Solved: SAX2 driver class org.apache.xerces.parsers.SAXParser not found; SVGConverter.error.while.rasterizing.file; cytoscape java.io.IOException: The AElfred parser is a SAX2

[Michi]

I had problems compiling the source code of cytoscape. I use Windows
XP and got the follwoing message:
SAX2 driver class org.apache.xerces.parsers.SAXParser not found
ans something like
SVGConverter.error.while.rasterizing.file

The compiler compiled the files with a lot of warnings but when you
run the code it was not possible to open cytoscape files.
The error was:
cytoscape java.io.IOException: The AElfred parser is a SAX2

I have found out that the problem was caused by the xerces lib files
that where not found during compilation.
I put the jar files for xerces, which can be downloaded at:
http://www.internet.bs/apache.org/xerces/j/ Xerces-J-bin.2.9.1.zip

to the following location
C:\Programme\Java\jre1.6.0_06\lib\ext
and then it worked well.

If someone knowd a better way, please let me know.

[Peng-Liang Wang]

Hi,

 

How did you compile Cytoscape? ant jar? Can you provide more detail about the output?

 

Thanks,

 

Peng

[Michi]

Hello Peng,

I am using Ecipse and it is using ant.
When I remove the lib's from lib/ext I get the following messages for
jar[default]:

