.pie.PieChartFactory;
+import edu.ucsf.rbvi.enhancedcg.internal.charts.stripe.StripeChartFactory;
public class CyActivator extends AbstractCyActivator {
+ private static Logger logger =
LoggerFactory.getLogger(edu.ucsf.rbvi.enhancedcg.internal.CyActivator.class);
public CyActivator() {
super();
}
@@ -43,9 +49,17 @@
CyCustomGraphicsFactory lineChartFactory = new
LineChartFactory();
Properties lineChartProps = new Properties();
registerService(bc, lineChartFactory,
CyCustomGraphicsFactory.class, lineChartProps);
- // CyCustomGraphicsFactory stripeChartFactory = new
StripeChartCustomGraphicsFactory();
+
+ CyCustomGraphicsFactory stripeChartFactory = new
StripeChartFactory();
+ Properties stripeChartProps = new Properties();
+ registerService(bc, stripeChartFactory,
CyCustomGraphicsFactory.class, stripeChartProps);
+
+ CyCustomGraphicsFactory heatStripChartFactory = new
HeatStripFactory();
+ Properties heatStripChartProps = new Properties();
+ registerService(bc, heatStripChartFactory,
CyCustomGraphicsFactory.class, heatStripChartProps);
+
// CyCustomGraphicsFactory stripChartFactory = new
StripChartCustomGraphicsFactory();
- System.out.println("Enhanced Custom Graphics started");
+ logger.info("Enhanced Custom Graphics started");
}
}
Modified:
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/bar/BarLayer.java
===================================================================
---
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/bar/BarLayer.java
2012-10-01 22:25:52 UTC (rev 30566)
+++
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/bar/BarLayer.java
2012-10-01 22:38:56 UTC (rev 30567)
@@ -42,6 +42,7 @@
import java.awt.geom.AffineTransform;
import java.awt.geom.Area;
+import java.awt.geom.Path2D;
import java.awt.geom.Point2D;
import java.awt.geom.Rectangle2D;
@@ -136,7 +137,16 @@
private Shape barShape() {
// System.out.println("sliceShape: bounds = "+bounds);
- return getBar(value);
+ Shape barShape = getBar(value);
+
+ // If this is our first bar, draw our axes
+ if (bar == 0) {
+ Area axes = getAxes();
+ axes.add(new Area(barShape));
+ return axes;
+ }
+ return barShape;
+
}
private Shape labelShape() {
@@ -175,7 +185,7 @@
else
max = -1.0 * min;
- double px1 = x + bar*sliceSize;
+ double px1 = x + bar*width/nBars;
double py1 = y + (0.5 * height);
if (val > 0.0)
@@ -187,4 +197,19 @@
return new Rectangle2D.Double(px1, py1, sliceSize, h);
}
+ private Area getAxes() {
+ // At this point, make it simple -- a line at 0.0
+ Rectangle2D firstBar = getBar(0.0);
+ int saveBar = bar;
+ bar = nBars-1;
+ Rectangle2D lastBar = getBar(0.0);
+ bar = saveBar;
+
+ Path2D xAxes = new Path2D.Double();
+ xAxes.moveTo(firstBar.getX(), firstBar.getY());
+ xAxes.lineTo(lastBar.getX()+lastBar.getWidth(), lastBar.getY());
+ BasicStroke stroke = new BasicStroke(0.5f/2.0f);
+ return new Area(stroke.createStrokedShape(xAxes));
+ }
+
}
Added:
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/heatstrip/HeatStripChart.java
===================================================================
---
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/heatstrip/HeatStripChart.java
(rev 0)
+++
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/heatstrip/HeatStripChart.java
2012-10-01 22:38:56 UTC (rev 30567)
@@ -0,0 +1,171 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2010 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package edu.ucsf.rbvi.enhancedcg.internal.charts.heatstrip;
+
+// System imports
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import java.awt.Color;
+import java.awt.Image;
+import java.awt.Paint;
+import java.awt.Shape;
+import java.awt.geom.Arc2D;
+import java.awt.geom.Area;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+// Cytoscape imports
+import org.cytoscape.model.CyIdentifiable;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+
+import edu.ucsf.rbvi.enhancedcg.internal.charts.AbstractChartCustomGraphics;
+
+/**
+ * The HeatStripChart creates a list of custom graphics where each custom
graphic represents
+ * a slice of the pie. The data for this is of the format:
label1:value1:color1, etc.,
+ * where value is numeric and the color is optional, but if specified, it must
be one of
+ * the named Java colors, hex RGB values, or hex RGBA values.
