Author: kono
Date: 2012-06-01 07:54:24 -0700 (Fri, 01 Jun 2012)
New Revision: 29419
Modified:
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/plugin.props
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/PSI25VisualStyleBuilder.java
Log:
Version 0.31 release.
Modified: csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/plugin.props
===================================================================
--- csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/plugin.props
2012-06-01 12:05:37 UTC (rev 29418)
+++ csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/plugin.props
2012-06-01 14:54:24 UTC (rev 29419)
@@ -11,7 +11,7 @@
pluginDescription=PSICQUIC Web Service Universal Client. You can import
interactions from all public databases supporting PSICQUIC standard. This
plugin works with Cytoscape 2.8.x.
# Plugin version number, this must be two numbers separated by a decimlal.
Ex. 0.2, 14.03
-pluginVersion=0.30
+pluginVersion=0.31
# Compatible Cytoscape version
cytoscapeVersion=2.8
Modified:
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/PSI25VisualStyleBuilder.java
===================================================================
---
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/PSI25VisualStyleBuilder.java
2012-06-01 12:05:37 UTC (rev 29418)
+++
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/PSI25VisualStyleBuilder.java
2012-06-01 14:54:24 UTC (rev 29419)
@@ -21,7 +21,6 @@
import cytoscape.visual.calculators.BasicCalculator;
import cytoscape.visual.calculators.Calculator;
import cytoscape.visual.mappings.DiscreteMapping;
-import cytoscape.visual.mappings.ObjectMapping;
import cytoscape.visual.mappings.PassThroughMapping;
import ding.view.ObjectPositionImpl;
@@ -35,9 +34,12 @@
// Presets
private static final Color NODE_COLOR = new Color(0xee, 0xee, 0xee);
+ private static final Color NODE_LABEL_COLOR = new Color(0x36, 0x36,
0x36);
+
private static final Color EDGE_COLOR = new Color(0x9c, 0x9c, 0x9c);
+ private static final int EDGE_OPACITY = 160;
private static final Color EDGE_LABEL_COLOR = new Color(0xA2, 0xB5,
0xCD);
- private static final int EDGE_LABEL_OPACITY = 130;
+ private static final int EDGE_LABEL_OPACITY = 160;
private static final int EDGE_LABEL_SIZE = 9;
// Color presets for some model organisms
@@ -79,26 +81,14 @@
GlobalAppearanceCalculator gac =
defStyle.getGlobalAppearanceCalculator();
// Default values
- final int edgeOp = 110;
- final Color nodeLineColor = new Color(40, 40, 40);
- final Color nodeLabelColor = new Color(30, 30, 30);
-
- final Color nodeCompoundColor = new Color(100, 100, 100);
- final Color nodeNestedColor = Color.white;
-
- final Color edgeColor = NODE_COLOR;
+ final Color nodeLineColor = new Color(46, 46, 46);
final Font nodeLabelFont = new Font("Helvetica", Font.PLAIN,
14);
- // final Color nodeLabelColor = new Color(105,105,105);
+ // Network background
gac.setDefaultBackgroundColor(Color.white);
final PassThroughMapping m = new
PassThroughMapping(String.class, Mitab25Mapper.PREDICTED_GENE_NAME);
final Calculator calc = new BasicCalculator(DEF_VS_NAME + "-" +
"NodeLabelMapping", m, NODE_LABEL);
- // PassThroughMapping me = new PassThroughMapping("",
ATTR_PREFIX +
- // "interaction type");
- //
- // EdgeCalculator calce = new EdgeCalculator(DEF_VS_NAME + "-"
- // + "EdgeLabelMapping", me, null, EDGE_LABEL);
nac.setCalculator(calc);
nac.getDefaultAppearance().set(VisualPropertyType.NODE_FILL_COLOR, NODE_COLOR);
nac.getDefaultAppearance().set(VisualPropertyType.NODE_SHAPE,
NodeShape.RECT);
@@ -108,10 +98,9 @@
nac.getDefaultAppearance().set(VisualPropertyType.NODE_BORDER_COLOR,
nodeLineColor);
nac.getDefaultAppearance().set(VisualPropertyType.NODE_WIDTH,
25);
nac.getDefaultAppearance().set(VisualPropertyType.NODE_HEIGHT,
15);
-
nac.getDefaultAppearance().set(VisualPropertyType.NODE_LABEL_COLOR,
nodeLabelColor);
+
nac.getDefaultAppearance().set(VisualPropertyType.NODE_LABEL_COLOR,
NODE_LABEL_COLOR);
nac.getDefaultAppearance().set(VisualPropertyType.NODE_FONT_FACE,
nodeLabelFont);
- // TODO: this is for 2.8.0
nac.getDefaultAppearance().set(VisualPropertyType.NODE_LABEL_POSITION,
new ObjectPositionImpl(Position.SOUTH,
Position.NORTH_WEST, Justification.JUSTIFY_CENTER, -7, 1.0));
@@ -133,51 +122,50 @@
