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From: <rv...@us...> - 2009-12-15 17:58:55
|
Revision: 367
http://treebase.svn.sourceforge.net/treebase/?rev=367&view=rev
Author: rvos
Date: 2009-12-15 17:58:49 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/images/
trunk/treebase-core/lib/images/colors/
trunk/treebase-core/lib/images/colors/0
trunk/treebase-core/lib/images/colors/0blank-off.gif
trunk/treebase-core/lib/images/colors/0blank-on.gif
trunk/treebase-core/lib/images/colors/0citationsTab.gif
trunk/treebase-core/lib/images/colors/0graphicsTab.gif
trunk/treebase-core/lib/images/colors/0infoBarBase.gif
trunk/treebase-core/lib/images/colors/0modulesTab.gif
trunk/treebase-core/lib/images/colors/0parametersTab.gif
trunk/treebase-core/lib/images/colors/0textTab.gif
trunk/treebase-core/lib/images/colors/1
trunk/treebase-core/lib/images/colors/1blank-off.gif
trunk/treebase-core/lib/images/colors/1blank-on.gif
trunk/treebase-core/lib/images/colors/1citationsTab.gif
trunk/treebase-core/lib/images/colors/1graphicsTab.gif
trunk/treebase-core/lib/images/colors/1infoBarBase.gif
trunk/treebase-core/lib/images/colors/1modulesTab.gif
trunk/treebase-core/lib/images/colors/1parametersTab.gif
trunk/treebase-core/lib/images/colors/1textTab.gif
trunk/treebase-core/lib/images/colors/2
trunk/treebase-core/lib/images/colors/2blank-off.gif
trunk/treebase-core/lib/images/colors/2blank-on.gif
trunk/treebase-core/lib/images/colors/2citationsTab.gif
trunk/treebase-core/lib/images/colors/2graphicsTab.gif
trunk/treebase-core/lib/images/colors/2infoBarBase.gif
trunk/treebase-core/lib/images/colors/2modulesTab.gif
trunk/treebase-core/lib/images/colors/2parametersTab.gif
trunk/treebase-core/lib/images/colors/2textTab.gif
trunk/treebase-core/lib/images/colors/3
trunk/treebase-core/lib/images/colors/3blank-off.gif
trunk/treebase-core/lib/images/colors/3blank-on.gif
trunk/treebase-core/lib/images/colors/3citationsTab.gif
trunk/treebase-core/lib/images/colors/3graphicsTab.gif
trunk/treebase-core/lib/images/colors/3infoBarBase.gif
trunk/treebase-core/lib/images/colors/3modulesTab.gif
trunk/treebase-core/lib/images/colors/3parametersTab.gif
trunk/treebase-core/lib/images/colors/3textTab.gif
Added: trunk/treebase-core/lib/images/colors/0
===================================================================
--- trunk/treebase-core/lib/images/colors/0 (rev 0)
+++ trunk/treebase-core/lib/images/colors/0 2009-12-15 17:58:49 UTC (rev 367)
@@ -0,0 +1,5 @@
+1.0 0.894 0.7686 bisquePALE Color scheme: sand/tan
+0.9333 0.9398 0.6667 paleGoldenRodLIGHT
+0.87 0.7216 0.5294 burlywoodMEDIUM
+0.6275 0.3216 0.1765 siennaDARK
+0.87 0.7216 0.5294 burlywoodPROJECT
Added: trunk/treebase-core/lib/images/colors/0blank-off.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/0blank-off.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/0blank-on.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/0blank-on.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/0citationsTab.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/0citationsTab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/0graphicsTab.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/0graphicsTab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/0infoBarBase.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/0infoBarBase.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/0modulesTab.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/0modulesTab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
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===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/0parametersTab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
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===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/0textTab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/1
===================================================================
--- trunk/treebase-core/lib/images/colors/1 (rev 0)
+++ trunk/treebase-core/lib/images/colors/1 2009-12-15 17:58:49 UTC (rev 367)
@@ -0,0 +1,6 @@
+0.8086 0.824 1.0 pale Color scheme: blue
+0.7267 0.8098 0.9333 LIGHT
+0.5294 0.5216 0.87 MEDIUM
+0.2000 0.2500 0.5875 DARK
+0.5294 0.5216 0.87 PROJECT
+
Added: trunk/treebase-core/lib/images/colors/1blank-off.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/1blank-off.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
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===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/1blank-on.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/1citationsTab.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/1citationsTab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/1graphicsTab.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/1graphicsTab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/1infoBarBase.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/1infoBarBase.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/1modulesTab.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/1modulesTab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/1parametersTab.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/1parametersTab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/1textTab.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/1textTab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/2
