Author: kono
Date: 2010-07-08 15:06:32 -0700 (Thu, 08 Jul 2010)
New Revision: 20860
Modified:
cytoscape/trunk/src/cytoscape/data/readers/CytoscapeSessionReader.java
cytoscape/trunk/src/cytoscape/data/writers/CytoscapeSessionWriter.java
cytoscape/trunk/src/cytoscape/visual/VisualMappingManager.java
cytoscape/trunk/src/cytoscape/visual/customgraphic/DefaultCyCustomGraphicsParser.java
cytoscape/trunk/src/cytoscape/visual/customgraphic/PersistImageTask.java
cytoscape/trunk/src/cytoscape/visual/customgraphic/URLImageCustomGraphicsParser.java
cytoscape/trunk/src/cytoscape/visual/customgraphic/impl/vector/GradientLayerCustomGraphics.java
cytoscape/trunk/src/cytoscape/visual/customgraphic/ui/CustomGraphicsBrowser.java
cytoscape/trunk/src/cytoscape/visual/customgraphic/ui/CustomGraphicsManagerDialog.java
cytoscape/trunk/src/cytoscape/visual/parsers/GraphicsParser.java
cytoscape/trunk/src/cytoscape/visual/properties/NodeCustomGraphicsProp.java
Log:
Comments are added to some classes related to Custom Graphics.
Modified: cytoscape/trunk/src/cytoscape/data/readers/CytoscapeSessionReader.java
===================================================================
--- cytoscape/trunk/src/cytoscape/data/readers/CytoscapeSessionReader.java
2010-07-08 21:13:33 UTC (rev 20859)
+++ cytoscape/trunk/src/cytoscape/data/readers/CytoscapeSessionReader.java
2010-07-08 22:06:32 UTC (rev 20860)
@@ -323,11 +323,13 @@
bookmarksFileURL = new URL("jar:" +
sourceURL.toString()
+ "!/" + entryName);
} else if (entryName.endsWith(".png")) {
+
// All bitmap images are saved as PNG
files.
final URL imageURL = new URL("jar:" +
sourceURL.toString()
+ "!/" + entryName);
- restoreCustomGraphics(entryName,
imageURL);
+ loadBitmapImageFiles(entryName,
imageURL);
} else if
(entryName.endsWith(CustomGraphicsManager.METADATA_FILE)) {
+ // This is the image property file.
imagePropsURL = new URL("jar:" +
sourceURL.toString()
+ "!/" + entryName);
} else
@@ -362,42 +364,55 @@
}
}
- private void restoreCustomGraphics(final String entryName,
- final URL imageURL) throws IOException {
+
+ private void loadBitmapImageFiles(final String entryName,
+ final URL imageFileURL) throws IOException {
final String[] ent = entryName.split(System
.getProperty("file.separator"));
final String displayName = ent[ent.length - 1];
String name = displayName.split("\\.")[0];
- imageMap.put(name, imageURL);
+ imageMap.put(name, imageFileURL);
}
- private void createCustomGraphics() throws IOException {
+ private void restoreCustomGraphics() throws IOException {
// Restore metadata
final Properties imageProps = new Properties();
imageProps.load(URLUtil.getBasicInputStream(imagePropsURL));
- // Remove all custom graphics
- final CustomGraphicsManager pool =
Cytoscape.getVisualMappingManager()
- .getCustomGraphicsPool();
- pool.removeAll();
+ // Remove all custom graphics from current session
+ final CustomGraphicsManager manager =
Cytoscape.getVisualMappingManager()
+ .getCustomGraphicsManager();
+ manager.removeAll();
+ // First, restore image-based custom graphics
for (String id : imageMap.keySet()) {
+
+ // Create Custom Graphics with specified ID.
final CyCustomGraphics graphics = new
URLImageCustomGraphics(Long.parseLong(id),
imageMap.get(id).toString());
+
+ // This property contains display name and tags.
final String propEntry = imageProps.getProperty(id);
+ if(propEntry == null)
+ continue;
- // Remove image prop.