Buildfile: H:\workspace_33\cytoscape-2.6.0\build.xml
prepare:
[mkdir] Created dir: H:\workspace_33\cytoscape-2.6.0\build
[mkdir] Created dir: H:\workspace_33\cytoscape-2.6.0\build\classes
[copy] Copying 126 files to H:\workspace_33\cytoscape-2.6.0\build
\classes\cytoscape\images
[copy] Copying 126 files to H:\workspace_33\cytoscape-2.6.0\build
\classes\cytoscape\view\images
[copy] Copying 26 files to H:\workspace_33\cytoscape-2.6.0\build
\classes\cytoscape\dialogs\images
[copy] Copying 33 files to H:\workspace_33\cytoscape-2.6.0\build
\classes\cytoscape\visual\ui\images
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\classes
Trying to override old definition of task xjc
Trying to override old definition of task rasterize
splash:
[echo]
[echo] ---------------------------------------
[echo] Creating splash and about screens
[echo] ---------------------------------------
[echo]
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\classes\cytoscape\images
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\classes\cytoscape\images
createSplash:
[rasterize] Rasterizing 1 image from SVG to image/png.
[rasterize] java.io.IOException: SAX2 driver class
org.apache.xerces.parsers.SAXParser not found
[rasterize] at
org.apache.batik.dom.util.SAXDocumentFactory.createDocument(Unknown
Source)
[rasterize] at
org.apache.batik.dom.util.SAXDocumentFactory.createDocument(Unknown
Source)
[rasterize] at
org.apache.batik.dom.svg.SAXSVGDocumentFactory.createDocument(Unknown
Source)
[rasterize] at
org.apache.batik.dom.svg.SAXSVGDocumentFactory.createDocument(Unknown
Source)
[rasterize] at
org.apache.batik.transcoder.XMLAbstractTranscoder.transcode(Unknown
Source)
[rasterize] at
org.apache.batik.transcoder.SVGAbstractTranscoder.transcode(Unknown
Source)
[rasterize] at
org.apache.batik.apps.rasterizer.SVGConverter.transcode(Unknown
Source)
[rasterize] at
org.apache.batik.apps.rasterizer.SVGConverter.execute(Unknown Source)
[rasterize] at
org.apache.tools.ant.taskdefs.optional.RasterizerTask.execute(Unknown
Source)
[rasterize] at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
[rasterize] at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown
Source)
[rasterize] at
sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
[rasterize] at java.lang.reflect.Method.invoke(Unknown Source)
[rasterize] at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:
105)
[rasterize] at org.apache.tools.ant.Task.perform(Task.java:348)
[rasterize] at org.apache.tools.ant.Target.execute(Target.java:357)
[rasterize] at org.apache.tools.ant.Target.performTasks(Target.java:
385)
[rasterize] at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1329)
[rasterize] at
org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:
38)
[rasterize] at
org.eclipse.ant.internal.ui.antsupport.EclipseSingleCheckExecutor.executeTargets(EclipseSingleCheckExecutor.java:
30)
[rasterize] at
org.apache.tools.ant.Project.executeTargets(Project.java:1181)
[rasterize] at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:
416)
[rasterize] at
org.apache.tools.ant.taskdefs.CallTarget.execute(CallTarget.java:105)
[rasterize] at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
[rasterize] at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown
Source)
[rasterize] at
sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
[rasterize] at java.lang.reflect.Method.invoke(Unknown Source)
[rasterize] at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:
105)
[rasterize] at org.apache.tools.ant.Task.perform(Task.java:348)
[rasterize] at org.apache.tools.ant.Target.execute(Target.java:357)
[rasterize] at org.apache.tools.ant.Target.performTasks(Target.java:
385)
[rasterize] at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1329)
[rasterize] at
org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:
38)
[rasterize] at
org.eclipse.ant.internal.ui.antsupport.EclipseSingleCheckExecutor.executeTargets(EclipseSingleCheckExecutor.java:
30)
[rasterize] at
org.apache.tools.ant.Project.executeTargets(Project.java:1181)
[rasterize] at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:
416)
[rasterize] at
org.apache.tools.ant.taskdefs.CallTarget.execute(CallTarget.java:105)
[rasterize] at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
[rasterize] at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown
Source)
[rasterize] at
sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
[rasterize] at java.lang.reflect.Method.invoke(Unknown Source)
[rasterize] at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:
105)
[rasterize] at org.apache.tools.ant.Task.perform(Task.java:348)
[rasterize] at org.apache.tools.ant.Target.execute(Target.java:357)
[rasterize] at org.apache.tools.ant.Target.performTasks(Target.java:
385)
[rasterize] at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1329)
[rasterize] at
org.apache.tools.ant.Project.executeTarget(Project.java:1298)
[rasterize] at
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:
41)
[rasterize] at
org.eclipse.ant.internal.ui.antsupport.EclipseDefaultExecutor.executeTargets(EclipseDefaultExecutor.java:
32)
[rasterize] at
org.apache.tools.ant.Project.executeTargets(Project.java:1181)
[rasterize] at
org.eclipse.ant.internal.ui.antsupport.InternalAntRunner.run(InternalAntRunner.java:
423)
[rasterize] at
org.eclipse.ant.internal.ui.antsupport.InternalAntRunner.main(InternalAntRunner.java:
137)
[rasterize] org.apache.batik.transcoder.TranscoderException: null
[rasterize] Enclosed Exception:
[rasterize] SAX2 driver class org.apache.xerces.parsers.SAXParser not
found
[rasterize] at
org.apache.batik.transcoder.XMLAbstractTranscoder.transcode(Unknown
Source)
[rasterize] at
org.apache.batik.transcoder.SVGAbstractTranscoder.transcode(Unknown
Source)
[rasterize] at
org.apache.batik.apps.rasterizer.SVGConverter.transcode(Unknown
Source)
[rasterize] at
org.apache.batik.apps.rasterizer.SVGConverter.execute(Unknown Source)
[rasterize] at
org.apache.tools.ant.taskdefs.optional.RasterizerTask.execute(Unknown
Source)
[rasterize] at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
[rasterize] at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown
Source)
[rasterize] at
sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
[rasterize] at java.lang.reflect.Method.invoke(Unknown Source)
[rasterize] at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:
105)
[rasterize] at org.apache.tools.ant.Task.perform(Task.java:348)
[rasterize] at org.apache.tools.ant.Target.execute(Target.java:357)
[rasterize] at org.apache.tools.ant.Target.performTasks(Target.java:
385)
[rasterize] at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1329)
[rasterize] at
org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:
38)
[rasterize] at
org.eclipse.ant.internal.ui.antsupport.EclipseSingleCheckExecutor.executeTargets(EclipseSingleCheckExecutor.java:
30)
[rasterize] at
org.apache.tools.ant.Project.executeTargets(Project.java:1181)
[rasterize] at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:
416)
[rasterize] at
org.apache.tools.ant.taskdefs.CallTarget.execute(CallTarget.java:105)
[rasterize] at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
[rasterize] at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown
Source)
[rasterize] at
sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
[rasterize] at java.lang.reflect.Method.invoke(Unknown Source)
[rasterize] at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:
105)
[rasterize] at org.apache.tools.ant.Task.perform(Task.java:348)
[rasterize] at org.apache.tools.ant.Target.execute(Target.java:357)
[rasterize] at org.apache.tools.ant.Target.performTasks(Target.java:
385)
[rasterize] at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1329)
[rasterize] at
org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:
38)
[rasterize] at
org.eclipse.ant.internal.ui.antsupport.EclipseSingleCheckExecutor.executeTargets(EclipseSingleCheckExecutor.java:
30)
[rasterize] at
org.apache.tools.ant.Project.executeTargets(Project.java:1181)
[rasterize] at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:
416)
[rasterize] at
org.apache.tools.ant.taskdefs.CallTarget.execute(CallTarget.java:105)
[rasterize] at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
[rasterize] at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown
Source)
[rasterize] at
sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
[rasterize] at java.lang.reflect.Method.invoke(Unknown Source)
[rasterize] at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:
105)
[rasterize] at org.apache.tools.ant.Task.perform(Task.java:348)
[rasterize] at org.apache.tools.ant.Target.execute(Target.java:357)
[rasterize] at org.apache.tools.ant.Target.performTasks(Target.java:
385)
[rasterize] at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1329)
[rasterize] at
org.apache.tools.ant.Project.executeTarget(Project.java:1298)
[rasterize] at
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:
41)
[rasterize] at
org.eclipse.ant.internal.ui.antsupport.EclipseDefaultExecutor.executeTargets(EclipseDefaultExecutor.java:
32)
[rasterize] at
org.apache.tools.ant.Project.executeTargets(Project.java:1181)
[rasterize] at
org.eclipse.ant.internal.ui.antsupport.InternalAntRunner.run(InternalAntRunner.java:
423)
[rasterize] at
org.eclipse.ant.internal.ui.antsupport.InternalAntRunner.main(InternalAntRunner.java:
137)
[rasterize] Unable to rasterize image 'CytoscapeSplashScreen.svg' to
'H:\workspace_33\cytoscape-2.6.0\build\classes\cytoscape\images
\CytoscapeSplashScreen.png': SVGConverter.error.while.rasterizing.file
[rasterize] Rasterizing 1 image from SVG to image/png.
[rasterize] java.io.IOException: SAX2 driver class
org.apache.xerces.parsers.SAXParser not found
[rasterize] at
org.apache.batik.dom.util.SAXDocumentFactory.createDocument(Unknown
Source)
[rasterize] at
org.apache.batik.dom.util.SAXDocumentFactory.createDocument(Unknown
Source)
[rasterize] at
org.apache.batik.dom.svg.SAXSVGDocumentFactory.createDocument(Unknown
Source)
[rasterize] at
org.apache.batik.dom.svg.SAXSVGDocumentFactory.createDocument(Unknown
Source)
[rasterize] at
org.apache.batik.transcoder.XMLAbstractTranscoder.transcode(Unknown
Source)
[rasterize] at
org.apache.batik.transcoder.SVGAbstractTranscoder.transcode(Unknown
Source)
[rasterize] at
org.apache.batik.apps.rasterizer.SVGConverter.transcode(Unknown
Source)
[rasterize] at
org.apache.batik.apps.rasterizer.SVGConverter.execute(Unknown Source)
[rasterize] at
org.apache.tools.ant.taskdefs.optional.RasterizerTask.execute(Unknown
Source)
[rasterize] at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
[rasterize] at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown
Source)
[rasterize] at
sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
[rasterize] at java.lang.reflect.Method.invoke(Unknown Source)
[rasterize] at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:
105)
[rasterize] at org.apache.tools.ant.Task.perform(Task.java:348)
[rasterize] at org.apache.tools.ant.Target.execute(Target.java:357)
[rasterize] at org.apache.tools.ant.Target.performTasks(Target.java:
385)
[rasterize] at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1329)
[rasterize] at
org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:
38)
[rasterize] at
org.eclipse.ant.internal.ui.antsupport.EclipseSingleCheckExecutor.executeTargets(EclipseSingleCheckExecutor.java:
30)
[rasterize] at
org.apache.tools.ant.Project.executeTargets(Project.java:1181)
[rasterize] at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:
416)
[rasterize] at
org.apache.tools.ant.taskdefs.CallTarget.execute(CallTarget.java:105)
[rasterize] at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
[rasterize] at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown
Source)
[rasterize] at
sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
[rasterize] at java.lang.reflect.Method.invoke(Unknown Source)
[rasterize] at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:
105)
[rasterize] at org.apache.tools.ant.Task.perform(Task.java:348)
[rasterize] at org.apache.tools.ant.Target.execute(Target.java:357)
[rasterize] at org.apache.tools.ant.Target.performTasks(Target.java:
385)
[rasterize] at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1329)
[rasterize] at
org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:
38)
[rasterize] at
org.eclipse.ant.internal.ui.antsupport.EclipseSingleCheckExecutor.executeTargets(EclipseSingleCheckExecutor.java:
30)
[rasterize] at
org.apache.tools.ant.Project.executeTargets(Project.java:1181)
[rasterize] at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:
416)
[rasterize] at
org.apache.tools.ant.taskdefs.CallTarget.execute(CallTarget.java:105)
[rasterize] at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
[rasterize] at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown
Source)
[rasterize] at
sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
[rasterize] at java.lang.reflect.Method.invoke(Unknown Source)
[rasterize] at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:
105)
[rasterize] at org.apache.tools.ant.Task.perform(Task.java:348)
[rasterize] at org.apache.tools.ant.Target.execute(Target.java:357)
[rasterize] at org.apache.tools.ant.Target.performTasks(Target.java:
385)
[rasterize] at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1329)
[rasterize] at
org.apache.tools.ant.Project.executeTarget(Project.java:1298)
[rasterize] at
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:
41)
[rasterize] at
org.eclipse.ant.internal.ui.antsupport.EclipseDefaultExecutor.executeTargets(EclipseDefaultExecutor.java:
32)
[rasterize] at
org.apache.tools.ant.Project.executeTargets(Project.java:1181)
[rasterize] at
org.eclipse.ant.internal.ui.antsupport.InternalAntRunner.run(InternalAntRunner.java:
423)
[rasterize] at
org.eclipse.ant.internal.ui.antsupport.InternalAntRunner.main(InternalAntRunner.java:
137)
[rasterize] org.apache.batik.transcoder.TranscoderException: null
[rasterize] Enclosed Exception:
[rasterize] SAX2 driver class org.apache.xerces.parsers.SAXParser not
found
[rasterize] at
org.apache.batik.transcoder.XMLAbstractTranscoder.transcode(Unknown
Source)
[rasterize] at
org.apache.batik.transcoder.SVGAbstractTranscoder.transcode(Unknown
Source)
[rasterize] at
org.apache.batik.apps.rasterizer.SVGConverter.transcode(Unknown
Source)
[rasterize] at
org.apache.batik.apps.rasterizer.SVGConverter.execute(Unknown Source)
[rasterize] at
org.apache.tools.ant.taskdefs.optional.RasterizerTask.execute(Unknown
Source)
[rasterize] at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
[rasterize] at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown
Source)
[rasterize] at
sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
[rasterize] at java.lang.reflect.Method.invoke(Unknown Source)
[rasterize] at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:
105)
[rasterize] at org.apache.tools.ant.Task.perform(Task.java:348)
[rasterize] at org.apache.tools.ant.Target.execute(Target.java:357)
[rasterize] at org.apache.tools.ant.Target.performTasks(Target.java:
385)
[rasterize] at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1329)
[rasterize] at
org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:
38)
[rasterize] at
org.eclipse.ant.internal.ui.antsupport.EclipseSingleCheckExecutor.executeTargets(EclipseSingleCheckExecutor.java:
30)
[rasterize] at
org.apache.tools.ant.Project.executeTargets(Project.java:1181)
[rasterize] at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:
416)
[rasterize] at
org.apache.tools.ant.taskdefs.CallTarget.execute(CallTarget.java:105)
[rasterize] at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
[rasterize] at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown
Source)
[rasterize] at
sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
[rasterize] at java.lang.reflect.Method.invoke(Unknown Source)
[rasterize] at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:
105)
[rasterize] at org.apache.tools.ant.Task.perform(Task.java:348)
[rasterize] at org.apache.tools.ant.Target.execute(Target.java:357)
[rasterize] at org.apache.tools.ant.Target.performTasks(Target.java:
385)
[rasterize] at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1329)
[rasterize] at
org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:
38)
[rasterize] at
org.eclipse.ant.internal.ui.antsupport.EclipseSingleCheckExecutor.executeTargets(EclipseSingleCheckExecutor.java:
30)
[rasterize] at
org.apache.tools.ant.Project.executeTargets(Project.java:1181)
[rasterize] at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:
416)
[rasterize] at
org.apache.tools.ant.taskdefs.CallTarget.execute(CallTarget.java:105)
[rasterize] at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
[rasterize] at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown
Source)
[rasterize] at
sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
[rasterize] at java.lang.reflect.Method.invoke(Unknown Source)
[rasterize] at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:
105)
[rasterize] at org.apache.tools.ant.Task.perform(Task.java:348)
[rasterize] at org.apache.tools.ant.Target.execute(Target.java:357)
[rasterize] at org.apache.tools.ant.Target.performTasks(Target.java:
385)
[rasterize] at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1329)
[rasterize] at
org.apache.tools.ant.Project.executeTarget(Project.java:1298)
[rasterize] at
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:
41)
[rasterize] at
org.eclipse.ant.internal.ui.antsupport.EclipseDefaultExecutor.executeTargets(EclipseDefaultExecutor.java:
32)
[rasterize] at
org.apache.tools.ant.Project.executeTargets(Project.java:1181)
[rasterize] at
org.eclipse.ant.internal.ui.antsupport.InternalAntRunner.run(InternalAntRunner.java:
423)
[rasterize] at
org.eclipse.ant.internal.ui.antsupport.InternalAntRunner.main(InternalAntRunner.java:
137)
[rasterize] Unable to rasterize image 'CytoscapeCredits.svg' to 'H:
\workspace_33\cytoscape-2.6.0\build\classes\cytoscape\images
\CytoscapeCredits.png': SVGConverter.error.while.rasterizing.file
bind:
[xjc] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\generated is
not found and thus excluded from the dependency check
[xjc] Compiling file:/H:/workspace_33/cytoscape-2.6.0/resources/
schema/cysession.xsd
[xjc] Writing output to H:\workspace_33\cytoscape-2.6.0\src
[xjc] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\bookmarks is
not found and thus excluded from the dependency check
[xjc] Compiling file:/H:/workspace_33/cytoscape-2.6.0/resources/
schema/bookmarks.xsd
[xjc] Writing output to H:\workspace_33\cytoscape-2.6.0\src
[echo] Copying jaxb.properties from H:
\workspace_33\cytoscape-2.6.0/src/cytoscape/generated to build dir...
compile:
[javac] Compiling 739 source files to H:
\workspace_33\cytoscape-2.6.0\build\classes
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\view
\CytoscapeDesktop.java:79: warning: [deprecation]
cytoscape.visual.ui.VizMapUI in cytoscape.visual.ui has been
deprecated
[javac] import cytoscape.visual.ui.VizMapUI;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\view
\CyNetworkView.java:107: warning: [deprecation]
cytoscape.visual.ui.VizMapUI in cytoscape.visual.ui has been
deprecated
[javac] public cytoscape.visual.ui.VizMapUI getVizMapUI();
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\view
\CytoscapeDesktop.java:200: warning: [deprecation]
cytoscape.visual.ui.VizMapUI in cytoscape.visual.ui has been
deprecated
[javac] protected VizMapUI vizMapUI;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\EdgeAppearanceCalculator.java:49: warning: [deprecation]
cytoscape.visual.calculators.EdgeArrowCalculator in
cytoscape.visual.calculators has been deprecated
[javac] import cytoscape.visual.calculators.EdgeArrowCalculator;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\EdgeAppearanceCalculator.java:50: warning: [deprecation]
cytoscape.visual.calculators.EdgeColorCalculator in
cytoscape.visual.calculators has been deprecated
[javac] import cytoscape.visual.calculators.EdgeColorCalculator;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\EdgeAppearanceCalculator.java:51: warning: [deprecation]
cytoscape.visual.calculators.EdgeFontFaceCalculator in
cytoscape.visual.calculators has been deprecated
[javac] import
cytoscape.visual.calculators.EdgeFontFaceCalculator;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\EdgeAppearanceCalculator.java:52: warning: [deprecation]
cytoscape.visual.calculators.EdgeFontSizeCalculator in
cytoscape.visual.calculators has been deprecated
[javac] import
cytoscape.visual.calculators.EdgeFontSizeCalculator;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\EdgeAppearanceCalculator.java:53: warning: [deprecation]
cytoscape.visual.calculators.EdgeLabelCalculator in
cytoscape.visual.calculators has been deprecated
[javac] import cytoscape.visual.calculators.EdgeLabelCalculator;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\EdgeAppearanceCalculator.java:54: warning: [deprecation]
cytoscape.visual.calculators.EdgeLineTypeCalculator in
cytoscape.visual.calculators has been deprecated
[javac] import
cytoscape.visual.calculators.EdgeLineTypeCalculator;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\EdgeAppearanceCalculator.java:55: warning: [deprecation]
cytoscape.visual.calculators.EdgeToolTipCalculator in
cytoscape.visual.calculators has been deprecated
[javac] import cytoscape.visual.calculators.EdgeToolTipCalculator;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\VizMapUI.java:406: warning: [deprecation]
cytoscape.visual.ui.VizMapTab in cytoscape.visual.ui has been
deprecated
[javac] private void addTab(List<VizMapTab> tabs, JTabbedPane
pane, VizMapTab t) {
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\VizMapUI.java:406: warning: [deprecation]
cytoscape.visual.ui.VizMapTab in cytoscape.visual.ui has been
deprecated
[javac] private void addTab(List<VizMapTab> tabs, JTabbedPane
pane, VizMapTab t) {