===================================================================
--- trunk/treebase-core/lib/images/colors/2 (rev 0)
+++ trunk/treebase-core/lib/images/colors/2 2009-12-15 17:58:49 UTC (rev 367)
@@ -0,0 +1,21 @@
+0.8086 1.0 0.824 pale Color scheme: green
+0.7267 0.886 0.64 LIGHT
+0.5294 0.87 0.5216 MEDIUM
+0.1500 0.5075 0.1516 DARK
+0.5294 0.87 0.5216 PROJECT
+
+
+old version:
+0.8086 1.0 0.824 pale Color scheme: green
+0.7267 0.9333 0.8098 LIGHT
+0.5294 0.87 0.5216 MEDIUM
+0.2765 0.6275 0.3216 DARK
+0.5294 0.87 0.5216 PROJECT
+
+
+older version:
+0.7686 1.0 0.894 pale Color scheme: green
+0.6667 0.9333 0.9398 LIGHT
+0.5294 0.87 0.7216 MEDIUM
+0.1765 0.6275 0.3216 DARK
+0.5294 0.87 0.7216 PROJECT
Added: trunk/treebase-core/lib/images/colors/2blank-off.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/2blank-off.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/2blank-on.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/2blank-on.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/2citationsTab.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/2citationsTab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/2graphicsTab.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/2graphicsTab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/2infoBarBase.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/2infoBarBase.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/2modulesTab.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/2modulesTab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/2parametersTab.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/2parametersTab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/2textTab.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/2textTab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/3
===================================================================
--- trunk/treebase-core/lib/images/colors/3 (rev 0)
+++ trunk/treebase-core/lib/images/colors/3 2009-12-15 17:58:49 UTC (rev 367)
@@ -0,0 +1,5 @@
+1.0 0.794 1 PALE color scheme: violet
+0.9333 0.6667 0.9398 LIGHT
+0.87 0.5294 0.7816 MEDIUM
+0.4275 0.1765 0.4216 DARK
+0.87 0.5294 0.7816 PROJECT
Added: trunk/treebase-core/lib/images/colors/3blank-off.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/3blank-off.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/3blank-on.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/3blank-on.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/3citationsTab.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/3citationsTab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/3graphicsTab.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/3graphicsTab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/3infoBarBase.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/3infoBarBase.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/3modulesTab.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/3modulesTab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/3parametersTab.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/3parametersTab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colors/3textTab.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colors/3textTab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-12-15 17:50:45
|
Revision: 366
http://treebase.svn.sourceforge.net/treebase/?rev=366&view=rev
Author: rvos
Date: 2009-12-15 17:50:39 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/documentation.html
Added: trunk/treebase-core/lib/documentation.html
===================================================================
--- trunk/treebase-core/lib/documentation.html (rev 0)
+++ trunk/treebase-core/lib/documentation.html 2009-12-15 17:50:39 UTC (rev 366)
@@ -0,0 +1,27 @@
+<html>
+
+ <head>
+ <meta http-equiv="content-type" content="text/html;charset=iso-8859-1">
+ <meta name="generator" content="Adobe GoLive 4">
+ <title>Mesquite Read Me</title>
+ </head>
+
+ <body>
+ <h2>Mesquite: a modular system for evolutionary analysis</h2>
+ <p><font size="4"><b>The documentation for Mesquite can be found <a href="docs/mesquite/manual.html">here</a></b></font><font size="4"><b>.</b></font></p>
+
+<p><font size="4"><b>Developer documentation for Mesquite can be found <a href="http://mesquiteproject.org/mesquite/development/development.html">here</a>.</b></font></p>
+
+<p><font size="4"><b>Source code for Mesquite can be found <a href="http://mesquiteproject.org/mesquite/download/source.html">here</a>.</b></font></p>
