Author: scooter
Date: 2010-09-01 17:37:22 -0700 (Wed, 01 Sep 2010)
New Revision: 21664
Modified:
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/command/NodeChartCommandHandler.java
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/NodeChartViewer.java
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/PieChart.java
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/ValueUtils.java
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/ViewUtils.java
csplugins/trunk/ucsf/scooter/nodeCharts/test.com
Log:
Now have colors and offsets working. Still need to add color name lookups and
nodelist and attributelist support
Modified:
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/command/NodeChartCommandHandler.java
===================================================================
---
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/command/NodeChartCommandHandler.java
2010-09-02 00:15:38 UTC (rev 21663)
+++
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/command/NodeChartCommandHandler.java
2010-09-02 00:37:22 UTC (rev 21664)
@@ -60,9 +60,13 @@
*/
public class NodeChartCommandHandler extends AbstractCommandHandler {
CyLogger logger;
- private static String NODE = "node";
Map<String, NodeChartViewer> viewerMap;
+ // Global commands
+ private static String NODE = "node";
+ private static String POSITION = "position";
+
+
public NodeChartCommandHandler(String namespace, CyLogger logger) {
super(CyCommandManager.reserveNamespace(namespace));
@@ -92,11 +96,19 @@
if (node == null)
throw new CyCommandException("can't find node:
'"+nodeName+"'");
+ Object pos = null;
+ if (args.containsKey(POSITION)) {
+ String position = (String) args.get(POSITION);
+ pos = ViewUtils.getPosition(position);
+ if (pos == null)
+ throw new CyCommandException("unknown position
keyword or illegal position expression: "+position);
+ }
+
NodeChartViewer viewer = viewerMap.get(command);
CyNetworkView view = Cytoscape.getCurrentNetworkView();
- ViewUtils.addCustomGraphics(viewer.getCustomGraphics(args,
node, view), node, view);
+ ViewUtils.addCustomGraphics(viewer.getCustomGraphics(args,
node, view, pos), node, view);
return result;
}
Modified:
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/NodeChartViewer.java
===================================================================
---
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/NodeChartViewer.java
2010-09-02 00:15:38 UTC (rev 21663)
+++
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/NodeChartViewer.java
2010-09-02 00:37:22 UTC (rev 21664)
@@ -54,7 +54,7 @@
public Map<String,String> getOptions();
- public List<CustomGraphic> getCustomGraphics(Map<String,Object>args,
CyNode node, CyNetworkView view)
+ public List<CustomGraphic> getCustomGraphics(Map<String,Object>args,
CyNode node, CyNetworkView view, Object position)
throws CyCommandException;
}
Modified:
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/PieChart.java
===================================================================
---
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/PieChart.java
2010-09-02 00:15:38 UTC (rev 21663)
+++
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/PieChart.java
2010-09-02 00:37:22 UTC (rev 21664)
@@ -35,11 +35,9 @@
// System imports
import java.util.ArrayList;
import java.util.Arrays;
-import java.util.Calendar;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import java.util.Random;
import java.awt.Color;
import java.awt.Paint;
@@ -81,7 +79,7 @@
return options;
}
- public List<CustomGraphic> getCustomGraphics(Map<String, Object>args,
CyNode node, CyNetworkView view)
+ public List<CustomGraphic> getCustomGraphics(Map<String, Object>args,
CyNode node, CyNetworkView view, Object position)
throws CyCommandException {
// First, get our data values
if (!args.containsKey(VALUES))
@@ -97,11 +95,7 @@
List<String> labels = getLabels((String)args.get(LABELS));
// Get our colors
- List<Color> colors;
- if (args.containsKey(COLORS))
- colors = convertColor((String)args.get(COLORS));
- else
- colors = generateColors(values.size());
+ List<Color> colors =
ValueUtils.convertInputToColor(args.get(COLORS), labels.size());
// Sanity check
if (labels.size() != values.size() ||
@@ -113,7 +107,7 @@
List<CustomGraphic> cgList = new ArrayList<CustomGraphic>();
// We need to get our bounding box in order to scale our
graphic properly
- Rectangle2D bbox = ViewUtils.getNodeBoundingBox(node, view);
+ Rectangle2D bbox = ViewUtils.getNodeBoundingBox(node, view,
