Author: kono
Date: 2010-07-08 17:08:23 -0700 (Thu, 08 Jul 2010)
New Revision: 20863
Modified:
cytoscape/trunk/src/cytoscape/data/readers/CytoscapeSessionReader.java
cytoscape/trunk/src/cytoscape/visual/customgraphic/DefaultCyCustomGraphicsParser.java
cytoscape/trunk/src/cytoscape/visual/customgraphic/impl/vector/GradientLayerCustomGraphics.java
cytoscape/trunk/src/cytoscape/visual/customgraphic/impl/vector/GradientOvalLayer.java
cytoscape/trunk/src/cytoscape/visual/customgraphic/impl/vector/GradientRoundRectangleLayer.java
cytoscape/trunk/src/cytoscape/visual/parsers/GraphicsParser.java
Log:
Fixed vector graphics restore code. However, still update timing is broken.
Need to check redraw timing.
Modified: cytoscape/trunk/src/cytoscape/data/readers/CytoscapeSessionReader.java
===================================================================
--- cytoscape/trunk/src/cytoscape/data/readers/CytoscapeSessionReader.java
2010-07-08 22:57:16 UTC (rev 20862)
+++ cytoscape/trunk/src/cytoscape/data/readers/CytoscapeSessionReader.java
2010-07-09 00:08:23 UTC (rev 20863)
@@ -91,6 +91,7 @@
import cytoscape.visual.customgraphic.Taggable;
import cytoscape.visual.customgraphic.impl.AbstractDCustomGraphics;
import cytoscape.visual.customgraphic.impl.bitmap.URLImageCustomGraphics;
+import cytoscape.visual.parsers.GraphicsParser;
/**
* Reader to load CYtoscape Session file (.cys).<br>
@@ -405,6 +406,9 @@
// Split string into blocks.
// This line should have: class Name, ID, name, tags.
final String[] parts = propEntry.split(",");
+ if(parts.length < 3)
+ continue;
+
String name = parts[parts.length - 2];
if (name.contains("___"))
name = name.replace("___", ",");
@@ -446,7 +450,8 @@
System.out.println("Need to restore non-image graphics: " +
imageProps.size());
//TODO: Fix vector images
-
+ restoreNonImageGraphics(imageProps, manager);
+
// Reset the counter
final Long currentMax = manager.getIDSet().last();
IDGenerator.getIDGenerator().initCounter(currentMax+1);
@@ -456,14 +461,18 @@
for(Object key:imageProps.keySet()) {
-// System.out.println("Key = " + key +", val = " +
imageProps.getProperty(key.toString()));
-// final CyCustomGraphics cg =
parser.parseStringValue(imageProps.getProperty(key.toString()));
-//
-// if(cg != null)
-// manager.addGraphics(cg, null);
+ final String value =
imageProps.getProperty(key.toString());
+
+ System.out.println("Key = " + key +", val = " + value);
+ final CyCustomGraphics cg =
parser.parseStringValue(imageProps.getProperty(key.toString()));
+ System.out.println("CG result = " + cg);
+ if(cg != null)
+ manager.addGraphics(cg, null);
}
}
+ private final GraphicsParser parser = new GraphicsParser();
+
/**
* Read a session file.
Modified:
cytoscape/trunk/src/cytoscape/visual/customgraphic/DefaultCyCustomGraphicsParser.java
===================================================================
---
cytoscape/trunk/src/cytoscape/visual/customgraphic/DefaultCyCustomGraphicsParser.java
2010-07-08 22:57:16 UTC (rev 20862)
+++
cytoscape/trunk/src/cytoscape/visual/customgraphic/DefaultCyCustomGraphicsParser.java
2010-07-09 00:08:23 UTC (rev 20863)
@@ -1,5 +1,8 @@
package cytoscape.visual.customgraphic;
+import java.lang.reflect.Constructor;
+import java.lang.reflect.InvocationTargetException;
+
import cytoscape.Cytoscape;
public class DefaultCyCustomGraphicsParser implements CyCustomGraphicsParser {
@@ -15,15 +18,19 @@
final String className = parts[0];
final Long id = Long.parseLong(parts[1]);
+ final String name = parts[2];
- CyCustomGraphics cg = Cytoscape.getVisualMappingManager()
- .getCustomGraphicsManager().getByID(id);
+// CyCustomGraphics cg = Cytoscape.getVisualMappingManager()
+// .getCustomGraphicsManager().getByID(id);
+
+ CyCustomGraphics cg = null;
if(cg == null) {
// Create new one by reflection
try {
final Class<?> cls = Class.forName(className);
- cg = (CyCustomGraphics) cls.newInstance();
+ final Constructor<?> ct =
cls.getConstructor(Long.class, String.class);
+ cg = (CyCustomGraphics) ct.newInstance(id,
name);
cg.setDisplayName(parts[2]);
Cytoscape.getVisualMappingManager()
.getCustomGraphicsManager().addGraphics(cg,
null);
@@ -38,6 +45,18 @@
// TODO Auto-generated catch block
e.printStackTrace();
return null;
+ } catch (SecurityException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (NoSuchMethodException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (IllegalArgumentException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (InvocationTargetException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
}
}
Modified:
cytoscape/trunk/src/cytoscape/visual/customgraphic/impl/vector/GradientLayerCustomGraphics.java
===================================================================
---
cytoscape/trunk/src/cytoscape/visual/customgraphic/impl/vector/GradientLayerCustomGraphics.java
2010-07-08 22:57:16 UTC (rev 20862)
+++
cytoscape/trunk/src/cytoscape/visual/customgraphic/impl/vector/GradientLayerCustomGraphics.java
2010-07-09 00:08:23 UTC (rev 20863)
@@ -48,8 +48,8 @@
protected final Map<String, CustomGraphicsProperty<?>> props;
- public GradientLayerCustomGraphics(final String name) {
- super(name);
+ public GradientLayerCustomGraphics(final Long id, final String name) {
+ super(id, name);
width = DEF_W;
height = DEF_H;
props = new HashMap<String, CustomGraphicsProperty<?>>();
Modified:
cytoscape/trunk/src/cytoscape/visual/customgraphic/impl/vector/GradientOvalLayer.java
===================================================================
---
cytoscape/trunk/src/cytoscape/visual/customgraphic/impl/vector/GradientOvalLayer.java
2010-07-08 22:57:16 UTC (rev 20862)
+++
cytoscape/trunk/src/cytoscape/visual/customgraphic/impl/vector/GradientOvalLayer.java
2010-07-09 00:08:23 UTC (rev 20863)
@@ -5,7 +5,7 @@
import java.awt.geom.Ellipse2D;
import cytoscape.render.stateful.CustomGraphic;
-import cytoscape.visual.customgraphic.Layer;
+import cytoscape.visual.customgraphic.IDGenerator;
import cytoscape.visual.customgraphic.impl.DLayer;
import cytoscape.visual.customgraphic.paint.GradientPaintFactory;
@@ -14,10 +14,16 @@
// Name of this custom graphics.