+ */
+public class HeatStripChart extends
AbstractChartCustomGraphics<HeatStripLayer> {
+ private static final String COLORS = "colorlist";
+ private static final String SEPARATION = "separation";
+ private static final String REDGREEN = "redgreen";
+ private static final String YELLOWCYAN = "yellowcyan";
+
+ private List<Color> colorList = null;
+ private String colorString = null;
+ private int separation = 0;
+ private int labelSize = 4;
+
+ Color[] redGreen = {Color.GREEN, Color.BLACK, Color.RED};
+ Color[] yellowCyan = {Color.CYAN, Color.BLACK, Color.YELLOW};
+ Color[] colorScale = null;
+
+ // Parse the input string, which is always of the form:
+ // heatstripchart: [attributelist=value]
+ //
[colorlist=value]
+ //
[labellist=value]
+ // [position=value]
+ // [scale=0.90]
+ // [separation=value]
+ // [valuelist=value]
+ public HeatStripChart(String input) {
+ Map<String, String> args = parseInput(input);
+ // This will populate the values, attributes, and labels lists
+ populateValues(args);
+
+ colorScale = yellowCyan;
+ if (args.containsKey(COLORS)) {
+ // Get our colors
+ String colorSpec = args.get(COLORS).toString();
+ if (colorSpec.equalsIgnoreCase(YELLOWCYAN)) {
+ colorScale = yellowCyan;
+ } else if (colorSpec.equalsIgnoreCase(REDGREEN)) {
+ colorScale = redGreen;
+ } else {
+ colorScale = new Color[3];
+ String [] colorArray = colorSpec.split(",");
+ List<Color> colors =
parseUpDownColor(colorArray);
+ colorScale[1] = colors.get(2);
+ colorScale[0] = colors.get(1);
+ colorScale[2] = colors.get(0);
+ }
+ }
+
+ if (args.containsKey(SEPARATION)) {
+ separation = Integer.parseInt(args.get(SEPARATION));
+ }
+ }
+
+ public String toSerializableString() { return
this.getIdentifier().toString()+","+displayName; }
+
+ public Image getRenderedImage() { return null; }
+
+ @Override
+ public List<HeatStripLayer> getLayers(CyNetwork network, CyIdentifiable
node) {
+ // Create all of our pie slices. Each slice becomes a layer
+ if (attributes != null && attributes.size() > 0) {
+ if (!(node instanceof CyNode))
+ return null;
+
+ values = getDataFromAttributes (network, (CyNode)node,
attributes, labels);
+ }
+
+ if (labels != null && labels.size() > 0 &&
+ labels.size() != values.size()) {
+ logger.error("number of labels (" + labels.size()
+ + "), values (" + values.size() + ") don't
match");
+ }
+
+ List<HeatStripLayer> labelList = new
ArrayList<HeatStripLayer>();
+
+ double minValue = 0.000001;
+ double maxValue = -minValue;
+ for (double val: values) {
+ minValue = Math.min(minValue, val);
+ maxValue = Math.max(maxValue, val);
+ }
+
+ int nBars = values.size();
+ for (int bar = 0; bar < nBars; bar++) {
+ String label = null;
+ if (labels != null && labels.size() > 0)
+ label = labels.get(bar);
+ if (values.get(bar) == 0.0) continue;
+
+ // Create the slice
+ HeatStripLayer bl = new HeatStripLayer(bar, nBars,
separation, values.get(bar), minValue, maxValue, colorScale);
+ if (bl == null) continue;
+ layers.add(bl);
+
+ if (label != null) {
+ // Now, create the label
+ HeatStripLayer labelLayer = new
HeatStripLayer(bar, nBars, separation, minValue, maxValue, label, labelSize);
+ if (labelLayer != null)
+ labelList.add(labelLayer);
+ }
+ }
+
+ // Now add all of our labels so they will be on top of our
slices
+ if (labelList != null && labelList.size() > 0)
+ layers.addAll(labelList);
+ return layers;
+ }
+
+}
Added:
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/heatstrip/HeatStripFactory.java
===================================================================
---