+ <h2>
+ <hr>
+ Installation and getting started</h2>
+ <p>Installations instructions are available from the <a href="http://mesquiteproject.org/mesquite/download/download.html">download page</a>.</p>
+ <h2>Main class</h2>
+ <p>The main class is Mesquite Folder/mesquite/Mesquite.class. It can take as an argument the name of a data file to open.</p>
+ <p>
+ <hr>
+Copyright 1999-2007 W. & D. Maddison
+</body>
+
+</html>
Property changes on: trunk/treebase-core/lib/documentation.html
___________________________________________________________________
Added: svn:executable
+ *
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-12-15 17:50:20
|
Revision: 365
http://treebase.svn.sourceforge.net/treebase/?rev=365&view=rev
Author: rvos
Date: 2009-12-15 17:50:12 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/Run_Mesquite_Windows.bat
Added: trunk/treebase-core/lib/Run_Mesquite_Windows.bat
===================================================================
--- trunk/treebase-core/lib/Run_Mesquite_Windows.bat (rev 0)
+++ trunk/treebase-core/lib/Run_Mesquite_Windows.bat 2009-12-15 17:50:12 UTC (rev 365)
@@ -0,0 +1 @@
+java -Xmx400M -Djava.library.path=lib -cp . mesquite.Mesquite
Property changes on: trunk/treebase-core/lib/Run_Mesquite_Windows.bat
___________________________________________________________________
Added: svn:executable
+ *
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-12-15 17:50:09
|
Revision: 364
http://treebase.svn.sourceforge.net/treebase/?rev=364&view=rev
Author: rvos
Date: 2009-12-15 17:49:59 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/Run_Mesquite_OSX.command
Added: trunk/treebase-core/lib/Run_Mesquite_OSX.command
===================================================================
--- trunk/treebase-core/lib/Run_Mesquite_OSX.command (rev 0)
+++ trunk/treebase-core/lib/Run_Mesquite_OSX.command 2009-12-15 17:49:59 UTC (rev 364)
@@ -0,0 +1,2 @@
+dir=`dirname "$0"`
+java -Xmx400M -Djava.library.path=lib -cp "$dir" mesquite.Mesquite
Property changes on: trunk/treebase-core/lib/Run_Mesquite_OSX.command
___________________________________________________________________
Added: svn:executable
+ *
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-12-15 17:48:05
|
Revision: 363
http://treebase.svn.sourceforge.net/treebase/?rev=363&view=rev
Author: rvos
Date: 2009-12-15 17:47:59 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/jars/
trunk/treebase-core/lib/jars/JSci.zip
trunk/treebase-core/lib/jars/Jama-1.0.1.zip
trunk/treebase-core/lib/jars/ToLBaseClasses.jar
trunk/treebase-core/lib/jars/iText.jar
trunk/treebase-core/lib/jars/pal.zip
Added: trunk/treebase-core/lib/jars/JSci.zip
===================================================================
(Binary files differ)
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===================================================================
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___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/jars/ToLBaseClasses.jar
===================================================================
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___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-12-15 17:47:42
|
Revision: 362
http://treebase.svn.sourceforge.net/treebase/?rev=362&view=rev
Author: rvos
Date: 2009-12-15 17:47:37 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/lib/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-12-15 17:45:14
|
Revision: 361
http://treebase.svn.sourceforge.net/treebase/?rev=361&view=rev
Author: rvos
Date: 2009-12-15 17:45:07 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/org/
trunk/treebase-core/lib/org/apache/
trunk/treebase-core/lib/org/apache/hivemind/
trunk/treebase-core/lib/org/apache/hivemind/util/
trunk/treebase-core/lib/org/apache/hivemind/util/ClassAdaptor.class
trunk/treebase-core/lib/org/apache/hivemind/util/PropertyAdaptor.class
trunk/treebase-core/lib/org/apache/hivemind/util/PropertyUtils.class
Added: trunk/treebase-core/lib/org/apache/hivemind/util/ClassAdaptor.class
===================================================================
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Added: svn:mime-type
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This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
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From: <rv...@us...> - 2009-12-15 17:44:58
|
Revision: 360
http://treebase.svn.sourceforge.net/treebase/?rev=360&view=rev
Author: rvos
Date: 2009-12-15 17:44:50 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/lesser.txt
Added: trunk/treebase-core/lib/lesser.txt
===================================================================
--- trunk/treebase-core/lib/lesser.txt (rev 0)
+++ trunk/treebase-core/lib/lesser.txt 2009-12-15 17:44:50 UTC (rev 360)
@@ -0,0 +1,504 @@
+ GNU LESSER GENERAL PUBLIC LICENSE
+ Version 2.1, February 1999
+
+ Copyright (C) 1991, 1999 Free Software Foundation, Inc.