private static final String NAME = "Glossy Oval Layer";
+
public GradientOvalLayer() {
- super(NAME);
+ this(IDGenerator.getIDGenerator().getNextId(), NAME);
}
+
+ public GradientOvalLayer(Long id, String name) {
+ super(id, name);
+ }
+
protected void renderImage(Graphics graphics) {
super.renderImage(graphics);
Modified:
cytoscape/trunk/src/cytoscape/visual/customgraphic/impl/vector/GradientRoundRectangleLayer.java
===================================================================
---
cytoscape/trunk/src/cytoscape/visual/customgraphic/impl/vector/GradientRoundRectangleLayer.java
2010-07-08 22:57:16 UTC (rev 20862)
+++
cytoscape/trunk/src/cytoscape/visual/customgraphic/impl/vector/GradientRoundRectangleLayer.java
2010-07-09 00:08:23 UTC (rev 20863)
@@ -5,6 +5,7 @@
import java.awt.geom.RoundRectangle2D;
import cytoscape.render.stateful.CustomGraphic;
+import cytoscape.visual.customgraphic.IDGenerator;
import cytoscape.visual.customgraphic.Layer;
import cytoscape.visual.customgraphic.impl.DLayer;
import cytoscape.visual.customgraphic.paint.GradientPaintFactory;
@@ -15,10 +16,16 @@
private static final String NAME = "Glossy Round Rectangle Layer";
private int r =20;
+
public GradientRoundRectangleLayer() {
- super(NAME);
+ this(IDGenerator.getIDGenerator().getNextId(), NAME);
}
+
+ public GradientRoundRectangleLayer(Long id, String name) {
+ super(id, name);
+ }
+
protected void renderImage(Graphics graphics) {
super.renderImage(graphics);
Modified: cytoscape/trunk/src/cytoscape/visual/parsers/GraphicsParser.java
===================================================================
--- cytoscape/trunk/src/cytoscape/visual/parsers/GraphicsParser.java
2010-07-08 22:57:16 UTC (rev 20862)
+++ cytoscape/trunk/src/cytoscape/visual/parsers/GraphicsParser.java
2010-07-09 00:08:23 UTC (rev 20863)
@@ -22,7 +22,6 @@
// Maybe injected from outside if we use DI framework.
private final CyCustomGraphicsParserFactory parserFactory;
-
private final CyCustomGraphicsParser defaultParser;
public GraphicsParser() {
@@ -41,32 +40,55 @@
return parse(value);
}
+
+ /**
+ * Parse given string.
+ *
+ * Syntax 1: (URL)
+ * Syntax 2: (Class Name, ID, Name, Tags)
+ *
+ * @param value
+ * @return
+ */
private CyCustomGraphics parse(String value) {
if(value == null || value.equals(NULL_CG))
return null;
- // Special case: URL String.
+ // Syntax 1: URL String.
try {
final URL url = new URL(value);
CyCustomGraphics graphics =
Cytoscape.getVisualMappingManager().getCustomGraphicsManager().getBySourceURL(url);
if(graphics == null) {
+ // Currently not in the Manager. Need to
create new instance.
graphics = new
URLImageCustomGraphics(url.toString());
+ // Use URL as display name
+ graphics.setDisplayName(value);
+
+ // Register to manager.
Cytoscape.getVisualMappingManager().getCustomGraphicsManager().addGraphics(graphics,
url);
}
return graphics;
} catch (IOException e) {
- logger.warn("Invalid URL found. This will be ignored: "
+ value);
+
+ // Syntax 2:
+ final String[] parts = value.split(",");
+ if(parts.length<4)
+ return null;
+
+ // Extract class name
+ final String className = parts[0];
+
+ // Get class-specific parser
+ final CyCustomGraphicsParser parser =
parserFactory.getParser(className);
+
+ if(parser == null)
+ return defaultParser.getInstance(value);
+ else
+ return parser.getInstance(value);
+
}
-
- final String[] parts = value.split(",");
- // Extract class
- final String className = parts[0];
- final CyCustomGraphicsParser parser =
parserFactory.getParser(className);
-
- if(parser == null)
- return defaultParser.getInstance(value);
- else
- return parser.getInstance(value);
}
+
+
}
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