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/heatstrip/HeatStripFactory.java
(rev 0)
+++
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/heatstrip/HeatStripFactory.java
2012-10-01 22:38:56 UTC (rev 30567)
@@ -0,0 +1,28 @@
+package edu.ucsf.rbvi.enhancedcg.internal.charts.heatstrip;
+
+import java.net.URL;
+
+import org.cytoscape.view.presentation.customgraphics.CyCustomGraphics;
+import org.cytoscape.view.presentation.customgraphics.CyCustomGraphicsFactory;
+import org.cytoscape.view.presentation.customgraphics.CustomGraphicLayer;
+
+public class HeatStripFactory implements CyCustomGraphicsFactory {
+ private static final Class<? extends CyCustomGraphics> TARGET_CLASS =
HeatStripChart.class;
+
+ public HeatStripFactory() {
+ }
+
+ public CyCustomGraphics<HeatStripLayer> getInstance(String input) {
+ return new HeatStripChart(input);
+ }
+
+ public CyCustomGraphics<HeatStripLayer> getInstance(URL input) { return
null; }
+
+ public String getPrefix() { return "heatstripchart"; }
+
+ public Class<? extends CyCustomGraphics> getSupportedClass() { return
TARGET_CLASS; }
+
+ public CyCustomGraphics<HeatStripLayer> parseSerializableString(String
string) { return null; }
+
+ public boolean supportsMime(String mimeType) { return false; }
+}
Added:
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/heatstrip/HeatStripLayer.java
===================================================================
---
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/heatstrip/HeatStripLayer.java
(rev 0)
+++
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/heatstrip/HeatStripLayer.java
2012-10-01 22:38:56 UTC (rev 30567)
@@ -0,0 +1,232 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2010 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package edu.ucsf.rbvi.enhancedcg.internal.charts.heatstrip;
+
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.LinearGradientPaint;
+import java.awt.Paint;
+import java.awt.Rectangle;
+import java.awt.Shape;
+import java.awt.Stroke;
+
+import java.awt.geom.AffineTransform;
+import java.awt.geom.Area;
+import java.awt.geom.Path2D;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+import java.util.Arrays;
+import java.util.Comparator;
+import java.util.List;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import org.cytoscape.view.presentation.customgraphics.PaintedShape;
+import edu.ucsf.rbvi.enhancedcg.internal.charts.ViewUtils;
+
+public class HeatStripLayer implements PaintedShape {
+ private boolean labelLayer = false;
+ private String label;
+ private Color[] colorScale;
+ private int fontSize;
+ protected Rectangle2D bounds;
+ private double value;
+ private double maxValue;
+ private double minValue;
+ private int bar;
+ private int nBars;
+ private int separation;
+ float[] dist = {0.0f, 0.5f, 1.0f};
+ private Logger logger = LoggerFactory.getLogger(this.getClass());
+
+ public HeatStripLayer(int bar, int nbars, int separation, double value,
+ double minValue, double maxValue, Color[] colorScale) {
+ labelLayer = false;
+ this.colorScale = colorScale;
+ this.bar = bar;
+ this.nBars = nbars;
+ this.separation = separation;
+ this.value = value;
+ this.minValue = minValue;
+ this.maxValue = maxValue;
+ bounds = new Rectangle2D.Double(0, 0, 100, 50);
+ }
+
+ public HeatStripLayer(int bar, int nbars, int separation, double
minValue, double maxValue,
+ String label, int fontSize) {
+ labelLayer = true;
+ this.bar = bar;
+ this.nBars = nbars;
+ this.separation = separation;
+ this.label = label;
+ this.fontSize = fontSize;
+ this.minValue = minValue;
+ this.maxValue = maxValue;