[javac]
^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\VizMapUI.java:967: warning: [deprecation]
cytoscape.visual.ui.VizMapTab in cytoscape.visual.ui has been
deprecated
[javac] VizMapTab checkCalcSelected(Calculator selectedCalc) {
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\actions
\ImportBioDataServerAction.java:43: warning: [deprecation]
cytoscape.data.servers.ui.GeneOntologyWizard in
cytoscape.data.servers.ui has been deprecated
[javac] import cytoscape.data.servers.ui.GeneOntologyWizard;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\actions
\ImportBioDataServerAction.java:59: warning: [deprecation]
cytoscape.data.servers.ui.GeneOntologyWizard in
cytoscape.data.servers.ui has been deprecated
[javac] GeneOntologyWizard wiz;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\ding
\DingNetworkView.java:59: warning: [deprecation]
cytoscape.visual.ui.VizMapUI in cytoscape.visual.ui has been
deprecated
[javac] import cytoscape.visual.ui.VizMapUI;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\ding
\DingNetworkView.java:192: warning: [deprecation]
cytoscape.visual.ui.VizMapUI in cytoscape.visual.ui has been
deprecated
[javac] public VizMapUI getVizMapUI() {
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\giny
\PhoebeNetworkView.java:395: warning: [deprecation]
cytoscape.visual.ui.VizMapUI in cytoscape.visual.ui has been
deprecated
[javac] public cytoscape.visual.ui.VizMapUI getVizMapUI() {
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\calculators\EdgeLineTypeCalculator.java:47: warning: [deprecation]
cytoscape.visual.LineType in cytoscape.visual has been deprecated
[javac] import cytoscape.visual.LineType;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\calculators\GenericEdgeLineTypeCalculator.java:48: warning:
[deprecation] cytoscape.visual.LineType in cytoscape.visual has been
deprecated
[javac] import cytoscape.visual.LineType;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\calculators\GenericNodeLineTypeCalculator.java:47: warning:
[deprecation] cytoscape.visual.LineType in cytoscape.visual has been
deprecated
[javac] import cytoscape.visual.LineType;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\calculators\NodeLineTypeCalculator.java:47: warning: [deprecation]
cytoscape.visual.LineType in cytoscape.visual has been deprecated
[javac] import cytoscape.visual.LineType;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\ContinuousMapping.java:47: warning: [deprecation]
cytoscape.visual.ShapeNodeRealizer in cytoscape.visual has been
deprecated
[javac] import cytoscape.visual.ShapeNodeRealizer;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\ContinuousMapping.java:56: warning: [deprecation]
cytoscape.visual.mappings.continuous.ContinuousUI in
cytoscape.visual.mappings.continuous has been deprecated
[javac] import cytoscape.visual.mappings.continuous.ContinuousUI;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\DiscreteMapping.java:56: warning: [deprecation]
cytoscape.visual.ShapeNodeRealizer in cytoscape.visual has been
deprecated
[javac] import cytoscape.visual.ShapeNodeRealizer;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\PassThroughMapping.java:47: warning: [deprecation]
cytoscape.visual.ShapeNodeRealizer in cytoscape.visual has been
deprecated
[javac] import cytoscape.visual.ShapeNodeRealizer;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\continuous\ContinuousUI.java:64: warning: [deprecation]
cytoscape.visual.ui.ValueDisplayer in cytoscape.visual.ui has been
deprecated
[javac] import cytoscape.visual.ui.ValueDisplayer;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\continuous\AddPointListener.java:59: warning: [deprecation]
cytoscape.visual.mappings.continuous.ContinuousUI in
cytoscape.visual.mappings.continuous has been deprecated
[javac] private ContinuousUI ui = null;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\continuous\DeletePointListener.java:57: warning:
[deprecation] cytoscape.visual.mappings.continuous.ContinuousUI in
cytoscape.visual.mappings.continuous has been deprecated
[javac] private ContinuousUI ui;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\continuous\ValueListener.java:50: warning: [deprecation]
cytoscape.visual.ui.ValueDisplayer in cytoscape.visual.ui has been
deprecated
[javac] import cytoscape.visual.ui.ValueDisplayer;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\continuous\ValueListener.java:58: warning: [deprecation]
cytoscape.visual.mappings.continuous.ContinuousUI in
cytoscape.visual.mappings.continuous has been deprecated
[javac] private ContinuousUI ui;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\continuous\ValueListener.java:68: warning: [deprecation]
cytoscape.visual.mappings.continuous.ContinuousUI in
cytoscape.visual.mappings.continuous has been deprecated
[javac] public ValueListener(ContinuousUI ui,
ContinuousMapping cm, int index,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\discrete\DiscreteUI.java:54: warning: [deprecation]
cytoscape.visual.ui.ValueDisplayer in cytoscape.visual.ui has been
deprecated
[javac] import cytoscape.visual.ui.ValueDisplayer;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\ValueDisplayer.java:43: warning: [deprecation]
cytoscape.visual.LineType in cytoscape.visual has been deprecated
[javac] import cytoscape.visual.LineType;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\discrete\DiscreteUI.java:206: warning: [deprecation]
cytoscape.visual.ui.ValueDisplayer in cytoscape.visual.ui has been
deprecated
[javac] void swapValueDisplayer(ValueDisplayer valueDisplayer,
int position,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\discrete\DiscreteUI.java:225: warning: [deprecation]
cytoscape.visual.ui.ValueDisplayer in cytoscape.visual.ui has been
deprecated
[javac] private ValueDisplayer getMapValue(Object
currentMapping) {
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\discrete\ValueChangeListener.java:47: warning: [deprecation]
cytoscape.visual.ui.ValueDisplayer in cytoscape.visual.ui has been
deprecated
[javac] import cytoscape.visual.ui.ValueDisplayer;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\parsers\LineTypeParser.java:47: warning: [deprecation]
cytoscape.visual.LineType in cytoscape.visual has been deprecated
[javac] import cytoscape.visual.LineType;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\parsers\LineTypeParser.java:77: warning: [deprecation]
cytoscape.visual.LineType in cytoscape.visual has been deprecated
[javac] public LineType parseLineType(String value) {
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\parsers\NodeShapeParser.java:48: warning: [deprecation]
cytoscape.visual.ShapeNodeRealizer in cytoscape.visual has been
deprecated
[javac] import cytoscape.visual.ShapeNodeRealizer;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\parsers\ObjectToString.java:49: warning: [deprecation]
cytoscape.visual.LineType in cytoscape.visual has been deprecated
[javac] import cytoscape.visual.LineType;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\parsers\ObjectToString.java:51: warning: [deprecation]
cytoscape.visual.ShapeNodeRealizer in cytoscape.visual has been
deprecated
[javac] import cytoscape.visual.ShapeNodeRealizer;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\parsers\ParserFactory.java:47: warning: [deprecation]
cytoscape.visual.LineType in cytoscape.visual has been deprecated
[javac] import cytoscape.visual.LineType;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\properties\EdgeLineWidthProp.java:40: warning: [deprecation]
cytoscape.visual.LineType in cytoscape.visual has been deprecated
[javac] import cytoscape.visual.LineType;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\DefaultPanel.java:95: warning: [deprecation]
cytoscape.visual.ui.VizMapUI in cytoscape.visual.ui has been
deprecated
[javac] public DefaultPanel(VizMapUI parentDialog,
VisualMappingManager vmm) {
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\EdgeBypass.java:45: warning: [deprecation] cytoscape.visual.LineType
in cytoscape.visual has been deprecated
[javac] import cytoscape.visual.LineType;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\IconSupport.java:47: warning: [deprecation]
cytoscape.visual.ui.ValueDisplayer in cytoscape.visual.ui has been
deprecated
[javac] import static cytoscape.visual.ui.ValueDisplayer.ARROW;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\IconSupport.java:48: warning: [deprecation]
cytoscape.visual.ui.ValueDisplayer in cytoscape.visual.ui has been
deprecated
[javac] import static cytoscape.visual.ui.ValueDisplayer.LINETYPE;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\IconSupport.java:49: warning: [deprecation]
cytoscape.visual.ui.ValueDisplayer in cytoscape.visual.ui has been
deprecated
[javac] import static
cytoscape.visual.ui.ValueDisplayer.NODESHAPE;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\IconSupport.java:64: warning: [deprecation] cytoscape.visual.LineType
in cytoscape.visual has been deprecated
[javac] import cytoscape.visual.LineType;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\ValueDisplayer.java:447: warning: [deprecation]
cytoscape.visual.ui.IconSupport in cytoscape.visual.ui has been
deprecated
[javac] private IconSupport is;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\ValueDisplayer.java:449: warning: [deprecation]
cytoscape.visual.ui.IconSupport in cytoscape.visual.ui has been
deprecated
[javac] IconListener(String title, String objectName,
IconSupport is,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\VizMapAttrTab.java:163: warning: [deprecation]
cytoscape.visual.ui.VizMapUI in cytoscape.visual.ui has been
deprecated
[javac] public VizMapAttrTab(VizMapUI mainUI, JTabbedPane
tabContainer, int tabIndex,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\VizMapAttrTab.java:806: warning: [deprecation]
cytoscape.visual.ui.VizMapTab in cytoscape.visual.ui has been
deprecated
[javac] VizMapTab checkCalcSelected(Calculator c) {
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\VizMapFontTab.java:81: warning: [deprecation]
cytoscape.visual.ui.VizMapUI in cytoscape.visual.ui has been
deprecated
[javac] public VizMapFontTab(VizMapUI mainUI, JTabbedPane
tabContainer,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\VizMapFontTab.java:137: warning: [deprecation]
cytoscape.visual.ui.VizMapTab in cytoscape.visual.ui has been
deprecated
[javac] VizMapTab checkCalcSelected(Calculator c) {
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\VizMapSizeTab.java:67: warning: [deprecation]
cytoscape.visual.ui.VizMapTab in cytoscape.visual.ui has been
deprecated
[javac] public class VizMapSizeTab extends VizMapTab {
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\VizMapSizeTab.java:71: warning: [deprecation]
cytoscape.visual.ui.VizMapAttrTab in cytoscape.visual.ui has been
deprecated
[javac] private VizMapAttrTab height;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\VizMapSizeTab.java:72: warning: [deprecation]
cytoscape.visual.ui.VizMapAttrTab in cytoscape.visual.ui has been
deprecated
[javac] private VizMapAttrTab width;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\VizMapSizeTab.java:73: warning: [deprecation]
cytoscape.visual.ui.VizMapAttrTab in cytoscape.visual.ui has been
deprecated
[javac] private VizMapAttrTab size;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\VizMapSizeTab.java:76: warning: [deprecation]
cytoscape.visual.ui.VizMapUI in cytoscape.visual.ui has been
deprecated
[javac] private VizMapUI mainUIDialog;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\VizMapSizeTab.java:93: warning: [deprecation]
cytoscape.visual.ui.VizMapUI in cytoscape.visual.ui has been
deprecated
[javac] public VizMapSizeTab(VizMapUI mainUI, JTabbedPane
tabContainer,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\VizMapSizeTab.java:117: warning: [deprecation]
cytoscape.visual.ui.VizMapUI in cytoscape.visual.ui has been
deprecated
[javac] public VizMapSizeTab(VizMapUI mainUI, JTabbedPane
tabContainer,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\VizMapSizeTab.java:272: warning: [deprecation]
cytoscape.visual.ui.VizMapTab in cytoscape.visual.ui has been
deprecated
[javac] VizMapTab checkCalcSelected(Calculator c) {
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\VizUIUtilities.java:45: warning: [deprecation]
cytoscape.visual.ShapeNodeRealizer in cytoscape.visual has been
deprecated
[javac] import cytoscape.visual.ShapeNodeRealizer;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\icon\LineTypeIcon.java:39: warning: [deprecation]
cytoscape.visual.LineType in cytoscape.visual has been deprecated
[javac] import cytoscape.visual.LineType;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\CyNode.java:
90: warning: [deprecation]
setGraphPerspective(giny.model.GraphPerspective) in giny.model.Node
has been deprecated
[javac] public boolean setGraphPerspective(GraphPerspective gp) {
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\CyNode.java:
78: warning: [deprecation] getGraphPerspective() in giny.model.Node
has been deprecated
[javac] public GraphPerspective getGraphPerspective() {
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\data
\SelectFilter.java:375: warning: [deprecation] getHiddenNodes() in
giny.model.GraphPerspectiveChangeEvent has been deprecated
[javac] Node[] hiddenNodes = event.getHiddenNodes();
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\view
\NetworkViewManager.java:104: warning: [deprecation] getHelpBroker()
in cytoscape.view.CytoscapeDesktop has been deprecated
[javac] cytoscapeDesktop.getHelpBroker().enableHelp(desktopPane,
"network-view-manager", null);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\VisualPropertyType.java:108: warning: [deprecation]
cytoscape.visual.LineType in cytoscape.visual has been deprecated
[javac] "defaultNodeLineType", LineType.class,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\VisualPropertyType.java:144: warning: [deprecation]
cytoscape.visual.LineType in cytoscape.visual has been deprecated
[javac] "defaultEdgeLineType", LineType.class,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\GlobalAppearanceCalculator.java:194: warning: [deprecation]
setSloppySelectionColor(java.awt.Color) in
cytoscape.visual.GlobalAppearance has been deprecated
[javac]
appr.setSloppySelectionColor(calculateSloppySelectionColor(network));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape
\CytoscapeInit.java:504: warning: [deprecation] toURL() in
java.io.File has been deprecated
[javac] URL sessionURL = shortName.toURL();
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\actions
\GinyUtils.java:96: warning: [deprecation]
getEdgeIndicesArray(int,int,boolean,boolean) in
giny.model.GraphPerspective has been deprecated
[javac]
.getEdgeIndicesArray(nview.getGraphPerspectiveIndex(),
na[i2],
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\actions
\GinyUtils.java:151: warning: [deprecation]
getEdgeIndicesArray(int,int,boolean) in giny.model.GraphPerspective
has been deprecated
[javac]
.getEdgeIndicesArray(nview.getGraphPerspectiveIndex(),
na[i2],
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\actions
\GinyUtils.java:254: warning: [deprecation]
neighborsList(giny.model.Node) in giny.model.GraphPerspective has been
deprecated
[javac] for (Iterator ni =
graphPerspective.neighborsList(n).iterator(); ni.hasNext();) {
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\actions
\ImportBioDataServerAction.java:84: warning: [deprecation]
cytoscape.data.servers.ui.GeneOntologyWizard in
cytoscape.data.servers.ui has been deprecated
[javac] wiz = new GeneOntologyWizard();
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\actions
\ImportExpressionMatrixAction.java:96: warning: [deprecation] show()
in java.awt.Dialog has been deprecated
[javac] amd.show();
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\dialogs
\plugins\PluginManageDialog.java:375: warning: [deprecation]
getLicenseText() in cytoscape.plugin.PluginInfo has been deprecated
[javac] if (pInfo.getLicenseText() != null) {
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\actions
\SelectFirstNeighborsAction.java:89: warning: [deprecation]
neighborsList(giny.model.Node) in giny.model.GraphPerspective has been
deprecated
[javac]
currentNetwork.setSelectedNodeState(currentNetwork.neighborsList((Node)
it.next()), true);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\data
\CyAttributesImpl.java:772: warning: [deprecation]
getAttributeMap(java.lang.String,java.lang.String) in
cytoscape.data.CyAttributes has been deprecated
[javac] public Map getAttributeMap(String id, String
attributeName) {
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\data
\CyAttributesImpl.java:670: warning: [deprecation]
setAttributeMap(java.lang.String,java.lang.String,java.util.Map) in
cytoscape.data.CyAttributes has been deprecated
[javac] public void setAttributeMap(String id, String
attributeName, Map map) {
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\data
\CyAttributesImpl.java:621: warning: [deprecation]
getAttributeList(java.lang.String,java.lang.String) in
cytoscape.data.CyAttributes has been deprecated
[javac] public List getAttributeList(String id, String
attributeName) {
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\data
\CyAttributesImpl.java:529: warning: [deprecation]
setAttributeList(java.lang.String,java.lang.String,java.util.List) in
cytoscape.data.CyAttributes has been deprecated
[javac] public void setAttributeList(String id, String
attributeName, List list) {
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\data\readers
\CytoscapeSessionReader.java:196: warning: [deprecation] toURL() in
java.io.File has been deprecated
[javac] this(new File(fileName).toURL(), monitor);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\data\readers
\CytoscapeSessionReader.java:207: warning: [deprecation] toURL() in
java.io.File has been deprecated
[javac] this(new File(fileName).toURL(), (TaskMonitor)null);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\data\readers
\CytoscapeSessionReader.java:933: warning: [deprecation] toURL() in
java.io.File has been deprecated
[javac] return tempFile.toURL();
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\plugin
\PluginTracker.java:660: warning: [deprecation] getLicenseText() in
cytoscape.plugin.PluginInfo has been deprecated
[javac] License.addContent( new
Element("text").setText(obj.getLicenseText()) );
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\data\writers
\InteractionWriter.java:122: warning: [deprecation]
getAdjacentEdgesList(giny.model.Node,boolean,boolean,boolean) in
giny.model.GraphPerspective has been deprecated
[javac] List edges = network.getAdjacentEdgesList(node, true,
true, true);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\ding
\DingNetworkView.java:416: warning: [deprecation]
setSelected(giny.view.EdgeView[]) in cytoscape.view.CyNetworkView has
been deprecated
[javac] public boolean setSelected(EdgeView[] edge_views) {
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\ding
\DingNetworkView.java:395: warning: [deprecation]
setSelected(cytoscape.CyEdge[]) in cytoscape.view.CyNetworkView has
been deprecated
[javac] public boolean setSelected(CyEdge[] edges) {
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\ding
\DingNetworkView.java:280: warning: [deprecation]
setSelected(giny.view.NodeView[]) in cytoscape.view.CyNetworkView has
been deprecated
[javac] public boolean setSelected(NodeView[] node_views) {
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\ding
\DingNetworkView.java:259: warning: [deprecation]
setSelected(cytoscape.CyNode[]) in cytoscape.view.CyNetworkView has
been deprecated
[javac] public boolean setSelected(CyNode[] nodes) {
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\dialogs
\URLimportAdvancedDialog.java:348: warning: [deprecation] toURL() in
java.io.File has been deprecated
[javac] tmpBookmarks =
BookmarksUtil.getBookmarks(tmpBookmarkFile.toURL());
[javac]
^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\dialogs
\plugins\PluginUpdateDialog.java:218: warning: [deprecation]
isLicenseRequired() in cytoscape.plugin.PluginInfo has been deprecated
[javac] if (pInfo.isLicenseRequired() &&
pInfo.getLicenseText() != null) {
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\dialogs
\plugins\PluginUpdateDialog.java:218: warning: [deprecation]
getLicenseText() in cytoscape.plugin.PluginInfo has been deprecated
[javac] if (pInfo.isLicenseRequired() &&
pInfo.getLicenseText() != null) {
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\dialogs
\preferences\BookmarkDialog.java:608: warning: [deprecation] toURL()
in java.io.File has been deprecated
[javac] tmpBookmarks =
BookmarksUtil.getBookmarks(tmpBookmarkFile.toURL());
[javac]
^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\giny
\FingCyNetwork.java:70: warning: [deprecation]
getConnectingNodeIndicesArray(int[]) in giny.model.GraphPerspective
has been deprecated
[javac] public class FingCyNetwork extends
FingExtensibleGraphPerspective implements CyNetwork,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\giny
\FingCyNetwork.java:70: warning: [deprecation]
getAdjacentEdgesList(giny.model.Node,boolean,boolean,boolean) in
giny.model.GraphPerspective has been deprecated
[javac] public class FingCyNetwork extends
FingExtensibleGraphPerspective implements CyNetwork,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\giny
\FingCyNetwork.java:70: warning: [deprecation] getEdgeIndex(int) in
giny.model.GraphPerspective has been deprecated
[javac] public class FingCyNetwork extends
FingExtensibleGraphPerspective implements CyNetwork,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\giny
\FingCyNetwork.java:70: warning: [deprecation] getNodeIndex(int) in
giny.model.GraphPerspective has been deprecated
[javac] public class FingCyNetwork extends
FingExtensibleGraphPerspective implements CyNetwork,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\giny
\FingCyNetwork.java:70: warning: [deprecation]
getEdgeIndicesArray(int,int,boolean) in giny.model.GraphPerspective
has been deprecated
[javac] public class FingCyNetwork extends
FingExtensibleGraphPerspective implements CyNetwork,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\giny
\FingCyNetwork.java:70: warning: [deprecation]
edgesList(int,int,boolean) in giny.model.GraphPerspective has been
deprecated
[javac] public class FingCyNetwork extends
FingExtensibleGraphPerspective implements CyNetwork,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\giny
\FingCyNetwork.java:70: warning: [deprecation]
neighborsList(giny.model.Node) in giny.model.GraphPerspective has been
deprecated
[javac] public class FingCyNetwork extends
FingExtensibleGraphPerspective implements CyNetwork,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\giny
\FingCyNetwork.java:70: warning: [deprecation]
createGraphPerspective(int[],int[]) in giny.model.GraphPerspective has
been deprecated
[javac] public class FingCyNetwork extends
FingExtensibleGraphPerspective implements CyNetwork,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\giny
\FingCyNetwork.java:70: warning: [deprecation]
createGraphPerspective(giny.model.Node[],giny.model.Edge[]) in
giny.model.GraphPerspective has been deprecated
[javac] public class FingCyNetwork extends
FingExtensibleGraphPerspective implements CyNetwork,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\giny
\FingCyNetwork.java:70: warning: [deprecation]
restoreEdges(java.util.List) in giny.model.GraphPerspective has been
deprecated
[javac] public class FingCyNetwork extends
FingExtensibleGraphPerspective implements CyNetwork,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\giny
\FingCyNetwork.java:70: warning: [deprecation]
hideEdges(java.util.List) in giny.model.GraphPerspective has been
deprecated
[javac] public class FingCyNetwork extends
FingExtensibleGraphPerspective implements CyNetwork,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\giny
\FingCyNetwork.java:70: warning: [deprecation]
restoreNodes(int[],boolean) in giny.model.GraphPerspective has been
deprecated
[javac] public class FingCyNetwork extends
FingExtensibleGraphPerspective implements CyNetwork,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\giny
\FingCyNetwork.java:70: warning: [deprecation]
restoreNodes(java.util.List,boolean) in giny.model.GraphPerspective
has been deprecated
[javac] public class FingCyNetwork extends
FingExtensibleGraphPerspective implements CyNetwork,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\giny
\FingCyNetwork.java:70: warning: [deprecation]
restoreNodes(java.util.List) in giny.model.GraphPerspective has been
deprecated
[javac] public class FingCyNetwork extends
FingExtensibleGraphPerspective implements CyNetwork,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\giny
\FingCyNetwork.java:70: warning: [deprecation]
hideNodes(java.util.List) in giny.model.GraphPerspective has been
deprecated
[javac] public class FingCyNetwork extends
FingExtensibleGraphPerspective implements CyNetwork,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\giny
\FingCyNetwork.java:70: warning: [deprecation]
getEdgeIndicesArray(int,int,boolean,boolean) in
giny.model.GraphPerspective has been deprecated
[javac] public class FingCyNetwork extends
FingExtensibleGraphPerspective implements CyNetwork,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\layout
\algorithms\GridNodeLayout.java:169: warning: [deprecation]
getAdjacentEdgesList(giny.model.Node,boolean,boolean,boolean) in
giny.model.GraphPerspective has been deprecated
[javac] edgeList =
network.getAdjacentEdgesList(nView.getNode(),true,true,true);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\plugin
\PluginFileReader.java:303: warning: [deprecation]
setLicense(java.lang.String,boolean) in cytoscape.plugin.PluginInfo
has been deprecated
[javac] obj.setLicense(License.getChildTextTrim(licenseText),
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\plugin
\PluginFileReader.java:309: warning: [deprecation]
setLicense(java.lang.String,boolean) in cytoscape.plugin.PluginInfo
has been deprecated
[javac] obj.setLicense(LicenseText, RequireAlways);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\util
\BookmarksUtil.java:189: warning: [deprecation] toURL() in
java.io.File has been deprecated
[javac] theBookmarks =
BookmarksUtil.getBookmarks(pBookmarkFile.toURL());
[javac]
^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\view
\BasicGraphViewHandler.java:612: warning: [deprecation]
getGraphPerspective() in giny.model.Node has been deprecated
[javac] GraphPerspective childGP = node.getGraphPerspective();
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\ContinuousMapping.java:101: warning: [deprecation]
cytoscape.visual.ShapeNodeRealizer in cytoscape.visual has been
deprecated
[javac] defaultObj = ShapeNodeRealizer.getNodeShape(((Byte)
defaultObj).byteValue());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\ContinuousMapping.java:282: warning: [deprecation]
cytoscape.visual.mappings.continuous.ContinuousUI in
cytoscape.visual.mappings.continuous has been deprecated
[javac] ContinuousUI ui = new ContinuousUI(dialog, defaultObj,
network, this);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\ContinuousMapping.java:282: warning: [deprecation]
cytoscape.visual.mappings.continuous.ContinuousUI in
cytoscape.visual.mappings.continuous has been deprecated
[javac] ContinuousUI ui = new ContinuousUI(dialog, defaultObj,
network, this);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\DiscreteMapping.java:105: warning: [deprecation]
cytoscape.visual.ShapeNodeRealizer in cytoscape.visual has been
deprecated
[javac] defObj = ShapeNodeRealizer.getNodeShape(((Byte)
defObj).byteValue());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\DiscreteMapping.java:158: warning: [deprecation]
cytoscape.visual.ShapeNodeRealizer in cytoscape.visual has been
deprecated
[javac] value = ShapeNodeRealizer.getNodeShape(((Byte)
value).byteValue());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\PassThroughMapping.java:106: warning: [deprecation]
cytoscape.visual.ShapeNodeRealizer in cytoscape.visual has been
deprecated
[javac] defaultObj = ShapeNodeRealizer.getNodeShape(((Byte)
defaultObj).byteValue());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\PassThroughMapping.java:122: warning: [deprecation]
cytoscape.visual.ShapeNodeRealizer in cytoscape.visual has been
deprecated
[javac] defaultObj = ShapeNodeRealizer.getNodeShape(((Byte)
defaultObj).byteValue());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\continuous\ValueListener.java:81: warning: [deprecation]
cytoscape.visual.ui.ValueDisplayer in cytoscape.visual.ui has been
deprecated
[javac] System.out.println("SIGNAL______________________"
+ ((ValueDisplayer) e.getItemSelectable()).getValue());

