Author: scooter
Date: 2010-12-21 13:04:24 -0800 (Tue, 21 Dec 2010)
New Revision: 23259
Modified:
csplugins/trunk/ucsf/scooter/nodeCharts/pom.xml
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/command/NodeChartCommandHandler.java
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/command/ValueUtils.java
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/BarChart.java
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/LineChart.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/StripeChart.java
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/ViewUtils.java
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/resources/nodeCharts/plugin.props
Log:
0.93: added ability to skip labels and a scale argument to allow for the
graphics to be larger or smaller than the default 90% of the node size
Modified: csplugins/trunk/ucsf/scooter/nodeCharts/pom.xml
===================================================================
--- csplugins/trunk/ucsf/scooter/nodeCharts/pom.xml 2010-12-21 20:38:00 UTC
(rev 23258)
+++ csplugins/trunk/ucsf/scooter/nodeCharts/pom.xml 2010-12-21 21:04:24 UTC
(rev 23259)
@@ -14,7 +14,7 @@
<groupId>cytoscape.csplugins</groupId>
<artifactId>nodeCharts</artifactId>
<packaging>jar</packaging>
- <version>0.91</version>
+ <version>0.93</version>
<name>Node Charts Plugin</name>
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
2010-12-21 20:38:00 UTC (rev 23258)
+++
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/command/NodeChartCommandHandler.java
2010-12-21 21:04:24 UTC (rev 23259)
@@ -81,6 +81,7 @@
public static final String NODE = "node";
public static final String NODELIST = "nodelist";
public static final String POSITION = "position";
+ public static final String SCALE = "scale";
public static final String SELECTED = "selected";
public static final String VALUES = "valuelist";
@@ -168,9 +169,6 @@
if (args.containsKey(VALUES) && args.containsKey(ATTRIBUTELIST))
throw new CyCommandException("nodecharts can't handle
both attributeslist and valuelist");
- if (!args.containsKey(LABELS) &&
!args.containsKey(ATTRIBUTELIST))
- throw new CyCommandException("nodecharts requires
either a labels list or an attribute list");
-
// Now get our actual viewer
NodeChartViewer viewer = viewerMap.get(command);
@@ -187,6 +185,15 @@
labels = ValueUtils.getStringList(args.get(LABELS));
}
+ double scale = 0.90;
+ if (args.containsKey(SCALE)) {
+ try {
+ scale =
ValueUtils.getDoubleValue(args.get(SCALE));
+ } catch (NumberFormatException e) {
+ throw new CyCommandException("Can't convert
"+args.get(SCALE).toString()+" to double");
+ }
+ }
+
// Get our position
Object pos = null;
if (args.containsKey(POSITION)) {
@@ -203,7 +210,7 @@
if (args.containsKey(ATTRIBUTELIST))
values = ValueUtils.getDataFromAttributes
(node, args.get(ATTRIBUTELIST), labels);
- List<CustomGraphic> cgList =
viewer.getCustomGraphics(args, values, labels, node, view, pos);
+ List<CustomGraphic> cgList =
viewer.getCustomGraphics(args, values, labels, node, view, pos, scale);
ViewUtils.addCustomGraphics(cgList, node, view);
result.addMessage("Created "+viewer.getName()+" chart
for node "+node.getIdentifier());
// If we succeeded, serialize the command and save it
in the appropriate nodeAttribute
@@ -223,6 +230,7 @@
addArgument(viewer.getName(), NODELIST);
addArgument(viewer.getName(), POSITION);
addArgument(viewer.getName(), VALUES);
+ addArgument(viewer.getName(), SCALE, "0.90");
// Get the specific commands handled by the viewer
Map<String,String> args = viewer.getOptions();
Modified:
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/command/ValueUtils.java
===================================================================
---
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/command/ValueUtils.java
2010-12-21 20:38:00 UTC (rev 23258)
+++
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/command/ValueUtils.java
2010-12-21 21:04:24 UTC (rev 23259)
@@ -190,6 +190,16 @@
return new ArrayList<String>();
}
+ public static double getDoubleValue(Object input) throws
NumberFormatException {
+ if (input instanceof Double)
+ return ((Double)input).doubleValue();
+ else if (input instanceof Integer)
+ return ((Integer)input).doubleValue();
+ else if (input instanceof String)
+ return Double.parseDouble((String)input);