+ bounds = new Rectangle2D.Double(0, 0, 100, 50);
+ }
+
+ public Paint getPaint() {
+ if (labelLayer)
+ return Color.BLACK;
+ return createGradPaint();
+ }
+
+ public Paint getPaint(Rectangle2D bounds) {
+ if (labelLayer)
+ return Color.BLACK;
+ return createGradPaint();
+ }
+
+ public Shape getShape() {
+ // create the slice or the label, as appropriate
+ if (labelLayer)
+ return labelShape();
+ else
+ return barShape();
+ }
+
+ public Stroke getStroke() {
+ // We only stroke the slice
+ if (!labelLayer)
+ return new BasicStroke(0.5f);
+ return null;
+ }
+
+ public Paint getStrokePaint() {
+ return Color.BLACK;
+ }
+
+ public Rectangle2D getBounds2D() {
+ return bounds;
+ }
+
+ public HeatStripLayer transform(AffineTransform xform) {
+ Shape newBounds = xform.createTransformedShape(bounds);
+ HeatStripLayer bl;
+ if (labelLayer)
+ bl = new HeatStripLayer(bar, nBars, separation,
minValue, maxValue, label, fontSize);
+ else
+ bl = new HeatStripLayer(bar, nBars, separation, value,
minValue, maxValue, colorScale);
+ bl.bounds = newBounds.getBounds2D();
+ return bl;
+ }
+
+ private Shape barShape() {
+ Shape strip = getHeatStrip(value);
+
+ // If this is our first bar, draw our axes
+ if (bar == 0) {
+ Area axes = getAxes();
+ axes.add(new Area(strip));
+ return axes;
+ }
+
+ return strip;
+ }
+
+ private Shape labelShape() {
+ // Get a bar that's in the right position and the maximum height
+ Rectangle2D bar = getHeatStrip(minValue);
+
+ ViewUtils.TextAlignment tAlign =
ViewUtils.TextAlignment.ALIGN_LEFT;
+ Point2D labelPosition = new Point2D.Double(bar.getCenterX(),
bar.getMaxY()+fontSize/2);
+
+ Shape textShape = ViewUtils.getLabelShape(label, null, 0,
fontSize);
+
+ double maxHeight = bar.getWidth();
+
+ textShape = ViewUtils.positionLabel(textShape, labelPosition,
tAlign, maxHeight, 0.0, 70.0);
+ if (textShape == null) {
+ return null;
+ }
+
+ return textShape;
+ }
+
+ private Rectangle2D getHeatStrip(double val) {
+ double x = bounds.getX()-bounds.getWidth()/2;
+ double y = bounds.getY()-bounds.getHeight()/2;
+ double width = bounds.getWidth();
+ double height = bounds.getHeight();
+
+ double yMid = y + (0.5 * height);
+ double sliceSize = (width / nBars) - (nBars * separation) +
separation; // only have n-1 separators
+
+ double min = minValue;
+ double max = maxValue;
+
+ if (Math.abs(max) > Math.abs(min))
+ min = -1.0 * max;
+ else
+ max = -1.0 * min;
+
+ double px1 = x + bar*width/nBars;
+ double py1 = y + (0.5 * height);
+
+ if (val > 0.0)
+ py1 = py1 - ((0.5 * height) * (val / max));
+ else
+ val = -val;
+
+ double h = (0.5 * height) * (val/max);
+ return new Rectangle2D.Double(px1, py1, sliceSize, h);
+ }
+
+ private Paint createGradPaint() {
+ double x = bounds.getX()-bounds.getWidth()/2;
+ double y = bounds.getY()-bounds.getHeight()/2;
+ double width = bounds.getWidth();
+ double height = bounds.getHeight();
+ return new LinearGradientPaint((float)x, (float)(y+height),
(float)x, (float)y, dist, colorScale);
+ }
+
+ private Area getAxes() {
+ // At this point, make it simple -- a line at 0.0
+ Rectangle2D firstBar = getHeatStrip(0.0);
+ int saveBar = bar;
+ bar = nBars-1;
+ Rectangle2D lastBar = getHeatStrip(0.0);
+ bar = saveBar;
+
+ Path2D xAxes = new Path2D.Double();
+ xAxes.moveTo(firstBar.getX(), firstBar.getY());
+ xAxes.lineTo(lastBar.getX()+lastBar.getWidth(), lastBar.getY());
+ BasicStroke stroke = new BasicStroke(0.5f/2.0f);
+ return new Area(stroke.createStrokedShape(xAxes));
+
+ }
+
+}
Added:
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/stripe/StripeChart.java