+ 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+[This is the first released version of the Lesser GPL. It also counts
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+ Copyright (C) <year> <name of author>
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+ License as published by the Free Software Foundation; either
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+
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+ but WITHOUT ANY WARRANTY; without even the implied warranty of
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+
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+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the library, if
+necessary. Here is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the
+ library `Frob' (a library for tweaking knobs) written by James Random Hacker.
+
+ <signature of Ty Coon>, 1 April 1990
+ Ty Coon, President of Vice
+
+That's all there is to it!
+
+
Property changes on: trunk/treebase-core/lib/lesser.txt
___________________________________________________________________
Added: svn:executable
+ *
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-12-15 17:44:46
|
Revision: 359
http://treebase.svn.sourceforge.net/treebase/?rev=359&view=rev
Author: rvos
Date: 2009-12-15 17:44:34 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/startingMesquiteAndMemoryAllocation.txt
Added: trunk/treebase-core/lib/startingMesquiteAndMemoryAllocation.txt
===================================================================
--- trunk/treebase-core/lib/startingMesquiteAndMemoryAllocation.txt (rev 0)
+++ trunk/treebase-core/lib/startingMesquiteAndMemoryAllocation.txt 2009-12-15 17:44:34 UTC (rev 359)
@@ -0,0 +1,48 @@
+To Run Mesquite
+
+To run Mesquite, you need Java installed. Mesquite 2 runs only on Java 1.4 and higher. We suggest Java 1.5 or higher.
+
+Once Mesquite_Folder is unzipped, you can start Mesquite as follows:
+
+==================
+Mac OS X
+There are 4 ways to start Mesquite under OS X:
+
+1. Default: Double click Mesquite OSX.app
+
+2. To run java 1.4: Double click Mesquite OSX (Java 1.4).app
+
+3. To run Mesquite with more memory: Double click Mesquite OSX (hi-mem).app (Hint: if you want to adjust the memory allocated, right click on the application's icon, go to info.plist in Contents, and change Xmx512M to Xmx700M or higher)
+
+4. Or, to adjust how exactly Mesquite starts, including memory allocation:
+Run Mesquite by double clicking the file run_mesquiteOSX.command. If double clicking this file does not start Mesquite, select the file in the Finder, choose Get Info, and change the "Open With" to "Terminal.app", which is in /Applications/Utilities/
+
+To give Mesquite even more memory, open the file with a text editor and edit the line:
+
+java -Xmx400M -Djava.library.path=lib -cp . mesquite.Mesquite
+
+to raise the number 400 higher, but don't introduce any spaces!
+
+
+==================
+Windows
+
+There are 3 ways to start Mesquite under Windows:
+
+1. Default: use the installer and double click Mesquite.exe
+
+2. To run Mesquite with more memory: use the alternative high memory installer (available at mesquiteproject.org), reinstall Mesquite, and double click Mesquite.exe.
+
+3. Or, to adjust how exactly Mesquite starts, including memory allocation:
+Run Mesquite by double clicking the file run_mesquiteWindows.bat. To give Mesquite even more memory, open the file with a text editor and edit the line:
+
+java -Xmx400M -Djava.library.path=lib -cp . mesquite.Mesquite
+
+to raise the number 400 higher.
+
+
+==================
+Linux etc.
+
+Run Mesquite by double clicking run_mesquite.sh
+
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-12-15 17:44:28
|
Revision: 358
http://treebase.svn.sourceforge.net/treebase/?rev=358&view=rev
Author: rvos
Date: 2009-12-15 17:44:21 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/run_mesquite.sh
Added: trunk/treebase-core/lib/run_mesquite.sh
===================================================================
--- trunk/treebase-core/lib/run_mesquite.sh (rev 0)
+++ trunk/treebase-core/lib/run_mesquite.sh 2009-12-15 17:44:21 UTC (rev 358)
@@ -0,0 +1,57 @@
+#!/bin/bash
+
+#Script to identify java VM. Also modifies classpath on cygwin.