+ throw new NumberFormatException("input can not be converted to
double");
+ }
+
/**
* Takes a map of objects indexed by a string keyword and returns
* a map of strings indexed by that keyword. This involves figuring
Modified:
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/BarChart.java
===================================================================
---
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/BarChart.java
2010-12-21 20:38:00 UTC (rev 23258)
+++
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/BarChart.java
2010-12-21 21:04:24 UTC (rev 23259)
@@ -53,7 +53,7 @@
public List<CustomGraphic> getCustomGraphics(Map<String, Object> args,
List<Double> values, List<String> labels, CyNode node,
- CyNetworkView view, Object position) throws
CyCommandException {
+ CyNetworkView view, Object position, double scale)
throws CyCommandException {
// Get our colors
List<Color> colors =
ValueUtils.convertInputToColor(args.get(COLORS), values);
@@ -68,7 +68,9 @@
}
// Sanity check
- if (labels.size() != values.size() || labels.size() !=
colors.size())
+ if (labels != null && labels.size() > 0 &&
+ (labels.size() != values.size() ||
+ labels.size() != colors.size()))
throw new CyCommandException("number of labels (" +
labels.size()
+ "), values (" + values.size() + "),
and colors ("
+ colors.size() + ") don't match");
@@ -78,7 +80,7 @@
// We need to get our bounding box in order to scale our graphic
// properly
- Rectangle2D bbox = ViewUtils.getNodeBoundingBox(node, view,
position);
+ Rectangle2D bbox = ViewUtils.getNodeBoundingBox(node, view,
position, scale);
double height = bbox.getHeight();
double width = bbox.getWidth();
@@ -138,25 +140,26 @@
cgList.add(c);
}
- // Now, create the labels. We want to do this here so we can
adjust the label for the slice
- for (int i = 0; i < values.size(); i++) {
-
- // add labels
- TextAlignment tAlign = TextAlignment.ALIGN_LEFT;
-
- // Now, create the label. Put the label on the outer
edge of the circle.
- Point2D labelPosition = new
Point2D.Double(barArray[i].getCenterX(), maxY);
- // vals[1] = ViewUtils.getLabelCustomGraphic(label,
null, 0, 0, labelPosition, tAlign, view);
- Shape textShape =
ViewUtils.getLabelShape(labels.get(i), null, 0, 0, view);
-
- double maxHeight = barArray[i].getWidth();
- textShape = ViewUtils.positionLabel(textShape,
labelPosition, tAlign, maxHeight, 0.0, 70.0);
- if (textShape == null) continue;
-
-// vals[1] = new CustomGraphic(textArea, new
DefaultPaintFactory(Color.BLACK));
- CustomGraphic c1 = new CustomGraphic(textShape, new
DefaultPaintFactory(Color.BLACK));
- cgList.add(c1);
-
+ if (labels != null && labels.size() > 0) {
+ // Now, create the labels. We want to do this here so
we can adjust the label for the slice
+ for (int i = 0; i < values.size(); i++) {
+
+ // add labels
+ TextAlignment tAlign = TextAlignment.ALIGN_LEFT;
+
+ // Now, create the label. Put the label on the
outer edge of the circle.
+ Point2D labelPosition = new
Point2D.Double(barArray[i].getCenterX(), maxY);
+ // vals[1] =
ViewUtils.getLabelCustomGraphic(label, null, 0, 0, labelPosition, tAlign, view);
+ Shape textShape =
ViewUtils.getLabelShape(labels.get(i), null, 0, 0, view);
+
+ double maxHeight = barArray[i].getWidth();
+ textShape = ViewUtils.positionLabel(textShape,
labelPosition, tAlign, maxHeight, 0.0, 70.0);
+ if (textShape == null) continue;
+
+ // vals[1] = new CustomGraphic(textArea, new
DefaultPaintFactory(Color.BLACK));
+ CustomGraphic c1 = new
CustomGraphic(textShape, new DefaultPaintFactory(Color.BLACK));
+ cgList.add(c1);
+ }
}
return cgList;
}
Modified:
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/LineChart.java
===================================================================
---
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/LineChart.java
2010-12-21 20:38:00 UTC (rev 23258)
+++
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/LineChart.java
2010-12-21 21:04:24 UTC (rev 23259)
@@ -42,13 +42,15 @@
public List<CustomGraphic> getCustomGraphics(Map<String, Object> args,
List<Double> values, List<String> labels, CyNode node,
- CyNetworkView view, Object position) throws
CyCommandException {
+ CyNetworkView view, Object position, double scale)
throws CyCommandException {
// Get our color
// Get our colors
List<Color> colors =