[javac]
^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\continuous\ValueListener.java:83: warning: [deprecation]
cytoscape.visual.ui.ValueDisplayer in cytoscape.visual.ui has been
deprecated
[javac] Object o = ((ValueDisplayer)
e.getItemSelectable()).getValue();
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\continuous\ValueListener.java:87: warning: [deprecation]
cytoscape.visual.mappings.continuous.ContinuousUI in
cytoscape.visual.mappings.continuous has been deprecated
[javac] if (offset == ContinuousUI.LESSER)
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\continuous\ValueListener.java:89: warning: [deprecation]
cytoscape.visual.mappings.continuous.ContinuousUI in
cytoscape.visual.mappings.continuous has been deprecated
[javac] else if (offset == ContinuousUI.EQUAL) {
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\continuous\ValueListener.java:106: warning: [deprecation]
cytoscape.visual.mappings.continuous.ContinuousUI in
cytoscape.visual.mappings.continuous has been deprecated
[javac] } else if (offset == ContinuousUI.GREATER)
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\discrete\DiscreteUI.java:153: warning: [deprecation]
cytoscape.visual.ui.ValueDisplayer in cytoscape.visual.ui has been
deprecated
[javac] ValueDisplayer valueDisplayer =
getMapValue(currentMapping);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\discrete\DiscreteUI.java:189: warning: [deprecation]
cytoscape.visual.ui.ValueDisplayer in cytoscape.visual.ui has been
deprecated
[javac] ValueDisplayer newValueDisplayer =
ValueDisplayer.getDisplayFor(parentDialog,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\discrete\DiscreteUI.java:189: warning: [deprecation]
cytoscape.visual.ui.ValueDisplayer in cytoscape.visual.ui has been
deprecated
[javac] ValueDisplayer newValueDisplayer =
ValueDisplayer.getDisplayFor(parentDialog,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\discrete\DiscreteUI.java:226: warning: [deprecation]
cytoscape.visual.ui.ValueDisplayer in cytoscape.visual.ui has been
deprecated
[javac] ValueDisplayer mapValue;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\discrete\DiscreteUI.java:230: warning: [deprecation]
cytoscape.visual.ui.ValueDisplayer in cytoscape.visual.ui has been
deprecated
[javac] mapValue =
ValueDisplayer.getBlankDisplayFor(parentDialog,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\discrete\DiscreteUI.java:233: warning: [deprecation]
cytoscape.visual.ui.ValueDisplayer in cytoscape.visual.ui has been
deprecated
[javac] mapValue =
ValueDisplayer.getDisplayFor(parentDialog, USER_MSG,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\discrete\ValueChangeListener.java:77: warning: [deprecation]
cytoscape.visual.ui.ValueDisplayer in cytoscape.visual.ui has been
deprecated
[javac] ValueDisplayer v = (ValueDisplayer)
e.getItemSelectable();
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\mappings\discrete\ValueChangeListener.java:77: warning: [deprecation]
cytoscape.visual.ui.ValueDisplayer in cytoscape.visual.ui has been
deprecated
[javac] ValueDisplayer v = (ValueDisplayer)
e.getItemSelectable();
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\parsers\LineTypeParser.java:79: warning: [deprecation]
cytoscape.visual.LineType in cytoscape.visual has been deprecated
[javac] return LineType.parseLineTypeText(value);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\parsers\ObjectToString.java:73: warning: [deprecation]
cytoscape.visual.LineType in cytoscape.visual has been deprecated
[javac] else if (o instanceof LineType)
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\parsers\ObjectToString.java:76: warning: [deprecation]
cytoscape.visual.ShapeNodeRealizer in cytoscape.visual has been
deprecated
[javac] return
ShapeNodeRealizer.getNodeShapeText((Byte) o);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\icon\LineTypeIcon.java:72: warning: [deprecation]
cytoscape.visual.LineType in cytoscape.visual has been deprecated
[javac] this((BasicStroke) ((LineType)
VisualPropertyType.EDGE_LINETYPE.getDefault(Cytoscape.getVisualMappingManager()
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\icon\LineTypeIcon.java:75: warning: [deprecation]
cytoscape.visual.LineType in cytoscape.visual has been deprecated
[javac] ((LineType) VisualPropertyType.EDGE_LINETYPE
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\icon\LineTypeIcon.java:87: warning: [deprecation]
cytoscape.visual.LineType in cytoscape.visual has been deprecated
[javac] this((BasicStroke) ((LineType) lineType).getStroke(),
DEFAULT_ICON_SIZE * 3,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\icon\LineTypeIcon.java:89: warning: [deprecation]
cytoscape.visual.LineType in cytoscape.visual has been deprecated
[javac] ((LineType) lineType).getType().toString(),
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\properties\EdgeLineTypeProp.java:71: warning: [deprecation]
cytoscape.visual.LineType in cytoscape.visual has been deprecated
[javac] final LineTypeIcon icon = new
LineTypeIcon((LineType)value);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\properties\EdgeLineTypeProp.java:90: warning: [deprecation]
cytoscape.visual.LineType in cytoscape.visual has been deprecated
[javac] final Stroke newLine = ((LineType)o).getStroke();
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\properties\EdgeLineTypeProp.java:105: warning: [deprecation]
cytoscape.visual.LineType in cytoscape.visual has been deprecated
[javac] public Object getDefaultAppearanceObject() { return
LineType.LINE_1; }
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\properties\NodeLineTypeProp.java:99: warning: [deprecation]
cytoscape.visual.LineType in cytoscape.visual has been deprecated
[javac] final Stroke newBorderLine =
((LineType)o).getStroke();
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual
\properties\NodeLineTypeProp.java:114: warning: [deprecation]
cytoscape.visual.LineType in cytoscape.visual has been deprecated
[javac] public Object getDefaultAppearanceObject() { return
LineType.LINE_1; }
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\PopupStringChooser.java:69: warning: [deprecation]
cytoscape.visual.ui.ValueDisplayer in cytoscape.visual.ui has been
deprecated
[javac] case ValueDisplayer.DOUBLE:
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\PopupStringChooser.java:83: warning: [deprecation]
cytoscape.visual.ui.ValueDisplayer in cytoscape.visual.ui has been
deprecated
[javac] case ValueDisplayer.INT:
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\VizMapSizeTab.java:149: warning: [deprecation]
cytoscape.visual.ui.VizMapAttrTab in cytoscape.visual.ui has been
deprecated
[javac] height = new VizMapAttrTab(mainUI, tabContainer,
tabIndex, VMM,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\VizMapSizeTab.java:151: warning: [deprecation]
cytoscape.visual.ui.VizMapAttrTab in cytoscape.visual.ui has been
deprecated
[javac] width = new VizMapAttrTab(mainUI, tabContainer,
tabIndex, VMM,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\VizMapSizeTab.java:156: warning: [deprecation]
cytoscape.visual.ui.VizMapAttrTab in cytoscape.visual.ui has been
deprecated
[javac] size = new VizMapAttrTab(mainUI, tabContainer,
tabIndex, VMM,
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\VizMapSizeTab.java:190: warning: [deprecation] getCalculator(byte) in
cytoscape.visual.AppearanceCalculator has been deprecated
[javac] private Calculator widthCalc =
nodeCalc.getCalculator((byte)VisualPropertyType.NODE_WIDTH.ordinal());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\VizMapSizeTab.java:191: warning: [deprecation] getCalculator(byte) in
cytoscape.visual.AppearanceCalculator has been deprecated
[javac] private Calculator heightCalc =
nodeCalc.getCalculator((byte)VisualPropertyType.NODE_HEIGHT.ordinal());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\VizMapSizeTab.java:194: warning: [deprecation] getCalculator(byte) in
cytoscape.visual.AppearanceCalculator has been deprecated
[javac] private Calculator lockCalc =
nodeCalc.getCalculator((byte)VisualPropertyType.NODE_SIZE.ordinal());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\VizMapSizeTab.java:210: warning: [deprecation] getCalculator(byte) in
cytoscape.visual.AppearanceCalculator has been deprecated
[javac] this.widthCalc =
nodeCalc.getCalculator((byte)VisualPropertyType.NODE_WIDTH.ordinal());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\VizMapSizeTab.java:213: warning: [deprecation] getCalculator(byte) in
cytoscape.visual.AppearanceCalculator has been deprecated
[javac] this.heightCalc =
nodeCalc.getCalculator((byte)VisualPropertyType.NODE_HEIGHT.ordinal());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\VizMapSizeTab.java:228: warning: [deprecation] getCalculator(byte) in
cytoscape.visual.AppearanceCalculator has been deprecated
[javac] this.lockCalc =
nodeCalc.getCalculator((byte)VisualPropertyType.NODE_SIZE.ordinal());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\src\cytoscape\visual\ui
\VizMapSizeTab.java:280: warning: [deprecation]
cytoscape.visual.ui.VizMapTab in cytoscape.visual.ui has been
deprecated
[javac] VizMapTab ret = height.checkCalcSelected(c);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\data
\ontology\readers\OBOFlatFileReaderTest.java:72: warning:
[deprecation] toURL() in java.io.File has been deprecated
[javac] URL oboUrl = sampleOBO.toURL();
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\data
\readers\XGMMLReaderTest.java:109: warning: [deprecation]
removeNodes(java.util.List) in giny.model.RootGraph has been
deprecated
[javac] network.removeNodes(network.nodesList());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\plugin
\PluginFileReaderTest.java:107: warning: [deprecation]
getLicenseText() in cytoscape.plugin.PluginInfo has been deprecated
[javac] assertNotNull(All.get(0).getLicenseText());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\plugin
\PluginManagerTest.java:563: warning: [deprecation] getLicenseText()
in cytoscape.plugin.PluginInfo has been deprecated
[javac] assertNotNull(CurrentPlugin.getLicenseText());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:114: warning: [deprecation]
getColor() in cytoscape.visual.EdgeAppearance has been deprecated
[javac] assertTrue("color", ea.getColor().equals(Color.BLACK));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:117: warning: [deprecation]
getLineType() in cytoscape.visual.EdgeAppearance has been deprecated
[javac] assertTrue("lineType", ea.getLineType() ==
LineType.LINE_1);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:117: warning: [deprecation]
cytoscape.visual.LineType in cytoscape.visual has been deprecated
[javac] assertTrue("lineType", ea.getLineType() ==
LineType.LINE_1);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:120: warning: [deprecation]
getSourceArrow() in cytoscape.visual.EdgeAppearance has been
deprecated
[javac] assertTrue("src arrow", ea.getSourceArrow() ==
Arrow.NONE);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:121: warning: [deprecation]
getTargetArrow() in cytoscape.visual.EdgeAppearance has been
deprecated
[javac] assertTrue("trg arrow", ea.getTargetArrow() ==
Arrow.NONE);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:122: warning: [deprecation]
getLabel() in cytoscape.visual.EdgeAppearance has been deprecated
[javac] assertTrue("label", ea.getLabel().equals(""));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:123: warning: [deprecation]
getToolTip() in cytoscape.visual.EdgeAppearance has been deprecated
[javac] assertTrue("tooltip", ea.getToolTip().equals(""));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:124: warning: [deprecation]
getFont() in cytoscape.visual.EdgeAppearance has been deprecated
[javac] assertTrue("font size", ea.getFont().getSize() == 10);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:125: warning: [deprecation]
getFont() in cytoscape.visual.EdgeAppearance has been deprecated
[javac] assertTrue("font style", ea.getFont().getStyle() ==
Font.PLAIN);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:139: warning: [deprecation]
getColor() in cytoscape.visual.EdgeAppearance has been deprecated
[javac] System.out.println("color " + ea.getColor());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:142: warning: [deprecation]
getLineType() in cytoscape.visual.EdgeAppearance has been deprecated
[javac] System.out.println("linetype " +
ea.getLineType().toString());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:144: warning: [deprecation]
getSourceArrow() in cytoscape.visual.EdgeAppearance has been
deprecated
[javac] System.out.println("src arrow " + ea.getSourceArrow());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:145: warning: [deprecation]
getTargetArrow() in cytoscape.visual.EdgeAppearance has been
deprecated
[javac] System.out.println("trg arrow " + ea.getTargetArrow());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:146: warning: [deprecation]
getLabel() in cytoscape.visual.EdgeAppearance has been deprecated
[javac] System.out.println("label " + ea.getLabel());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:147: warning: [deprecation]
getToolTip() in cytoscape.visual.EdgeAppearance has been deprecated
[javac] System.out.println("tooltip " + ea.getToolTip());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:148: warning: [deprecation]
getFont() in cytoscape.visual.EdgeAppearance has been deprecated
[javac] System.out.println("font size " +
ea.getFont().getSize());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:149: warning: [deprecation]
getFont() in cytoscape.visual.EdgeAppearance has been deprecated
[javac] System.out.println("font style " +
ea.getFont().getStyle());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:151: warning: [deprecation]
getColor() in cytoscape.visual.EdgeAppearance has been deprecated
[javac] assertTrue("color " + ea.getColor(),
ea.getColor().equals(
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:151: warning: [deprecation]
getColor() in cytoscape.visual.EdgeAppearance has been deprecated
[javac] assertTrue("color " + ea.getColor(),
ea.getColor().equals(
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:162: warning: [deprecation]
getTargetArrow() in cytoscape.visual.EdgeAppearance has been
deprecated
[javac] assertTrue("trg arrow " + ea.getTargetArrow(),
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:163: warning: [deprecation]
getTargetArrow() in cytoscape.visual.EdgeAppearance has been
deprecated
[javac] ea.getTargetArrow() == Arrow.NONE);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:165: warning: [deprecation]
getLabel() in cytoscape.visual.EdgeAppearance has been deprecated
[javac] assertTrue("label " + ea.getLabel(),
ea.getLabel().equals("0.4"));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:165: warning: [deprecation]
getLabel() in cytoscape.visual.EdgeAppearance has been deprecated
[javac] assertTrue("label " + ea.getLabel(),
ea.getLabel().equals("0.4"));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:166: warning: [deprecation]
getToolTip() in cytoscape.visual.EdgeAppearance has been deprecated
[javac] assertTrue("tooltip " + ea.getToolTip(),
ea.getToolTip().equals(""));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:166: warning: [deprecation]
getToolTip() in cytoscape.visual.EdgeAppearance has been deprecated
[javac] assertTrue("tooltip " + ea.getToolTip(),
ea.getToolTip().equals(""));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:167: warning: [deprecation]
getFont() in cytoscape.visual.EdgeAppearance has been deprecated
[javac] assertTrue("font size " + ea.getFont().getSize(),
ea.getFont()
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:167: warning: [deprecation]
getFont() in cytoscape.visual.EdgeAppearance has been deprecated
[javac] assertTrue("font size " + ea.getFont().getSize(),
ea.getFont()
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:169: warning: [deprecation]
getFont() in cytoscape.visual.EdgeAppearance has been deprecated
[javac] assertTrue("font style " + ea.getFont().getStyle(),
ea.getFont()
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\EdgeAppearanceCalculatorTest.java:169: warning: [deprecation]
getFont() in cytoscape.visual.EdgeAppearance has been deprecated
[javac] assertTrue("font style " + ea.getFont().getStyle(),
ea.getFont()
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:124: warning: [deprecation]
getFillColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertTrue("a color " + na.getFillColor() + " expect "
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:125: warning: [deprecation]
getFillColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] + Color.WHITE.toString(),
na.getFillColor().equals(Color.WHITE));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:126: warning: [deprecation]
getBorderColor() in cytoscape.visual.NodeAppearance has been
deprecated
[javac] assertTrue("a border color " + na.getBorderColor() + "
expect "
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:127: warning: [deprecation]
getBorderColor() in cytoscape.visual.NodeAppearance has been
deprecated
[javac] + Color.BLACK.toString(), na.getBorderColor().equals(
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:129: warning: [deprecation]
cytoscape.visual.LineType in cytoscape.visual has been deprecated
[javac] assertEquals("a lineType ", LineType.LINE_1,
na.getBorderLineType());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:129: warning: [deprecation]
getBorderLineType() in cytoscape.visual.NodeAppearance has been
deprecated
[javac] assertEquals("a lineType ", LineType.LINE_1,
na.getBorderLineType());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:130: warning: [deprecation]
cytoscape.visual.ShapeNodeRealizer in cytoscape.visual has been
deprecated
[javac] assertEquals("a shape ", ShapeNodeRealizer.RECT,
na.getShape());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:130: warning: [deprecation]
getShape() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("a shape ", ShapeNodeRealizer.RECT,
na.getShape());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:133: warning: [deprecation]
getWidth() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("a width ", 35.0, na.getWidth());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:134: warning: [deprecation]
getHeight() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("a height ", 35.0, na.getHeight());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:135: warning: [deprecation]
getSize() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("a size ", 35.0, na.getSize());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:137: warning: [deprecation]
getLabel() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("a label ", "", na.getLabel());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:138: warning: [deprecation]
getToolTip() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("a tooltip ", "", na.getToolTip());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:139: warning: [deprecation]
getFont() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("a font size ", 12,
na.getFont().getSize());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:140: warning: [deprecation]
getFont() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("a font style ", Font.PLAIN,
na.getFont().getStyle());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:141: warning: [deprecation]
getLabelColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertTrue("a label color " + na.getLabelColor() + "
expect "
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:142: warning: [deprecation]
getLabelColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] + Color.BLACK,
na.getLabelColor().equals(Color.BLACK));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:147: warning: [deprecation]
getFillColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertTrue("b color " + nb.getFillColor() + " expect "
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:148: warning: [deprecation]
getFillColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] + Color.WHITE.toString(),
nb.getFillColor().equals(Color.WHITE));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:149: warning: [deprecation]
getBorderColor() in cytoscape.visual.NodeAppearance has been
deprecated
[javac] assertTrue("b border color " + nb.getBorderColor() + "
expect "
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:150: warning: [deprecation]
getBorderColor() in cytoscape.visual.NodeAppearance has been
deprecated
[javac] + Color.BLACK.toString(), nb.getBorderColor().equals(
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:152: warning: [deprecation]
cytoscape.visual.LineType in cytoscape.visual has been deprecated
[javac] assertEquals("b lineType ", LineType.LINE_1,
nb.getBorderLineType());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:152: warning: [deprecation]
getBorderLineType() in cytoscape.visual.NodeAppearance has been
deprecated
[javac] assertEquals("b lineType ", LineType.LINE_1,
nb.getBorderLineType());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:153: warning: [deprecation]
cytoscape.visual.ShapeNodeRealizer in cytoscape.visual has been
deprecated
[javac] assertEquals("b shape ", ShapeNodeRealizer.RECT,
nb.getShape());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:153: warning: [deprecation]
getShape() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("b shape ", ShapeNodeRealizer.RECT,
nb.getShape());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:155: warning: [deprecation]
getWidth() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("b width ", 35.0, nb.getWidth());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:156: warning: [deprecation]
getHeight() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("b height ", 35.0, nb.getHeight());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:157: warning: [deprecation]
getSize() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("b size ", 35.0, nb.getSize());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:159: warning: [deprecation]
getLabel() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("b label ", "", nb.getLabel());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:160: warning: [deprecation]
getToolTip() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("b tooltip ", "", nb.getToolTip());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:161: warning: [deprecation]
getFont() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("b font size ", 12,
nb.getFont().getSize());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:162: warning: [deprecation]
getFont() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("b font style ", Font.PLAIN,
nb.getFont().getStyle());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:163: warning: [deprecation]
getLabelColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertTrue("b label color " + nb.getLabelColor() + "
expect "
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:164: warning: [deprecation]
getLabelColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] + Color.BLACK,
nb.getLabelColor().equals(Color.BLACK));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:170: warning: [deprecation]
getFillColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertTrue("c color " + nc.getFillColor() + " expect "
