Received: by 10.101.11.18 with SMTP id o18mr4801738ani.47.1313511182326;
        Tue, 16 Aug 2011 09:13:02 -0700 (PDT)
X-BeenThere: cytoscape-discuss@googlegroups.com
Received: by 10.101.168.35 with SMTP id v35ls3562925ano.3.gmail; Tue, 16 Aug
 2011 09:13:00 -0700 (PDT)
Received: by 10.236.79.166 with SMTP id i26mr5030671yhe.5.1313511180277;
        Tue, 16 Aug 2011 09:13:00 -0700 (PDT)
Received: by 10.236.79.166 with SMTP id i26mr5030668yhe.5.1313511180269;
        Tue, 16 Aug 2011 09:13:00 -0700 (PDT)
Return-Path: <christian.fo...@utsouthwestern.edu>
Received: from zixvpm01.utsouthwestern.edu (zixvpm01.utsouthwestern.edu [199.242.239.75])
        by gmr-mx.google.com with ESMTPS id p47si150308yhl.2.2011.08.16.09.12.59
        (version=TLSv1/SSLv3 cipher=OTHER);
        Tue, 16 Aug 2011 09:12:59 -0700 (PDT)
Received-SPF: pass (google.com: domain of christian.fo...@utsouthwestern.edu designates 199.242.239.75 as permitted sender) client-ip=199.242.239.75;
Authentication-Results: gmr-mx.google.com; spf=pass (google.com: domain of christian.fo...@utsouthwestern.edu designates 199.242.239.75 as permitted sender) smtp.mail=christian.fo...@utsouthwestern.edu
Received: from zixvpm01.utsouthwestern.edu (ZixVPM [127.0.0.1])
	by Outbound.utsouthwestern.edu (Proprietary) with ESMTP id DB89E2E8154
	for <cytoscape-discuss@googlegroups.com>; Tue, 16 Aug 2011 11:12:58 -0500 (CDT)
Received: from swlxsmtp1.swmed.edu (swlxsmtp1.swmed.edu [199.165.152.166])
	(using TLSv1 with cipher DHE-RSA-AES256-SHA (256/256 bits))
	(No client certificate requested)
	by zixvpm01.utsouthwestern.edu (Proprietary) with ESMTP id 02F732000A0
	for <cytoscape-discuss@googlegroups.com>; Tue, 16 Aug 2011 11:06:38 -0500 (CDT)
Received: from [129.112.153.8]
	by swlxsmtp1.swmed.edu with esmtp (Exim 4.76)
	(envelope-from <christian.fo...@utsouthwestern.edu>)
	id 1QtMA1-0005KS-Pq
	for cytoscape-discuss@googlegroups.com; Tue, 16 Aug 2011 11:06:37 -0500
From: Christian Forst <christian.fo...@utsouthwestern.edu>
To: cytoscape-discuss@googlegroups.com
In-Reply-To: <CAMHNpFEvZwZt-tuZ1rYhux+8i6AqDowKtkd-feLzv9njx+Q...@mail.gmail.com>
References: <CAMHNpFEvZwZt-tuZ1rYhux+8i6AqDowKtkd-feLzv9njx+Q...@mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Date: Tue, 16 Aug 2011 11:06:44 -0500
Message-ID: <1313510804.3216.297.camel@aiv>
Mime-Version: 1.0
X-Mailer: Evolution 2.28.1
Content-Transfer-Encoding: 7bit
X-Scan-Signature: b6acd0fa8483bd36aa3e334d62e9d97e
Subject: Repairing a Cytoscape Session file?

Is there a way to repair a Cytoscape session file, or do I have to start
from scratch.
I have an apparently corrupt session file inducing the following java
exceptions:

java.lang.NullPointerException: Colors cannot be null
	at java.awt.GradientPaint.<init>(GradientPaint.java:71)
	at
cytoscape.visual.ui.editors.continuous.CyGradientTrackRenderer.drawGradient(CyGradientTrackRenderer.java:271)
	at
cytoscape.visual.ui.editors.continuous.CyGradientTrackRenderer.drawIcon(CyGradientTrackRenderer.java:407)
	at
cytoscape.visual.ui.editors.continuous.CyGradientTrackRenderer.getTrackGraphicIcon(CyGradientTrackRenderer.java:339)
	at
cytoscape.visual.ui.editors.continuous.GradientEditorPanel.getIcon(GradientEditorPanel.java:154)
	at
cytoscape.visual.ui.editors.continuous.ContinuousMappingEditorPanel.getIcon(ContinuousMappingEditorPanel.java:157)
	at
cytoscape.visual.ui.VizMapperMainPanel.buildProperty(VizMapperMainPanel.java:1377)
	at
cytoscape.visual.ui.VizMapperMainPanel.setPropertyFromCalculator(VizMapperMainPanel.java:1445)
	at
cytoscape.visual.ui.VizMapperMainPanel.setPropertyTable(VizMapperMainPanel.java:1263)
	at
cytoscape.visual.ui.VizMapperMainPanel.switchVS(VizMapperMainPanel.java:752)
	at
cytoscape.visual.ui.VizMapperMainPanel.initVizmapperGUI(VizMapperMainPanel.java:848)
	at cytoscape.CytoscapeInit.loadSessionFile(CytoscapeInit.java:483)
	at cytoscape.CytoscapeInit.init(CytoscapeInit.java:215)
	at cytoscape.CyMain.<init>(CyMain.java:144)
	at cytoscape.CyMain.main(CyMain.java:108)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at com.exe4j.runtime.LauncherEngine.launch(Unknown Source)
	at com.install4j.runtime.Launcher.main(Unknown Source)
Exception in thread "Thread-3" java.lang.NullPointerException
	at
cytoscape.visual.customgraphic.PersistImageTask.run(PersistImageTask.java:45)
	at cytoscape.task.util.TaskWrapper.run(TaskManager.java:160)


Thanks
	Christian