+#Written by Travis Wheeler (www.traviswheeler.com)
+
+#If you find bugs or modify the script to improve functionality,
+# please let us know so we can improve the script for everyone
+
+
+# Thanks to William Cook (http://www.cs.utexas.edu/users/wcook/) for the bit that
+# identifies the path containing this script, and uses it to set the classpath.
+# (the exact site of the work that served as inspiration for this code is lost to antiquity)
+
+
+#figure out where java lives
+if [ $MESQUITE_JAVA_HOME ]
+then
+ java="$MESQUITE_JAVA_HOME/bin/java"
+elif [ $JAVA_HOME ]
+then
+ java="$JAVA_HOME/bin/java"
+else
+ tmp=`java -version 2>&1`
+ if echo "$tmp" | grep -q "command not found" # no "java", so try "jre"
+ then
+ tmp=`jre -version 2>&1`
+ if echo "$tmp" | grep -q "command not found"
+ then
+ echo "Can't find java. Try setting either the JAVA_HOME environment variable"
+ exit
+ else
+ java="jre"
+ fi
+ else
+ java="java"
+ fi
+fi
+
+
+# figure out where I live, then run java w/ my containing dir as classpath
+dir=`dirname "$0"`
+os=`uname`
+if test ${os:0:6} = "CYGWIN"
+then
+ if test ${dir:1:8} = "cygdrive"
+ then
+ dir="${dir:10:1}:/${dir:12}"
+ fi
+ chmod -R u+w "$dir/com/"
+ cp -r "$dir/../Resources/com/"* "$dir/com/" >& /dev/null
+ $java -Djava.library.path=lib -cp "$dir" mesquite.Mesquite $*
+else
+ chmod -R u+w "$dir/com/"
+ cp -r "$dir/../Resources/com/"* "$dir/com/" >& /dev/null
+ $java -Djava.library.path=lib -cp "$dir" mesquite.Mesquite $*
+fi
+
Property changes on: trunk/treebase-core/lib/run_mesquite.sh
___________________________________________________________________
Added: svn:executable
+ *
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-12-15 17:17:12
|
Revision: 357
http://treebase.svn.sourceforge.net/treebase/?rev=357&view=rev
Author: rvos
Date: 2009-12-15 17:16:56 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/edu/
trunk/treebase-core/lib/edu/stanford/
trunk/treebase-core/lib/edu/stanford/ejalbert/
trunk/treebase-core/lib/edu/stanford/ejalbert/BrowserLauncher.class
Added: trunk/treebase-core/lib/edu/stanford/ejalbert/BrowserLauncher.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/edu/stanford/ejalbert/BrowserLauncher.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-12-15 17:16:46
|
Revision: 356
http://treebase.svn.sourceforge.net/treebase/?rev=356&view=rev
Author: rvos
Date: 2009-12-15 17:16:33 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/docs/
trunk/treebase-core/lib/docs/mesquite/
trunk/treebase-core/lib/docs/mesquite/BeanTree/
trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/
trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/BeanTree.class
trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/BeanTreeControls.class
trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/Branch.class
trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/TreeCanvas.class
trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/TreeClass.class
trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/com/
trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/com/metrowerks/
trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/com/metrowerks/AppletFrame.class
trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.html
trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.java
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/AncestralStates.html
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/Pagel94.html
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/ProcessCharEvol.html
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/charEvolution.html
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/ancStates.gif
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/anceStates.jpg
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/anolesPlot2D.jpg
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/anolesPlot3D.jpg
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/mirrorTree.jpg
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/p94Table1.jpg