===================================================================
---
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/stripe/StripeChart.java
(rev 0)
+++
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/stripe/StripeChart.java
2012-10-01 22:38:56 UTC (rev 30567)
@@ -0,0 +1,109 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2010 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package edu.ucsf.rbvi.enhancedcg.internal.charts.stripe;
+
+// System imports
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import java.awt.Color;
+import java.awt.Image;
+import java.awt.Paint;
+import java.awt.Shape;
+import java.awt.geom.Arc2D;
+import java.awt.geom.Area;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+// Cytoscape imports
+import org.cytoscape.model.CyIdentifiable;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+
+import edu.ucsf.rbvi.enhancedcg.internal.charts.AbstractChartCustomGraphics;
+
+/**
+ * The StripeChart creates a list of custom graphics where each custom graphic
represents
+ * a slice of the pie. The data for this is of the format:
label1:value1:color1, etc.,
+ * where value is numeric and the color is optional, but if specified, it must
be one of
+ * the named Java colors, hex RGB values, or hex RGBA values.
+ */
+public class StripeChart extends AbstractChartCustomGraphics<StripeLayer> {
+ private static final String COLORS = "colorlist";
+
+ private List<Color> colorList = null;
+ private int labelSize = 4;
+ private String colorString = null;
+
+ // Parse the input string, which is always of the form:
+ // linechart: [colorlist=value]
+ // [position=value]
+ // [scale=0.90]
+ public StripeChart(String input) {
+ Map<String, String> args = parseInput(input);
+ // This will populate the values, attributes, and labels lists
+ // populateValues(args);
+
+ if (args.containsKey(COLORS)) {
+ if (attributes == null)
+ colorList =
convertInputToColor(args.get(COLORS), new ArrayList<Double>());
+ else
+ colorString = args.get(COLORS);
+ }
+ }
+
+ public String toSerializableString() { return
this.getIdentifier().toString()+","+displayName; }
+
+ public Image getRenderedImage() { return null; }
+
+ @Override
+ public List<StripeLayer> getLayers(CyNetwork network, CyIdentifiable
node) {
+ int nStripes = colorList.size();
+ for (int stripe = 0; stripe < nStripes; stripe++) {
+ Color color = colorList.get(stripe);
+
+ // Create the stripe
+ StripeLayer bl = new StripeLayer(stripe, nStripes,
color);
+ if (bl == null) continue;
+ layers.add(bl);
+
+ }
+
+ return layers;
+ }
+
+}
Added:
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/stripe/StripeChartFactory.java
===================================================================
---
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/stripe/StripeChartFactory.java
(rev 0)
+++
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/stripe/StripeChartFactory.java
2012-10-01 22:38:56 UTC (rev 30567)
@@ -0,0 +1,28 @@
+package edu.ucsf.rbvi.enhancedcg.internal.charts.stripe;
+
+import java.net.URL;
+
+import org.cytoscape.view.presentation.customgraphics.CyCustomGraphics;
+import org.cytoscape.view.presentation.customgraphics.CyCustomGraphicsFactory;
+import org.cytoscape.view.presentation.customgraphics.CustomGraphicLayer;
+
+public class StripeChartFactory implements CyCustomGraphicsFactory {
+ private static final Class<? extends CyCustomGraphics> TARGET_CLASS =
StripeChart.class;
+
+ public StripeChartFactory() {
+ }
+
+ public CyCustomGraphics<StripeLayer> getInstance(String input) {
+ return new StripeChart(input);
+ }
+