VisualPropertyType.NODE_FILL_COLOR);
nac.setCalculator(nodeColorCalc);
- DiscreteMapping nodeShapeMapping = new
DiscreteMapping(NodeShape.RECT, Mitab25Mapper.ATTR_PREFIX + "interactor type",
- ObjectMapping.NODE_MAPPING);
+ DiscreteMapping nodeShapeMapping = new
DiscreteMapping(NodeShape.class, Mitab25Mapper.ATTR_PREFIX
+ + "interactor type");
nodeShapeMapping.putMapValue("compound", NodeShape.ELLIPSE);
nodeShapeMapping.putMapValue("nested", NodeShape.ROUND_RECT);
final Calculator nodeShapeCalc = new
BasicCalculator(DEF_VS_NAME + "-" + "NodeShapeMapping", nodeShapeMapping,
VisualPropertyType.NODE_SHAPE);
nac.setCalculator(nodeShapeCalc);
- DiscreteMapping nodeWidthMapping = new DiscreteMapping(30,
Mitab25Mapper.ATTR_PREFIX + "interactor type",
- ObjectMapping.NODE_MAPPING);
+ DiscreteMapping nodeWidthMapping = new
DiscreteMapping(Number.class, Mitab25Mapper.ATTR_PREFIX
+ + "interactor type");
nodeWidthMapping.putMapValue("compound", 15);
nodeWidthMapping.putMapValue("nested", 100);
final Calculator nodeWidthCalc = new
BasicCalculator(DEF_VS_NAME + "-" + "NodeWidthMapping", nodeWidthMapping,
VisualPropertyType.NODE_WIDTH);
nac.setCalculator(nodeWidthCalc);
- DiscreteMapping nodeHeightMapping = new DiscreteMapping(30,
Mitab25Mapper.ATTR_PREFIX + "interactor type",
- ObjectMapping.NODE_MAPPING);
+ DiscreteMapping nodeHeightMapping = new
DiscreteMapping(Number.class, Mitab25Mapper.ATTR_PREFIX
+ + "interactor type");
nodeHeightMapping.putMapValue("compound", 15);
nodeHeightMapping.putMapValue("nested", 100);
final Calculator nodeHeightCalc = new
BasicCalculator(DEF_VS_NAME + "-" + "NodeHeightMapping",
nodeHeightMapping,
VisualPropertyType.NODE_HEIGHT);
nac.setCalculator(nodeHeightCalc);
- final PassThroughMapping edgeLabelMapping = new
PassThroughMapping(String.class, Mitab25Mapper.INTERACTION_TYPE_ATTR_NAME);
- final Calculator edgeCalc = new BasicCalculator(DEF_VS_NAME +
"-" + "EdgeLabelMapping", edgeLabelMapping, VisualPropertyType.EDGE_LABEL);
+ final PassThroughMapping edgeLabelMapping = new
PassThroughMapping(String.class,
+ Mitab25Mapper.INTERACTION_TYPE_ATTR_NAME);
+ final Calculator edgeCalc = new BasicCalculator(DEF_VS_NAME +
"-" + "EdgeLabelMapping", edgeLabelMapping,
+ VisualPropertyType.EDGE_LABEL);
eac.setCalculator(edgeCalc);
-
+
// eac.setCalculator(calce);
eac.getDefaultAppearance().set(VisualPropertyType.EDGE_COLOR,
EDGE_COLOR);
eac.getDefaultAppearance().set(VisualPropertyType.EDGE_LABEL_COLOR,
EDGE_LABEL_COLOR);
eac.getDefaultAppearance().set(VisualPropertyType.EDGE_FONT_SIZE,
EDGE_LABEL_SIZE);
- eac.getDefaultAppearance().set(VisualPropertyType.EDGE_OPACITY,
edgeOp);
-
eac.getDefaultAppearance().set(VisualPropertyType.EDGE_SRCARROW_OPACITY,
edgeOp);
-
eac.getDefaultAppearance().set(VisualPropertyType.EDGE_TGTARROW_OPACITY,
edgeOp);
+ eac.getDefaultAppearance().set(VisualPropertyType.EDGE_OPACITY,
EDGE_OPACITY);
+
eac.getDefaultAppearance().set(VisualPropertyType.EDGE_SRCARROW_OPACITY,
EDGE_OPACITY);
+
eac.getDefaultAppearance().set(VisualPropertyType.EDGE_TGTARROW_OPACITY,
EDGE_OPACITY);
eac.getDefaultAppearance().set(VisualPropertyType.EDGE_LABEL_OPACITY,
EDGE_LABEL_OPACITY);
eac.getDefaultAppearance().set(VisualPropertyType.EDGE_LINE_WIDTH, 1);
// Interaction Type mapping
- DiscreteMapping lineStyle = new
DiscreteMapping(LineStyle.SOLID, Mitab25Mapper.ATTR_PREFIX + "interaction type",
- ObjectMapping.EDGE_MAPPING);
- DiscreteMapping lineWidth = new DiscreteMapping(1.0,
Mitab25Mapper.ATTR_PREFIX + "interaction type",
- ObjectMapping.EDGE_MAPPING);
- DiscreteMapping edgeColorMap = new DiscreteMapping(Color.black,
Mitab25Mapper.ATTR_PREFIX + "interaction type",
- ObjectMapping.EDGE_MAPPING);
+ DiscreteMapping lineStyle = new
DiscreteMapping(LineStyle.class, Mitab25Mapper.ATTR_PREFIX + "interaction
type");
+ DiscreteMapping lineWidth = new DiscreteMapping(Number.class,
Mitab25Mapper.ATTR_PREFIX + "interaction type");
+ DiscreteMapping edgeColorMap = new DiscreteMapping(Color.class,
Mitab25Mapper.ATTR_PREFIX + "interaction type");
generateInteractionTypeMap(lineStyle, lineWidth, edgeColorMap);
final Calculator lineStyleCalc = new
BasicCalculator(DEF_VS_NAME + "-" + "EdgeLineStyleMapping", lineStyle,
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