+ // Remove this prop.
imageProps.remove(id);
- String[] parts = propEntry.split(",");
+ // Split string into blocks.
+ // This line should have: class Name, ID, name, tags.
+ final String[] parts = propEntry.split(",");
String name = parts[parts.length - 2];
if (name.contains("___"))
name = name.replace("___", ",");
+
+ // Set display name
graphics.setDisplayName(name);
+ // Restore tags
String tagStr = null;
if (parts.length > 3 && graphics instanceof Taggable) {
tagStr = parts[3];
@@ -406,19 +421,24 @@
+
AbstractDCustomGraphics.LIST_DELIMITER);
for (String tag : tagParts)
tags.add(tag.trim());
+
+ // Add all restored tags.
((Taggable) graphics).getTags().addAll(tags);
}
+
+ // If name is a valid URL, store as data source.
try {
final URL nameAsURL = new URL(name);
// The name is URL. Use as its source.
- final CyCustomGraphics currentValue =
pool.getBySourceURL(nameAsURL);
+ final CyCustomGraphics currentValue =
manager.getBySourceURL(nameAsURL);
// Add only if the graphics does not exist in
memory.
if(currentValue == null)
- pool.addGraphics(graphics, nameAsURL);
+ manager.addGraphics(graphics,
nameAsURL);
} catch (MalformedURLException e) {
- pool.addGraphics(graphics, null);
+ // Name is not an URL. These should be added
always.
+ manager.addGraphics(graphics, null);
}
}
@@ -426,17 +446,24 @@
System.out.println("Need to restore non-image graphics: " +
imageProps.size());
//TODO: Fix vector images
-// for(Object key:imageProps.keySet()) {
-// System.out.println("Key = " + key +", val = " +
imageProps.getProperty(key.toString()));
-// CyCustomGraphics<?> nonImage =
parser.parseStringValue(imageProps.getProperty(key.toString()));
-// pool.addGraphics(nonImage, null);
-// }
-
+
// Reset the counter
- final Long currentMax = pool.getIDSet().last();
+ final Long currentMax = manager.getIDSet().last();
IDGenerator.getIDGenerator().initCounter(currentMax+1);
}
+ private void restoreNonImageGraphics(final Properties imageProps, final
CustomGraphicsManager manager) {
+
+
+ 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);
+ }
+ }
+
/**
* Read a session file.
@@ -597,8 +624,9 @@
throw e;
}
+ // Need to restore custom graphics BEFORE Visual Styles.
if (imagePropsURL != null)
- createCustomGraphics();
+ restoreCustomGraphics();
if (loadVizmap) {
// restore vizmap.props
Modified: cytoscape/trunk/src/cytoscape/data/writers/CytoscapeSessionWriter.java
===================================================================
--- cytoscape/trunk/src/cytoscape/data/writers/CytoscapeSessionWriter.java
2010-07-08 21:13:33 UTC (rev 20859)
+++ cytoscape/trunk/src/cytoscape/data/writers/CytoscapeSessionWriter.java
2010-07-08 22:06:32 UTC (rev 20860)
@@ -364,7 +364,7 @@
private void zipCustomGraphics() throws IOException,
InterruptedException {
- final CustomGraphicsManager pool =
Cytoscape.getVisualMappingManager().getCustomGraphicsPool();
+ final CustomGraphicsManager pool =
Cytoscape.getVisualMappingManager().getCustomGraphicsManager();
// Collect all custom graphics
final Collection<CyCustomGraphics> customGraphics =
pool.getAll();
Modified: cytoscape/trunk/src/cytoscape/visual/VisualMappingManager.java
===================================================================
--- cytoscape/trunk/src/cytoscape/visual/VisualMappingManager.java
2010-07-08 21:13:33 UTC (rev 20859)