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:171: warning: [deprecation]
getFillColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] + Color.WHITE.toString(),
nc.getFillColor().equals(Color.WHITE));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:172: warning: [deprecation]
getBorderColor() in cytoscape.visual.NodeAppearance has been
deprecated
[javac] assertTrue("c border color " + nc.getBorderColor() + "
expect "
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:173: warning: [deprecation]
getBorderColor() in cytoscape.visual.NodeAppearance has been
deprecated
[javac] + Color.BLACK.toString(), nc.getBorderColor().equals(
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:175: warning: [deprecation]
cytoscape.visual.LineType in cytoscape.visual has been deprecated
[javac] assertEquals("c lineType ", LineType.LINE_1,
nc.getBorderLineType());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:175: warning: [deprecation]
getBorderLineType() in cytoscape.visual.NodeAppearance has been
deprecated
[javac] assertEquals("c lineType ", LineType.LINE_1,
nc.getBorderLineType());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:176: warning: [deprecation]
cytoscape.visual.ShapeNodeRealizer in cytoscape.visual has been
deprecated
[javac] assertEquals("c shape ", ShapeNodeRealizer.RECT,
nc.getShape());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:176: warning: [deprecation]
getShape() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("c shape ", ShapeNodeRealizer.RECT,
nc.getShape());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:178: warning: [deprecation]
getWidth() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("c width ", 70.0, nc.getWidth());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:179: warning: [deprecation]
getHeight() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("c height ", 30.0, nc.getHeight());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:180: warning: [deprecation]
getSize() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("c size ", 35.0, nc.getSize());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:181: warning: [deprecation]
getLabel() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("c label ", "", nc.getLabel());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:182: warning: [deprecation]
getToolTip() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("c tooltip ", "", nc.getToolTip());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:183: warning: [deprecation]
getFont() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("c font size ", 12,
nc.getFont().getSize());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:184: warning: [deprecation]
getFont() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("c font style ", Font.PLAIN,
nc.getFont().getStyle());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:185: warning: [deprecation]
getLabelColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertTrue("c label color " + nc.getLabelColor() + "
expect "
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:186: warning: [deprecation]
getLabelColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] + Color.BLACK,
nc.getLabelColor().equals(Color.BLACK));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:189: warning: [deprecation]
setFillColor(java.awt.Color) in cytoscape.visual.NodeAppearance has
been deprecated
[javac] def.setFillColor(Color.GREEN);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:190: warning: [deprecation]
setBorderColor(java.awt.Color) in cytoscape.visual.NodeAppearance has
been deprecated
[javac] def.setBorderColor(Color.BLUE);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:191: warning: [deprecation]
setWidth(double) in cytoscape.visual.NodeAppearance has been
deprecated
[javac] def.setWidth(47.0);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:192: warning: [deprecation]
setHeight(double) in cytoscape.visual.NodeAppearance has been
deprecated
[javac] def.setHeight(23.0);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:195: warning: [deprecation]
getFillColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertTrue("color " + na.getFillColor() + " expect "
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:196: warning: [deprecation]
getFillColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] + Color.GREEN.toString(),
na.getFillColor().equals(Color.GREEN));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:197: warning: [deprecation]
getBorderColor() in cytoscape.visual.NodeAppearance has been
deprecated
[javac] assertTrue("border color " + na.getBorderColor() + "
expect "
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:198: warning: [deprecation]
getBorderColor() in cytoscape.visual.NodeAppearance has been
deprecated
[javac] + Color.BLUE.toString(),
na.getBorderColor().equals(Color.BLUE));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:199: warning: [deprecation]
getWidth() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("width ", 47.0, na.getWidth());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:200: warning: [deprecation]
getHeight() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("height ", 23.0, na.getHeight());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:203: warning: [deprecation]
getFillColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertTrue("color " + nb.getFillColor() + " expect "
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:204: warning: [deprecation]
getFillColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] + Color.GREEN.toString(),
nb.getFillColor().equals(Color.GREEN));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:205: warning: [deprecation]
getBorderColor() in cytoscape.visual.NodeAppearance has been
deprecated
[javac] assertTrue("border color " + nb.getBorderColor() + "
expect "
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:206: warning: [deprecation]
getBorderColor() in cytoscape.visual.NodeAppearance has been
deprecated
[javac] + Color.BLUE.toString(),
nb.getBorderColor().equals(Color.BLUE));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:207: warning: [deprecation]
getWidth() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("width ", 47.0, nb.getWidth());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:208: warning: [deprecation]
getHeight() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("height ", 23.0, nb.getHeight());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:234: warning: [deprecation]
getFillColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] "a color " + na.getFillColor() + " expect " +
ca.toString(),
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:235: warning: [deprecation]
getFillColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] na.getFillColor().equals(ca));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:236: warning: [deprecation]
getBorderColor() in cytoscape.visual.NodeAppearance has been
deprecated
[javac] assertTrue("a border color " + na.getBorderColor() + "
expect "
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:237: warning: [deprecation]
getBorderColor() in cytoscape.visual.NodeAppearance has been
deprecated
[javac] + Color.BLACK.toString(), na.getBorderColor().equals(
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:239: warning: [deprecation]
cytoscape.visual.LineType in cytoscape.visual has been deprecated
[javac] assertEquals("a lineType ", LineType.LINE_1,
na.getBorderLineType());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:239: warning: [deprecation]
getBorderLineType() in cytoscape.visual.NodeAppearance has been
deprecated
[javac] assertEquals("a lineType ", LineType.LINE_1,
na.getBorderLineType());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:240: warning: [deprecation]
cytoscape.visual.ShapeNodeRealizer in cytoscape.visual has been
deprecated
[javac] assertEquals("a shape ", ShapeNodeRealizer.RECT,
na.getShape());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:240: warning: [deprecation]
getShape() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("a shape ", ShapeNodeRealizer.RECT,
na.getShape());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:241: warning: [deprecation]
getWidth() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("a width ", 70.0, na.getWidth());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:242: warning: [deprecation]
getHeight() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("a height ", 10.0, na.getHeight()); //
only height has a
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:244: warning: [deprecation]
getSize() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("a size ", 35.0, na.getSize()); // props
don't set size
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:245: warning: [deprecation]
getLabel() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("a label ", "a", na.getLabel());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:246: warning: [deprecation]
getToolTip() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("a tooltip ", "", na.getToolTip());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:247: warning: [deprecation]
getFont() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("a font size ", 12,
na.getFont().getSize());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:248: warning: [deprecation]
getFont() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("a font style ", Font.PLAIN,
na.getFont().getStyle());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:249: warning: [deprecation]
getLabelColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertTrue("a label color " + na.getLabelColor() + "
expect "
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:250: warning: [deprecation]
getLabelColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] + Color.BLACK,
na.getLabelColor().equals(Color.BLACK));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:258: warning: [deprecation]
getFillColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] "b color " + nb.getFillColor() + " expect " +
cb.toString(),
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:259: warning: [deprecation]
getFillColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] nb.getFillColor().equals(cb));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:260: warning: [deprecation]
getBorderColor() in cytoscape.visual.NodeAppearance has been
deprecated
[javac] assertTrue("b border color " + nb.getBorderColor() + "
expect "
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:261: warning: [deprecation]
getBorderColor() in cytoscape.visual.NodeAppearance has been
deprecated
[javac] + Color.BLACK,
nb.getBorderColor().equals(Color.BLACK));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:268: warning: [deprecation]
cytoscape.visual.ShapeNodeRealizer in cytoscape.visual has been
deprecated
[javac] assertEquals("b shape ", ShapeNodeRealizer.RECT,
nb.getShape());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:268: warning: [deprecation]
getShape() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("b shape ", ShapeNodeRealizer.RECT,
nb.getShape());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:269: warning: [deprecation]
getWidth() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("b width ", 70.0, nb.getWidth());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:270: warning: [deprecation]
getHeight() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("b height ", 30.0, nb.getHeight());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:271: warning: [deprecation]
getSize() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("b size ", 35.0, nb.getSize()); // props
don't set size
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:272: warning: [deprecation]
getLabel() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("b label ", "b", nb.getLabel());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:273: warning: [deprecation]
getToolTip() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("b tooltip ", "", nb.getToolTip());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:274: warning: [deprecation]
getFont() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("b font size ", 12,
nb.getFont().getSize());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:275: warning: [deprecation]
getFont() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("b font style ", Font.PLAIN,
nb.getFont().getStyle());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:276: warning: [deprecation]
getLabelColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertTrue("b label color " + nb.getLabelColor() + "
expect "
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:277: warning: [deprecation]
getLabelColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] + Color.BLACK.toString(), nb.getLabelColor()
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:287: warning: [deprecation]
getFillColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] "c color " + nc.getFillColor() + " expect " +
cc.toString(),
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:288: warning: [deprecation]
getFillColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] nc.getFillColor().equals(cc));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:289: warning: [deprecation]
getBorderColor() in cytoscape.visual.NodeAppearance has been
deprecated
[javac] assertTrue("c border color " + nc.getBorderColor() + "
expect "
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:290: warning: [deprecation]
getBorderColor() in cytoscape.visual.NodeAppearance has been
deprecated
[javac] + Color.BLACK,
nc.getBorderColor().equals(Color.BLACK));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:292: warning: [deprecation]
getBorderLineType() in cytoscape.visual.NodeAppearance has been
deprecated
[javac] assertEquals("c line width ", 1.0f,
nc.getBorderLineType().getWidth());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:294: warning: [deprecation]
cytoscape.visual.ShapeNodeRealizer in cytoscape.visual has been
deprecated
[javac] assertEquals("c shape ", ShapeNodeRealizer.RECT,
nc.getShape());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:294: warning: [deprecation]
getShape() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("c shape ", ShapeNodeRealizer.RECT,
nc.getShape());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:295: warning: [deprecation]
getWidth() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("c width ", 35.0, nc.getWidth()); // since
node size is
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:297: warning: [deprecation]
getHeight() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("c height ", 35.0, nc.getHeight()); //
since node size
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:299: warning: [deprecation]
getSize() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("c size ", 35.0, nc.getSize());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:300: warning: [deprecation]
getLabel() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("c label ", "c", nc.getLabel());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:301: warning: [deprecation]
getToolTip() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("c tooltip ", "", nc.getToolTip());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:302: warning: [deprecation]
getFont() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("c font size ", 12,
nc.getFont().getSize());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:303: warning: [deprecation]
getFont() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("c font style ", Font.PLAIN,
nc.getFont().getStyle());
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:304: warning: [deprecation]
getLabelColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertTrue("c label color " + nc.getLabelColor() + "
expect "
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:305: warning: [deprecation]
getLabelColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] + Color.BLACK.toString(), nc.getLabelColor()
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:372: warning: [deprecation]
cytoscape.visual.ShapeNodeRealizer in cytoscape.visual has been
deprecated
[javac] byte shape = ShapeNodeRealizer.DIAMOND;
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:411: warning: [deprecation]
getFillColor() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertTrue(secondApp.getFillColor().equals(fillColor));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:412: warning: [deprecation]
getBorderColor() in cytoscape.visual.NodeAppearance has been
deprecated
[javac]
assertTrue(secondApp.getBorderColor().equals(borderColor));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:420: warning: [deprecation]
getShape() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertTrue(secondApp.getShape() == shape);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:421: warning: [deprecation]
getWidth() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("width ", secondApp.getWidth(), width,
0.0001);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:422: warning: [deprecation]
getHeight() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("height ", secondApp.getHeight(), height,
0.0001);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:423: warning: [deprecation]
getLabel() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertTrue(secondApp.getLabel().equals(label));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:424: warning: [deprecation]
getToolTip() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertTrue(secondApp.getToolTip().equals(toolTip));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:425: warning: [deprecation]
getFont() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertTrue(secondApp.getFont().equals(font));
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceCalculatorTest.java:429: warning: [deprecation]
getWidth() in cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("width", secondApp.getWidth(), 32.0,
0.0001);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceTest.java:108: warning: [deprecation] getSize() in
cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("node uniform size", 35.0, na.getSize(),
SLACK);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceTest.java:109: warning: [deprecation] getWidth() in
cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("node width", 35.0, na.getWidth(), SLACK);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceTest.java:110: warning: [deprecation] getHeight() in
cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("node height", 35.0, na.getHeight(),
SLACK);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceTest.java:114: warning: [deprecation] getSize() in
cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("node uniform size", 35.0, na.getSize(),
SLACK);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceTest.java:115: warning: [deprecation] getWidth() in
cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("node width", 70.0, na.getWidth(), SLACK);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceTest.java:116: warning: [deprecation] getHeight() in
cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("node height", 30.0, na.getHeight(),
SLACK);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceTest.java:118: warning: [deprecation] setWidth(double)
in cytoscape.visual.NodeAppearance has been deprecated
[javac] na.setWidth(40.0);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceTest.java:120: warning: [deprecation] getSize() in
cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("node uniform size", 35.0, na.getSize(),
SLACK);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceTest.java:121: warning: [deprecation] getWidth() in
cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("node width", 40.0, na.getWidth(), SLACK);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceTest.java:123: warning: [deprecation] setHeight(double)
in cytoscape.visual.NodeAppearance has been deprecated
[javac] na.setHeight(50.0);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceTest.java:125: warning: [deprecation] getSize() in
cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("node uniform size", 35.0, na.getSize(),
SLACK);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceTest.java:126: warning: [deprecation] getHeight() in
cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("node heigth", 50.0, na.getHeight(),
SLACK);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceTest.java:130: warning: [deprecation] setWidth(double)
in cytoscape.visual.NodeAppearance has been deprecated
[javac] na.setWidth(20.0);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceTest.java:132: warning: [deprecation] getSize() in
cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("node uniform size", 20.0, na.getSize(),
SLACK);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceTest.java:133: warning: [deprecation] getWidth() in
cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("node width", 20.0, na.getWidth(), SLACK);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceTest.java:135: warning: [deprecation] setHeight(double)
in cytoscape.visual.NodeAppearance has been deprecated
[javac] na.setHeight(80.0);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceTest.java:137: warning: [deprecation] getSize() in
cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("node uniform size", 80.0, na.getSize(),
SLACK);
[javac] ^
[javac] H:\workspace_33\cytoscape-2.6.0\tests\cytoscape\visual
\NodeAppearanceTest.java:138: warning: [deprecation] getHeight() in
cytoscape.visual.NodeAppearance has been deprecated
[javac] assertEquals("node heigth", 80.0, na.getHeight(),
SLACK);
[javac] ^
[javac] Note: Some input files use unchecked or unsafe operations.
[javac] Note: Recompile with -Xlint:unchecked for details.
[javac] 339 warnings
[rmic] RMI Compiling 1 class to H:
\workspace_33\cytoscape-2.6.0\build\classes
[echo] Copying resources/ directory to build
[copy] Copying 32 files to H:\workspace_33\cytoscape-2.6.0\build
\classes\cytoscape\resources
Trying to override old definition of task xjc
Trying to override old definition of task rasterize
help:
buildHelp:
[echo] Copying javahelp files: helpset, html files, images
[copy] Copying 29 files to H:\workspace_33\cytoscape-2.6.0\build
\classes\cytoscape\help
[mkdir] Created dir: H:\workspace_33\cytoscape-2.6.0\build\classes
\cytoscape\help\images
[copy] Copying 228 files to H:\workspace_33\cytoscape-2.6.0\build
\classes\cytoscape\help\images
[echo] Indexing help files and creating search db
generate_manifest:
[echo]
[echo]
***********************************************
[echo] Creating Cytoscape Manifest File
[echo]
***********************************************
[echo]
jar:
[echo]
[echo]
***********************************************
[echo] Creating Cytoscape JAR File
[echo]
***********************************************
[echo]
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\temp\META-INF\services
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\temp\META-INF\services
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\classes
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\classes
[jar] Building jar: H:
\workspace_33\cytoscape-2.6.0\cytoscape.jar
BUILD SUCCESSFUL
Total time: 1 minute 12 seconds