+ public CyCustomGraphics<StripeLayer> getInstance(URL input) { return
null; }
+
+ public String getPrefix() { return "stripechart"; }
+
+ public Class<? extends CyCustomGraphics> getSupportedClass() { return
TARGET_CLASS; }
+
+ public CyCustomGraphics<StripeLayer> parseSerializableString(String
string) { return null; }
+
+ public boolean supportsMime(String mimeType) { return false; }
+}
Added:
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/stripe/StripeLayer.java
===================================================================
---
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/stripe/StripeLayer.java
(rev 0)
+++
csplugins/trunk/ucsf/scooter/enhancedcg/src/main/java/edu/ucsf/rbvi/internal/charts/stripe/StripeLayer.java
2012-10-01 22:38:56 UTC (rev 30567)
@@ -0,0 +1,141 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2010 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package edu.ucsf.rbvi.enhancedcg.internal.charts.stripe;
+
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Paint;
+import java.awt.Rectangle;
+import java.awt.Shape;
+import java.awt.Stroke;
+
+import java.awt.geom.AffineTransform;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+import java.util.Arrays;
+import java.util.Comparator;
+import java.util.List;
+
+import org.cytoscape.view.presentation.customgraphics.PaintedShape;
+import edu.ucsf.rbvi.enhancedcg.internal.charts.ViewUtils;
+
+public class StripeLayer implements PaintedShape {
+ private boolean labelLayer = false;
+ private String label;
+ private Color color;
+ private int fontSize;
+ protected Rectangle2D bounds;
+ private int stripe;
+ private int nStripes;
+
+ public StripeLayer(int stripe, int nStripes, Color color) {
+ labelLayer = false;
+ this.color = color;
+ this.stripe = stripe;
+ this.nStripes = nStripes;
+ bounds = new Rectangle2D.Double(0, 0, 100, 50);
+ }
+
+ public StripeLayer(int stripe, int nStripes, String label, int
fontSize) {
+ labelLayer = true;
+ this.stripe = stripe;
+ this.nStripes = nStripes;
+ this.label = label;
+ this.fontSize = fontSize;
+ this.color = Color.BLACK;
+ bounds = new Rectangle2D.Double(0, 0, 100, 50);
+ }
+
+ public Paint getPaint() {
+ return color;
+ }
+
+ public Paint getPaint(Rectangle2D bounds) {
+ return color;
+ }
+
+ public Shape getShape() {
+ // create the slice or the label, as appropriate
+ if (labelLayer)
+ return labelShape();
+ else
+ return stripeShape();
+ }
+
+ public Stroke getStroke() {
+ // We only stroke the slice
+ if (!labelLayer)
+ return new BasicStroke(0.1f);
+ return null;
+ }
+
+ public Paint getStrokePaint() {
+ return Color.BLACK;
+ }
+
+ public Rectangle2D getBounds2D() {
+ return bounds;
+ }
+
+ public StripeLayer transform(AffineTransform xform) {
+ Shape newBounds = xform.createTransformedShape(bounds);
+ StripeLayer bl;
+ if (labelLayer)
+ bl = new StripeLayer(stripe, nStripes, label, fontSize);
+ else
+ bl = new StripeLayer(stripe, nStripes, color);
+ bl.bounds = newBounds.getBounds2D();
+ return bl;
+ }
+
+ private Shape stripeShape() {
+ // System.out.println("sliceShape: bounds = "+bounds);
+ return getStripe(stripe, nStripes);
+ }
+
+ private Shape labelShape() {
+ return null;
+ }
+
+ private Rectangle2D getStripe(int stripe, int nStripes) {
+ double x = bounds.getX()-bounds.getWidth()/2;
+ double y = bounds.getY()-bounds.getHeight()/2;
+ double width = bounds.getWidth();
+ double height = bounds.getHeight();
+ // Create the stripe
+ return new Rectangle2D.Double((x + (stripe * width/nStripes)),
y, width/nStripes, height);
+ }
+
+}
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