position);
for (int slice = 0; slice < nSlices; slice++) {
CustomGraphic cg = createSlice(bbox, arcStart,
labels.get(slice), values.get(slice), colors.get(slice));
@@ -143,26 +137,6 @@
return values;
}
- private List<Color> convertColor(String input) {
- String[] inputArray = input.split(",");
- return null;
- }
-
- private List<Color> generateColors(int nColors) {
- Calendar cal = Calendar.getInstance();
- int seed = cal.get(Calendar.SECOND);
- Random rand = new Random(seed);
-
- List<Color> result = new ArrayList<Color>(nColors);
- for (int index = 0; index < nColors; index++) {
- int r = rand.nextInt(255);
- int g = rand.nextInt(255);
- int b = rand.nextInt(255);
- result.add(index, new Color(r,g,b,200));
- }
- return result;
- }
-
private List<String> getLabels(String input) {
String[] inputArray = input.split(",");
return Arrays.asList(inputArray);
Modified:
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/ValueUtils.java
===================================================================
---
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/ValueUtils.java
2010-09-02 00:15:38 UTC (rev 21663)
+++
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/ValueUtils.java
2010-09-02 00:37:22 UTC (rev 21664)
@@ -35,8 +35,14 @@
// System imports
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Calendar;
+import java.util.HashMap;
import java.util.List;
+import java.util.Map;
+import java.util.Random;
+import java.awt.Color;
+
// Cytoscape imports
import cytoscape.command.CyCommandException;
@@ -91,4 +97,161 @@
String[] inputArray = input.split(",");
return convertStringList(Arrays.asList(inputArray));
}
+
+ public enum ColorKeyword {
+ RANDOM ("random"),
+ CONTRASTING ("contrasting"),
+ RAINBOW ("rainbow"),
+ MODULATED ("modulated");
+
+ private String label;
+ private static Map<String, ColorKeyword>cMap;
+
+ ColorKeyword(String label) {
+ this.label = label;
+ addKeyword(this);
+ }
+
+ public String getLabel() {
+ return label;
+ }
+
+ public String toString() {
+ return label;
+ }
+
+ private void addKeyword(ColorKeyword col) {
+ if (cMap == null) cMap = new
HashMap<String,ColorKeyword>();
+ cMap.put(col.getLabel(), col);
+ }
+
+ static ColorKeyword getColorKeyword(String label) {
+ if (cMap.containsKey(label))
+ return cMap.get(label);
+ return null;
+ }
+ }
+
+ public static List<Color> convertInputToColor(Object input, int
nColors) throws CyCommandException {
+ if (input == null) {
+ // give the default: contrasting colors
+ return generateContrastingColors(nColors);
+ }
+
+ // OK, we have three posibilities. The input could be a
keyword, a comma-separated list of colors, or
+ // a list of Color objects. We need to figure this out first...
+ if (input instanceof List) {
+ if ( ((List<Object>)input).get(0) instanceof Color)
+ return (List<Color>)input;
+ else
+ throw new CyCommandException("color list not of
type Color?");
+ } else if (input instanceof String) {
+ String inputString = (String) input;
+ // See if we have a csv
+ String [] colorArray = inputString.split(",");
+ if (colorArray.length > 1)
+ return parseColorList(colorArray);
+ else
+ return parseColorKeyword(inputString.trim(),
nColors);
+ } else
+ throw new CyCommandException("unknown type for color
list");
+ }
+
+ private static List<Color> parseColorKeyword(String input, int nColors)
throws CyCommandException {
+ ColorKeyword ckey = ColorKeyword.getColorKeyword(input);
+ if (ckey == null)
+ throw new CyCommandException("unknown color keyword");
+ switch (ckey) {
+ case RANDOM:
+ return generateRandomColors(nColors);
+ case RAINBOW:
+ return generateRainbowColors(nColors);
+ case MODULATED:
+ return generateModulatedRainbowColors(nColors);
+ case CONTRASTING:
+ default:
+ return generateContrastingColors(nColors);
+ }
+ }
+
+ private static List<Color> parseColorList(String[] inputArray) throws
CyCommandException {
+ List<Color> colors = new ArrayList<Color>();
+ // A color in the array can either be a hex value or a text
color
+ for (String colorString: inputArray) {
+ colorString = colorString.trim();
+ if
(colorString.matches("^#([A-Fa-f0-9]{8}|[A-Fa-f0-9]{6})$")) {
+ // We have a hex value with either 6 (rgb) or 8
(rgba) digits
+ int r =
Integer.parseInt(colorString.substring(1,3), 16);
+ int g =
Integer.parseInt(colorString.substring(3,5), 16);
+ int b =
Integer.parseInt(colorString.substring(5,7), 16);
+ if (colorString.length() > 7) {
+ int a =
Integer.parseInt(colorString.substring(7,9), 16);