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/p94Table2.jpg
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/pagel94.jpg
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/pairwise.jpg
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/pdapFelsContrH.jpg
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/scm.jpg
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/tcot.gif
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/traceAll.gif
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/traceOverTrees.gif
trunk/treebase-core/lib/docs/mesquite/Diversification/
trunk/treebase-core/lib/docs/mesquite/Diversification/BiSSESimParams.gif
trunk/treebase-core/lib/docs/mesquite/Diversification/diversification.html
trunk/treebase-core/lib/docs/mesquite/Help/
trunk/treebase-core/lib/docs/mesquite/Help/MesquiteFAQ.html
trunk/treebase-core/lib/docs/mesquite/Help/QualityTrees.html
trunk/treebase-core/lib/docs/mesquite/Help/images/
trunk/treebase-core/lib/docs/mesquite/Help/images/Thumbs.db
trunk/treebase-core/lib/docs/mesquite/Help/images/abcTree.GIF
trunk/treebase-core/lib/docs/mesquite/Help/images/ballsNSticksTree.GIF
trunk/treebase-core/lib/docs/mesquite/Help/images/branchesCollapsed.JPG
trunk/treebase-core/lib/docs/mesquite/Help/images/branchesToCollapse.JPG
trunk/treebase-core/lib/docs/mesquite/Help/images/collapseBranchTool.GIF
trunk/treebase-core/lib/docs/mesquite/Help/images/curvogramTree.GIF
trunk/treebase-core/lib/docs/mesquite/Help/images/diagonalTree.GIF
trunk/treebase-core/lib/docs/mesquite/Help/images/fourTreeForms.GIF
trunk/treebase-core/lib/docs/mesquite/Help/images/fragModelScaled.JPG
trunk/treebase-core/lib/docs/mesquite/Help/images/fragModelSim.GIF
trunk/treebase-core/lib/docs/mesquite/Help/images/fragModelSim.JPG
trunk/treebase-core/lib/docs/mesquite/Help/images/fragModelText.JPG
trunk/treebase-core/lib/docs/mesquite/Help/images/fragModelWindow.JPG
trunk/treebase-core/lib/docs/mesquite/Help/images/nodeNamer.GIF
trunk/treebase-core/lib/docs/mesquite/Help/images/observedStatistic.JPG
trunk/treebase-core/lib/docs/mesquite/Help/images/refugiaModel.JPG
trunk/treebase-core/lib/docs/mesquite/Help/images/refugiaModelScaled.JPG
trunk/treebase-core/lib/docs/mesquite/Help/images/refugiaModelSim.JPG
trunk/treebase-core/lib/docs/mesquite/Help/images/refugiaModelText.JPG
trunk/treebase-core/lib/docs/mesquite/Help/images/refugiaModelWindow.JPG
trunk/treebase-core/lib/docs/mesquite/Help/images/squareTree.GIF
trunk/treebase-core/lib/docs/mesquite/Help/slatkinMaddisonS.html
trunk/treebase-core/lib/docs/mesquite/Library/
trunk/treebase-core/lib/docs/mesquite/Library/MesquiteVersionNumber.lbi
trunk/treebase-core/lib/docs/mesquite/Library/Untitled.lbi
trunk/treebase-core/lib/docs/mesquite/Library/_notes/
trunk/treebase-core/lib/docs/mesquite/Library/styles.xml
trunk/treebase-core/lib/docs/mesquite/RandomSimul/
trunk/treebase-core/lib/docs/mesquite/RandomSimul/RandomSimul.html
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/chalceum.jpg
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/codeSnippet.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/exportMatrixBatch.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/fullmodel.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/gamma10reps.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/gamma15.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/gamma15dlog.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/gammaTest.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/sim1.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/simMatrix.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/snippetEg.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/templateEditor2.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/templateManager.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/textViewTab.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/treeCode.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/simChars.html