When I do the ant release ( I removed the test as it fails because
there are xml files missing for the plugin_test) I get:
Buildfile: H:\workspace_33\cytoscape-2.6.0\build.xml
prepare:
splash:
[echo]
[echo] ---------------------------------------
[echo] Creating splash and about screens
[echo] ---------------------------------------
[echo]
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\classes\cytoscape\images
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\classes\cytoscape\images
createSplash:
bind:
[xjc] files are up to date
[xjc] files are up to date
[echo] Copying jaxb.properties from H:
\workspace_33\cytoscape-2.6.0/src/cytoscape/generated to build dir...
compile:
[echo] Copying resources/ directory to build
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\classes\cytoscape\resources
help:
buildHelp:
generate_manifest:
[echo]
[echo]
***********************************************
[echo] Creating Cytoscape Manifest File
[echo]
***********************************************
[echo]
jar:
[echo]
[echo]
***********************************************
[echo] Creating Cytoscape JAR File
[echo]
***********************************************
[echo]
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\classes
[jar] Building jar: H:
\workspace_33\cytoscape-2.6.0\cytoscape.jar
release:
[echo]
[echo]
***********************************************
[echo] Creating Cytoscape Release
[echo]
***********************************************
[echo]
[mkdir] Created dir: H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0
[mkdir] Created dir: H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\plugins
[mkdir] Created dir: H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\sampleData
[echo]
[echo] ---------------------------------------
[echo] Copying over all necessary JAR files.
[echo] ---------------------------------------
[echo]
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0
[copy] Copying 64 files to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\lib
[echo]
[echo] ---------------------------------------
[echo] Copying over all OS-specific scripts.
[echo] ---------------------------------------
[echo]
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0
[echo]
[echo] ---------------------------------------
[echo] Copying over user documentation and Cytoscape
License.
[echo] ---------------------------------------
[echo]
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0
[mkdir] Created dir: H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\docs
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\docs
[copy] Copying 2 files to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\docs
[mkdir] Created dir: H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\docs\images
[copy] Copying 228 files to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\docs\images
[echo]
[echo] ---------------------------------------
[echo] Copying over sample data files.
[echo] ---------------------------------------
[echo]
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\sampleData
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\sampleData
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\sampleData
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\sampleData
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\sampleData
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\sampleData
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\sampleData
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\sampleData
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\sampleData
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\sampleData
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\sampleData
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\sampleData
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\sampleData
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\sampleData
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\sampleData
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\sampleData
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\sampleData
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\sampleData
[copy] Copying 1 file to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\sampleData
[echo]
[echo] ---------------------------------------
[echo] Copying over third party licenses.
[echo] ---------------------------------------
[echo]
[mkdir] Created dir: H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\licenses
[copy] Copying 5 files to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\licenses
[echo]
[echo] ---------------------------------------
[echo] Copying over PlugIns.
[echo] ---------------------------------------
[echo]
[copy] Copying 16 files to H:\workspace_33\cytoscape-2.6.0\build
\cytoscape-v2.6.0\plugins
BUILD SUCCESSFUL
Total time: 38 seconds