+ colors.add(new Color(r,g,b,a));
+ } else {
+ colors.add(new Color(r,g,b));
+ }
+ } else {
+ // Check for color string
+ }
+ }
+ return colors;
+ }
+
+ private static List<Color> generateRandomColors(int nColors) {
+ // System.out.println("Generating random colors");
+ Calendar cal = Calendar.getInstance();
+ int seed = cal.get(Calendar.SECOND);
+ Random rand = new Random(seed);
+
+ List<Color> result = new ArrayList<Color>(nColors);
+ for (int index = 0; index < nColors; index++) {
+ int r = rand.nextInt(255);
+ int g = rand.nextInt(255);
+ int b = rand.nextInt(255);
+ result.add(index, new Color(r,g,b,200));
+ }
+ return result;
+ }
+
+ // Rainbow colors just divide the Hue wheel into n pieces and return
them
+ private static List<Color> generateRainbowColors(int nColors) {
+ // System.out.println("Generating rainbow colors");
+ List<Color> values = new ArrayList<Color>();
+ for (float i = 0.0f; i < (float)nColors; i += 1.0f) {
+ values.add(new Color(Color.HSBtoRGB(i/(float)nColors,
1.0f, 1.0f)));
+ }
+ return values;
+ }
+
+ // Rainbow colors just divide the Hue wheel into n pieces and return
them, but
+ // in this case, we're going to change the saturation and intensity
+ private static List<Color> generateModulatedRainbowColors(int nColors) {
+ // System.out.println("Generating modulated colors");
+ List<Color> values = new ArrayList<Color>();
+ for (float i = 0.0f; i < (float)nColors; i += 1.0f) {
+ float sat = (Math.abs(((Number) Math.cos((8 * i) / (2 *
Math.PI))).floatValue()) * 0.7f)
+ + 0.3f;
+ float br = (Math.abs(((Number) Math.sin(((i) / (2 *
Math.PI)) + (Math.PI / 2)))
+ .floatValue()) * 0.7f) + 0.3f;
+
+ //
System.out.println("Color("+(i/(float)nColors)+","+sat+","+br+")");
+ values.add(new Color(Color.HSBtoRGB(i/(float)nColors,
sat, br)));
+ }
+ return values;
+ }
+
+ // This is like rainbow, but we alternate sides of the color wheel
+ private static List<Color> generateContrastingColors(int nColors) {
+ // System.out.println("Generating contrasting colors");
+ List<Color> values = new ArrayList<Color>();
+ float divs = ((float)nColors)/2.0f;
+ for (float i = 0.0f; i < divs; i += 1.0f) {
+ //
System.out.println("Color("+(i/divs)+","+1.0f+","+1.0f+")");
+ values.add(new Color(Color.HSBtoRGB(i/divs, 1.0f,
1.0f)));
+ //
System.out.println("Color("+((i/divs)+0.5f)+","+1.0f+","+1.0f+")");
+ values.add(new Color(Color.HSBtoRGB((i/divs)+0.5f,
1.0f, 1.0f)));
+ }
+ return values;
+ }
+
}
Modified:
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/ViewUtils.java
===================================================================
---
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/ViewUtils.java
2010-09-02 00:15:38 UTC (rev 21663)
+++
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/ViewUtils.java
2010-09-02 00:37:22 UTC (rev 21664)
@@ -32,9 +32,11 @@
*/
package nodeCharts.view;
+import java.awt.geom.Point2D;
import java.awt.geom.Rectangle2D;
// System imports
+import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -47,10 +49,52 @@
import ding.view.DNodeView;
import giny.view.NodeView;
+
/**
* The NodeChartViewer creates the actual custom graphics
*/
public class ViewUtils {
+
+ public enum Position {
+ CENTER ("center"),
+ EAST ("east"),
+ NORTH ("north"),
+ NORTHEAST ("northeast"),
+ NORTHWEST ("northwest"),
+ SOUTH ("south"),
+ SOUTHEAST ("southeast"),
+ SOUTHWEST ("southwest"),
+ WEST ("west");
+
+ private String label;
+ private static Map<String, Position>pMap;
+
+ Position(String label) {
+ this.label = label;
+ addPosition(this);
+ }
+
+ public String getLabel() {
+ return label;
+ }
+
+ public String toString() {
+ return label;
+ }
+
+ private void addPosition(Position pos) {
+ if (pMap == null) pMap = new HashMap<String,Position>();
+ pMap.put(pos.getLabel(), pos);
+ }
+
+ static Position getPosition(String label) {
+ if (pMap.containsKey(label))
+ return pMap.get(label);
+ return null;
+ }
+ }
+
+
public static void addCustomGraphics(List<CustomGraphic> cgList, CyNode
node, CyNetworkView view) {
// Get the DNodeView
NodeView nView = view.getNodeView(node);
@@ -59,7 +103,7 @@
}
}
- public static Rectangle2D getNodeBoundingBox(CyNode node, CyNetworkView
view) {
+ public static Rectangle2D getNodeBoundingBox(CyNode node, CyNetworkView
view, Object position) {
DNodeView nView = (DNodeView)view.getNodeView(node);
// Get the affine transform
@@ -67,6 +111,88 @@
double width = (nView.getWidth()-nView.getBorderWidth())*0.90;
// Create the bounding box.