ValueUtils.convertInputToColor(args.get(COLORS), values);
// Sanity check
- if (labels.size() != values.size() || labels.size() !=
colors.size())
+ if (labels != null && labels.size() > 0 &&
+ (labels.size() != values.size() ||
+ labels.size() != colors.size()))
throw new CyCommandException("number of labels (" +
labels.size()
+ "), values (" + values.size() + "),
and colors ("
+ colors.size() + ") don't match");
@@ -58,7 +60,7 @@
// We need to get our bounding box in order to scale our graphic
// properly
- Rectangle2D bbox = ViewUtils.getNodeBoundingBox(node, view,
position);
+ Rectangle2D bbox = ViewUtils.getNodeBoundingBox(node, view,
position, scale);
double height = bbox.getHeight();
double width = bbox.getWidth();
double x = bbox.getX();
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
2010-12-21 20:38:00 UTC (rev 23258)
+++
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/NodeChartViewer.java
2010-12-21 21:04:24 UTC (rev 23259)
@@ -55,7 +55,7 @@
public Map<String,String> getOptions();
public List<CustomGraphic> getCustomGraphics(Map<String,Object>args,
List<Double> values, List<String> labels,
- CyNode node, CyNetworkView
view, Object position)
+ CyNode node, CyNetworkView
view, Object position, double scale)
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
2010-12-21 20:38:00 UTC (rev 23258)
+++
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/PieChart.java
2010-12-21 21:04:24 UTC (rev 23259)
@@ -89,7 +89,7 @@
}
public List<CustomGraphic> getCustomGraphics(Map<String, Object>args,
List<Double> values, List<String> labels,
- CyNode node, CyNetworkView
view, Object position)
+ CyNode node, CyNetworkView
view, Object position, double scale)
throws CyCommandException {
// Get our colors
List<Color> colors =
ValueUtils.convertInputToColor(args.get(COLORS), values);
@@ -98,16 +98,10 @@
double arcStart = 0.0;
Object startObj = args.get(ARCSTART);
if (startObj != null) {
- if (startObj instanceof Double)
- arcStart = ((Double)startObj).doubleValue();
- else if (startObj instanceof Integer)
- arcStart = ((Integer)startObj).doubleValue();
- else if (startObj instanceof String) {
- try {
- arcStart =
Double.parseDouble((String)startObj);
- } catch (NumberFormatException e) {
- throw new CyCommandException("arcstart
must be a number: "+e.getMessage());
- }
+ try {
+ arcStart = ValueUtils.getDoubleValue(startObj);
+ } catch (NumberFormatException e) {
+ throw new CyCommandException("arcstart must be
a number: "+e.getMessage());
}
}
@@ -115,29 +109,34 @@
values= convertData(values);
// Sanity check
- if (labels.size() != values.size() ||
- labels.size() != colors.size())
+ if (labels != null && labels.size() > 0 &&
+ (labels.size() != values.size() ||
+ labels.size() != colors.size()))
throw new CyCommandException("number of labels
("+labels.size()+"), values ("+
values.size()+"), and
colors ("+colors.size()+") don't match");
- int nSlices = labels.size();
+ int nSlices = values.size();
List<CustomGraphic> cgList = new ArrayList<CustomGraphic>();
List<CustomGraphic> labelList = new ArrayList<CustomGraphic>();
// We need to get our bounding box in order to scale our
graphic properly
- Rectangle2D bbox = ViewUtils.getNodeBoundingBox(node, view,
position);
+ Rectangle2D bbox = ViewUtils.getNodeBoundingBox(node, view,
position, scale);
// System.out.println("Node: "+node);
for (int slice = 0; slice < nSlices; slice++) {
- CustomGraphic[] cg = createSlice(bbox, arcStart,
values.get(slice), labels.get(slice), colors.get(slice), view);
+ String label = null;
+ if (labels != null && labels.size() > 0)
+ label = labels.get(slice);
+ CustomGraphic[] cg = createSlice(bbox, arcStart,
values.get(slice), label, colors.get(slice), view);
cgList.add(cg[0]);
if (cg[1] != null)
labelList.add(cg[1]);
arcStart += values.get(slice).doubleValue();
}
- cgList.addAll(labelList);
+ if (labelList != null && labelList.size() > 0)
+ cgList.addAll(labelList);
return cgList;
}
@@ -177,29 +176,28 @@
TextAlignment tAlign = getLabelAlignment(midpointAngle);
- // create the label
- Shape textShape = ViewUtils.getLabelShape(label, null, 0, 0,
view);
+ vals[1] = null;
+ if (label != null) {
+ // create the label
+ Shape textShape = ViewUtils.getLabelShape(label, null,
0, 0, view);
- // Now, position the label. Put the label on the outer edge of
the circle.