When I run the generated version of cytoscape (I added cytoscape.jat
to the classpath) it now works,
I can open cytoscape files. Just the spalsh screen is not appearing.
Before I got this AElfred Message.
I check if I have added something else somewhere. The Message of the
successful cytoscape session is:
CytoscapeInit static initialization
init mode: 1
starting delete action
ending delete action
PreferenceAction()...
BookmarkAction()...
Updating plugins...
loading plugins....
- file: H:\workspace_33\cytoscape-2.6.0\build\cytoscape-v2.6.0\plugins
\biopax.jar

attempting to load plugin url:
jar:file:H:\workspace_33\cytoscape-2.6.0\build\cytoscape-v2.6.0\plugins
\biopax.jar!/
Loading from manifest
Successfully loaded: class org.mskcc.biopax_plugin.plugin.BioPaxPlugIn
Registering org.mskcc.biopax_plugin.plugin.BioPaxPlugIn@105562b
Registering org.mskcc.biopax_plugin.plugin.BioPaxPlugIn
Track plugin: true


loading session...
Got VMM Change event. Cur VS in VMM: Sample1
Creating Default Image for Sample1
Got VMM Change event. Cur VS in VMM: Solid
Creating Default Image for Solid
Got VMM Change event. Cur VS in VMM: Universe
Creating Default Image for Universe
Got VMM Change event. Cur VS in VMM: default
Creating Default Image for default
VS Switched --> default, Last = null
loading networks...
loading attributes...
loading expression files...

Cytoscape initialized successfully in: 4358 ms
VS Switched --> default, Last = null
Cytoscape Session Initialized.
Opening session file: H:\workspace_33\cytoscape-2.6.0\testData
\galFiltered.cys
extractEntry: 47 msec.
vizmapSource: 'jar:file:/H:/workspace_33/cytoscape-2.6.0/testData/
galFiltered.cys!/CytoscapeSession-2008_03_27-13_29/
session_vizmap.props'
Applying visual styles from: jar:file:/H:/workspace_33/cytoscape-2.6.0/
testData/galFiltered.cys!/CytoscapeSession-2008_03_27-13_29/
session_vizmap.props
XGMMLReader galFiltered.sif: 11794 msec.
loadCySession: 12372 msec.
Session loaded in 13122 msec.
Got VMM Change event. Cur VS in VMM: Sample1
Creating Default Image for Sample1
Got VMM Change event. Cur VS in VMM: Solid
Creating Default Image for Solid
Got VMM Change event. Cur VS in VMM: Universe
Creating Default Image for Universe
Got VMM Change event. Cur VS in VMM: default
Creating Default Image for default
Got VMM Change event. Cur VS in VMM: galFiltered Style
Creating Default Image for galFiltered Style


Michael

On 14 Mai, 17:50, "Peng-Liang Wang" <penwang2...@gmail.com> wrote:
> Hi,
>
> How did you compile Cytoscape? ant jar? Can you provide more detail about
> the output?
>
> Thanks,
>
> Peng
>

[Peng-Liang Wang]

Hi,

 

I just did a fresh checkout of Cytoscape (on Windows XP) and compile it with Java 1.6.0.06 within Eclipse. I got "build successful". I can not reproduce the error you got.

 

Peng

ca.toString(...

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