+++ cytoscape/trunk/src/cytoscape/visual/VisualMappingManager.java
2010-07-08 22:06:32 UTC (rev 20860)
@@ -442,7 +442,7 @@
myEdgeApp.applyAppearance(edgeView, activeVS.getDependency());
}
- public CustomGraphicsManager getCustomGraphicsPool() {
+ public CustomGraphicsManager getCustomGraphicsManager() {
return pool;
}
Modified:
cytoscape/trunk/src/cytoscape/visual/customgraphic/DefaultCyCustomGraphicsParser.java
===================================================================
---
cytoscape/trunk/src/cytoscape/visual/customgraphic/DefaultCyCustomGraphicsParser.java
2010-07-08 21:13:33 UTC (rev 20859)
+++
cytoscape/trunk/src/cytoscape/visual/customgraphic/DefaultCyCustomGraphicsParser.java
2010-07-08 22:06:32 UTC (rev 20860)
@@ -17,7 +17,7 @@
final Long id = Long.parseLong(parts[1]);
CyCustomGraphics cg = Cytoscape.getVisualMappingManager()
- .getCustomGraphicsPool().getByID(id);
+ .getCustomGraphicsManager().getByID(id);
if(cg == null) {
// Create new one by reflection
@@ -26,7 +26,7 @@
cg = (CyCustomGraphics) cls.newInstance();
cg.setDisplayName(parts[2]);
Cytoscape.getVisualMappingManager()
- .getCustomGraphicsPool().addGraphics(cg, null);
+ .getCustomGraphicsManager().addGraphics(cg,
null);
} catch (ClassNotFoundException e) {
e.printStackTrace();
return null;
Modified:
cytoscape/trunk/src/cytoscape/visual/customgraphic/PersistImageTask.java
===================================================================
--- cytoscape/trunk/src/cytoscape/visual/customgraphic/PersistImageTask.java
2010-07-08 21:13:33 UTC (rev 20859)
+++ cytoscape/trunk/src/cytoscape/visual/customgraphic/PersistImageTask.java
2010-07-08 22:06:32 UTC (rev 20860)
@@ -47,7 +47,7 @@
final long startTime = System.currentTimeMillis();
final CustomGraphicsManager pool =
Cytoscape.getVisualMappingManager()
- .getCustomGraphicsPool();
+ .getCustomGraphicsManager();
final ExecutorService exService = Executors
.newFixedThreadPool(NUM_THREADS);
Modified:
cytoscape/trunk/src/cytoscape/visual/customgraphic/URLImageCustomGraphicsParser.java
===================================================================
---
cytoscape/trunk/src/cytoscape/visual/customgraphic/URLImageCustomGraphicsParser.java
2010-07-08 21:13:33 UTC (rev 20859)
+++
cytoscape/trunk/src/cytoscape/visual/customgraphic/URLImageCustomGraphicsParser.java
2010-07-08 22:06:32 UTC (rev 20860)
@@ -36,7 +36,7 @@
final String imageName = entry[1];
CyCustomGraphics cg = Cytoscape.getVisualMappingManager()
-
.getCustomGraphicsPool().getByID(Long.parseLong(imageName));
+
.getCustomGraphicsManager().getByID(Long.parseLong(imageName));
cg.setDisplayName(entry[2]);
return cg;
}
Modified:
cytoscape/trunk/src/cytoscape/visual/customgraphic/impl/vector/GradientLayerCustomGraphics.java
===================================================================
---
cytoscape/trunk/src/cytoscape/visual/customgraphic/impl/vector/GradientLayerCustomGraphics.java
2010-07-08 21:13:33 UTC (rev 20859)
+++
cytoscape/trunk/src/cytoscape/visual/customgraphic/impl/vector/GradientLayerCustomGraphics.java
2010-07-08 22:06:32 UTC (rev 20860)
@@ -28,7 +28,7 @@
// Bound of this graphics
protected Shape bound;
- private static final float FIT = 1.0f;
+ private static final float FIT = 0.9f;
protected static final String COLOR1 = "Color 1";
protected static final String COLOR2 = "Color 2";
@@ -39,8 +39,8 @@
// Pre-Rendered image for icon.