- Point2D labelPosition = getLabelPosition(bbox, midpointAngle,
1.4);
- // vals[1] = ViewUtils.getLabelCustomGraphic(label, null, 0, 0,
labelPosition, tAlign, view);
- textShape = ViewUtils.positionLabel(textShape, labelPosition,
tAlign, 0.0, 0.0, 0.0);
- if (textShape == null) {
- vals[1] = null;
- return vals;
- }
+ // Now, position the label. Put the label on the outer
edge of the circle.
+ Point2D labelPosition = getLabelPosition(bbox,
midpointAngle, 1.4);
+ // vals[1] = ViewUtils.getLabelCustomGraphic(label,
null, 0, 0, labelPosition, tAlign, view);
+ textShape = ViewUtils.positionLabel(textShape,
labelPosition, tAlign, 0.0, 0.0, 0.0);
+ if (textShape != null) {
+ // Draw a line between our label and the slice
+ labelPosition = getLabelPosition(bbox,
midpointAngle, 1.0);
+ Shape labelLine =
ViewUtils.getLabelLine(textShape.getBounds2D(), labelPosition, tAlign);
- // Draw a line between our label and the slice
- labelPosition = getLabelPosition(bbox, midpointAngle, 1.0);
- Shape labelLine =
ViewUtils.getLabelLine(textShape.getBounds2D(), labelPosition, tAlign);
+ // Combine the shapes
+ Area textArea = new Area(textShape);
+ textArea.add(new Area(labelLine));
- // Combine the shapes
- Area textArea = new Area(textShape);
- textArea.add(new Area(labelLine));
+ vals[1] = new CustomGraphic(textArea, new
DefaultPaintFactory(Color.BLACK));
+ }
+ }
-
- vals[1] = new CustomGraphic(textArea, new
DefaultPaintFactory(Color.BLACK));
-
return vals;
}
Modified:
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/StripeChart.java
===================================================================
---
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/StripeChart.java
2010-12-21 20:38:00 UTC (rev 23258)
+++
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/StripeChart.java
2010-12-21 21:04:24 UTC (rev 23259)
@@ -81,7 +81,7 @@
}
public List<CustomGraphic> getCustomGraphics(Map<String, Object> args,
List<Double> values, List<String> labels, CyNode node,
- CyNetworkView view, Object position) throws
CyCommandException {
+ CyNetworkView view, Object position, double scale)
throws CyCommandException {
// Get our colors
List<Color> colors =
ValueUtils.convertInputToColor(args.get(COLORS), values);
@@ -91,7 +91,7 @@
// We need to get our bounding box in order to scale our graphic
// properly
- Rectangle2D bbox = ViewUtils.getNodeBoundingBox(node, view,
position);
+ Rectangle2D bbox = ViewUtils.getNodeBoundingBox(node, view,
position, scale);
// System.out.println("Node: "+node);
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
2010-12-21 20:38:00 UTC (rev 23258)
+++
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/java/nodeCharts/view/ViewUtils.java
2010-12-21 21:04:24 UTC (rev 23259)
@@ -135,12 +135,12 @@
}
}
- public static Rectangle2D getNodeBoundingBox(CyNode node, CyNetworkView
view, Object position) {
+ public static Rectangle2D getNodeBoundingBox(CyNode node, CyNetworkView
view, Object position, double nodePortion) {
DNodeView nView = (DNodeView)view.getNodeView(node);
// Get the affine transform
- double height = (nView.getHeight()-nView.getBorderWidth())*0.90;
- double width = (nView.getWidth()-nView.getBorderWidth())*0.90;
+ double height =
(nView.getHeight()-nView.getBorderWidth())*nodePortion;
+ double width =
(nView.getWidth()-nView.getBorderWidth())*nodePortion;
// Create the bounding box.
Rectangle2D.Double bbox = new Rectangle2D.Double(-width/2,
-height/2, width, height);
Modified:
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/resources/nodeCharts/plugin.props
===================================================================
---
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/resources/nodeCharts/plugin.props
2010-12-21 20:38:00 UTC (rev 23258)
+++
csplugins/trunk/ucsf/scooter/nodeCharts/src/main/resources/nodeCharts/plugin.props
2010-12-21 21:04:24 UTC (rev 23259)
@@ -11,7 +11,7 @@
pluginDescription=Paint a chart on a node
# Plugin version number, this must be two numbers separated by a decimlal.
Ex. 0.2, 14.03
-pluginVersion=0.91
+pluginVersion=0.93
# Compatible Cytoscape version
cytoscapeVersion=2.8
@@ -29,6 +29,6 @@
projectURL=http://www.rbvi.ucsf.edu/Research/cytoscape/
# Date this plugin/plugin version was released
-releaseDate=December 17, 2010
+releaseDate=December 21, 2010
# -- The following properties should be set ONLY BY CORE PLUGINS -- #
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