- return new Rectangle2D.Double(-width/2, -height/2, width,
height);
+ Rectangle2D.Double bbox = new Rectangle2D.Double(-width/2,
-height/2, width, height);
+ return positionAdjust(bbox, position);
}
+
+ /**
+ * getPosition will return either a Point2D or a Position, depending on
whether
+ * the user provided us with a position keyword or a specific value.
+ *
+ * @param position the position argument
+ * @return a Point2D representing the X,Y offset specified by the user
or a Position
+ * enum that corresponds to the provided keyword. <b>null</b> is
returned if the input
+ * is illegal.
+ */
+ public static Object getPosition(String position) {
+ Position pos = Position.getPosition(position);
+ if (pos != null)
+ return pos;
+
+ String [] xy = position.split(",");
+ if (xy.length != 2) {
+ return null;
+ }
+
+ try {
+ Double x = Double.valueOf(xy[0]);
+ Double y = Double.valueOf(xy[1]);
+ return new Point2D.Double(x.doubleValue(),
y.doubleValue());
+ } catch (NumberFormatException e) {
+ return null;
+ }
+ }
+
+ private static Rectangle2D positionAdjust(Rectangle2D.Double bbox,
Object pos) {
+ if (pos == null)
+ return bbox;
+
+ double height = bbox.getHeight();
+ double width = bbox.getWidth();
+ double x = bbox.getX();
+ double y = bbox.getY();
+
+ if (pos instanceof Position) {
+ Position p = (Position) pos;
+
+ switch (p) {
+ case EAST:
+ x = width/2;
+ break;
+ case WEST:
+ x = -width*1.5;
+ break;
+ case NORTH:
+ y = -height*1.5;
+ break;
+ case SOUTH:
+ y = height/2;
+ break;
+ case NORTHEAST:
+ x = width/2;
+ y = -height*1.5;
+ break;
+ case NORTHWEST:
+ x = -width*1.5;
+ y = -height*1.5;
+ break;
+ case SOUTHEAST:
+ x = width/2;
+ y = height/2;
+ break;
+ case SOUTHWEST:
+ x = -width*1.5;
+ y = height/2;
+ break;
+ case CENTER:
+ default:
+ }
+ } else if (pos instanceof Point2D.Double) {
+ x += ((Point2D.Double)pos).getX();
+ y += ((Point2D.Double)pos).getY();
+ }
+
+ return new Rectangle2D.Double(x,y,width,height);
+ }
+
}
Modified: csplugins/trunk/ucsf/scooter/nodeCharts/test.com
===================================================================
--- csplugins/trunk/ucsf/scooter/nodeCharts/test.com 2010-09-02 00:15:38 UTC
(rev 21663)
+++ csplugins/trunk/ucsf/scooter/nodeCharts/test.com 2010-09-02 00:37:22 UTC
(rev 21664)
@@ -1,3 +1,13 @@
-nodecharts pie node="YCL067C" labellist="A,B,C,D" valuelist="1.0,2.0,0.5,5"
+nodecharts pie node="YCL067C" labellist="A,B,C,D" valuelist="1.0,2.0,0.5,5"
colorlist="#FF0000,#00FF00,#0000FF,#0000FF80"
nodecharts pie node="YKL101W" labellist="A,B,C,D,E,F"
valuelist="3.0,2.0,0.5,5,1,1.5"
+nodecharts pie node="YHR084W" labellist="A,B,C,D,E,F"
valuelist="3.0,2.0,0.5,5,1,1.5" position="north" colorlist="random"
+nodecharts pie node="YDR461W" labellist="A,B,C,D,E,F"
valuelist="3.0,2.0,0.5,5,1,1.5" position="south" colorlist="rainbow"
+nodecharts pie node="YFL026W" labellist="A,B,C,D,E,F"
valuelist="3.0,2.0,0.5,5,1,1.5" position="east" colorlist="modulated"
+nodecharts pie node="YGL008C" labellist="A,B,C,D,E,F"
valuelist="3.0,2.0,0.5,5,1,1.5" position="west" colorlist="contrasting"
+nodecharts pie node="YBR112C" labellist="A,B,C,D,E,F"
valuelist="3.0,2.0,0.5,5,1,1.5" position="northwest"
+nodecharts pie node="YCR084C" labellist="A,B,C,D,E,F"
valuelist="3.0,2.0,0.5,5,1,1.5" position="southwest"
+nodecharts pie node="YNL145W" labellist="A,B,C,D,E,F"
valuelist="3.0,2.0,0.5,5,1,1.5" position="northeast"
+nodecharts pie node="YIL015W" labellist="A,B,C,D,E,F"
valuelist="3.0,2.0,0.5,5,1,1.5" position="southeast"
+nodecharts pie node="YBL069W" labellist="A,B,C,D,E,F"
valuelist="3.0,2.0,0.5,5,1,1.5" position="10,10"
+
network view update
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