protected BufferedImage rendered;
- private static final Color transparentWhite = new Color(255, 255, 255,
150);
- private static final Color transparentBlack = new Color(150, 150, 150,
100);
+ private static final Color transparentWhite = new Color(255, 255, 255,
100);
+ private static final Color transparentBlack = new Color(100, 100, 100,
100);
private static final int DEF_W = 100;
private static final int DEF_H = 100;
Modified:
cytoscape/trunk/src/cytoscape/visual/customgraphic/ui/CustomGraphicsBrowser.java
===================================================================
---
cytoscape/trunk/src/cytoscape/visual/customgraphic/ui/CustomGraphicsBrowser.java
2010-07-08 21:13:33 UTC (rev 20859)
+++
cytoscape/trunk/src/cytoscape/visual/customgraphic/ui/CustomGraphicsBrowser.java
2010-07-08 22:06:32 UTC (rev 20860)
@@ -56,7 +56,7 @@
* @throws IOException
*/
public CustomGraphicsBrowser() throws IOException {
- pool =
Cytoscape.getVisualMappingManager().getCustomGraphicsPool();
+ pool =
Cytoscape.getVisualMappingManager().getCustomGraphicsManager();
initComponents();
addAllImages();
Modified:
cytoscape/trunk/src/cytoscape/visual/customgraphic/ui/CustomGraphicsManagerDialog.java
===================================================================
---
cytoscape/trunk/src/cytoscape/visual/customgraphic/ui/CustomGraphicsManagerDialog.java
2010-07-08 21:13:33 UTC (rev 20859)
+++
cytoscape/trunk/src/cytoscape/visual/customgraphic/ui/CustomGraphicsManagerDialog.java
2010-07-08 22:06:32 UTC (rev 20860)
@@ -38,7 +38,7 @@
/** Creates new form CustomGraphicsManagerDialog */
public CustomGraphicsManagerDialog(java.awt.Frame parent, boolean
modal) {
super(parent, modal);
- pool =
Cytoscape.getVisualMappingManager().getCustomGraphicsPool();
+ pool =
Cytoscape.getVisualMappingManager().getCustomGraphicsManager();
initComponents();
try {
browser = new CustomGraphicsBrowser();
Modified: cytoscape/trunk/src/cytoscape/visual/parsers/GraphicsParser.java
===================================================================
--- cytoscape/trunk/src/cytoscape/visual/parsers/GraphicsParser.java
2010-07-08 21:13:33 UTC (rev 20859)
+++ cytoscape/trunk/src/cytoscape/visual/parsers/GraphicsParser.java
2010-07-08 22:06:32 UTC (rev 20860)
@@ -48,10 +48,10 @@
// Special case: URL String.
try {
final URL url = new URL(value);
- CyCustomGraphics graphics =
Cytoscape.getVisualMappingManager().getCustomGraphicsPool().getBySourceURL(url);
+ CyCustomGraphics graphics =
Cytoscape.getVisualMappingManager().getCustomGraphicsManager().getBySourceURL(url);
if(graphics == null) {
graphics = new
URLImageCustomGraphics(url.toString());
-
Cytoscape.getVisualMappingManager().getCustomGraphicsPool().addGraphics(graphics,
url);
+
Cytoscape.getVisualMappingManager().getCustomGraphicsManager().addGraphics(graphics,
url);
}
return graphics;
} catch (IOException e) {
Modified:
cytoscape/trunk/src/cytoscape/visual/properties/NodeCustomGraphicsProp.java
===================================================================
--- cytoscape/trunk/src/cytoscape/visual/properties/NodeCustomGraphicsProp.java
2010-07-08 21:13:33 UTC (rev 20859)
+++ cytoscape/trunk/src/cytoscape/visual/properties/NodeCustomGraphicsProp.java
2010-07-08 22:06:32 UTC (rev 20860)
@@ -272,7 +272,7 @@
public Map<Object, Icon> getIconSet() {
final Map<Object, Icon> customGraphicsIcons = new
HashMap<Object, Icon>();
final CustomGraphicsManager pool =
Cytoscape.getVisualMappingManager()
- .getCustomGraphicsPool();
+ .getCustomGraphicsManager();
for (CyCustomGraphics graphics : pool.getAll()) {
VisualPropertyIcon icon = (VisualPropertyIcon)
getIcon(graphics);
icon.setName(graphics.getDisplayName());
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