trunk/treebase-core/lib/docs/mesquite/RandomSimul/simDNA.html
trunk/treebase-core/lib/docs/mesquite/RandomSimul/simTrees.html
trunk/treebase-core/lib/docs/mesquite/Templates/
trunk/treebase-core/lib/docs/mesquite/Templates/Template.dwt
trunk/treebase-core/lib/docs/mesquite/Templates/TemplateBlank.dwt
trunk/treebase-core/lib/docs/mesquite/Templates/mesq.ico
trunk/treebase-core/lib/docs/mesquite/changes.html
trunk/treebase-core/lib/docs/mesquite/characters.html
trunk/treebase-core/lib/docs/mesquite/charts.html
trunk/treebase-core/lib/docs/mesquite/continuous/
trunk/treebase-core/lib/docs/mesquite/continuous/continuous.html
trunk/treebase-core/lib/docs/mesquite/continuous/images/
trunk/treebase-core/lib/docs/mesquite/continuous/images/cvaflies.jpg
trunk/treebase-core/lib/docs/mesquite/continuous/images/landmarks.jpg
trunk/treebase-core/lib/docs/mesquite/credits.html
trunk/treebase-core/lib/docs/mesquite/glossary.html
trunk/treebase-core/lib/docs/mesquite/help.html
trunk/treebase-core/lib/docs/mesquite/howMesquiteWorks.html
trunk/treebase-core/lib/docs/mesquite/images/
trunk/treebase-core/lib/docs/mesquite/images/BembMatrix.gif
trunk/treebase-core/lib/docs/mesquite/images/DNAMatrix.gif
trunk/treebase-core/lib/docs/mesquite/images/DNAMatrix.jpg
trunk/treebase-core/lib/docs/mesquite/images/NSERClogo.jpg
trunk/treebase-core/lib/docs/mesquite/images/a_logo.gif
trunk/treebase-core/lib/docs/mesquite/images/addCharsTool.gif
trunk/treebase-core/lib/docs/mesquite/images/addTaxaTool.gif
trunk/treebase-core/lib/docs/mesquite/images/analyses.gif
trunk/treebase-core/lib/docs/mesquite/images/annot.gif
trunk/treebase-core/lib/docs/mesquite/images/annot.jpg
trunk/treebase-core/lib/docs/mesquite/images/annotation.gif
trunk/treebase-core/lib/docs/mesquite/images/arrow.gif
trunk/treebase-core/lib/docs/mesquite/images/babyMesquite.jpg
trunk/treebase-core/lib/docs/mesquite/images/basics.gif
trunk/treebase-core/lib/docs/mesquite/images/bigModularity.gif
trunk/treebase-core/lib/docs/mesquite/images/blue-ball-small.gif
trunk/treebase-core/lib/docs/mesquite/images/bruchine.jpg
trunk/treebase-core/lib/docs/mesquite/images/cellPictures.gif
trunk/treebase-core/lib/docs/mesquite/images/cellPictures.jpg
trunk/treebase-core/lib/docs/mesquite/images/charList.jpg
trunk/treebase-core/lib/docs/mesquite/images/charWand.gif
trunk/treebase-core/lib/docs/mesquite/images/closeTab.jpg
trunk/treebase-core/lib/docs/mesquite/images/color.gif
trunk/treebase-core/lib/docs/mesquite/images/colorLegend.gif
trunk/treebase-core/lib/docs/mesquite/images/construction.gif
trunk/treebase-core/lib/docs/mesquite/images/dataWindow.gif
trunk/treebase-core/lib/docs/mesquite/images/demail.jpg
trunk/treebase-core/lib/docs/mesquite/images/depthVsImbalance.jpg
trunk/treebase-core/lib/docs/mesquite/images/email.jpg
trunk/treebase-core/lib/docs/mesquite/images/employeeTree.gif
trunk/treebase-core/lib/docs/mesquite/images/employees.jpg
trunk/treebase-core/lib/docs/mesquite/images/exampleWindow.jpg
trunk/treebase-core/lib/docs/mesquite/images/eyeDropper.gif
trunk/treebase-core/lib/docs/mesquite/images/fadeDown.gif
trunk/treebase-core/lib/docs/mesquite/images/fadeLeft.gif
trunk/treebase-core/lib/docs/mesquite/images/fadeRight.gif
trunk/treebase-core/lib/docs/mesquite/images/fadeUp.gif
trunk/treebase-core/lib/docs/mesquite/images/favicon.ico
trunk/treebase-core/lib/docs/mesquite/images/gcSequence.jpg
trunk/treebase-core/lib/docs/mesquite/images/green-ball-small.gif
trunk/treebase-core/lib/docs/mesquite/images/helpButton.gif
trunk/treebase-core/lib/docs/mesquite/images/iBeamTool.gif
trunk/treebase-core/lib/docs/mesquite/images/iemail.jpg
trunk/treebase-core/lib/docs/mesquite/images/infoBar.gif
trunk/treebase-core/lib/docs/mesquite/images/introduction.gif
trunk/treebase-core/lib/docs/mesquite/images/keySelector.gif
trunk/treebase-core/lib/docs/mesquite/images/listC.gif
trunk/treebase-core/lib/docs/mesquite/images/listT.gif
trunk/treebase-core/lib/docs/mesquite/images/littleModularity.gif
trunk/treebase-core/lib/docs/mesquite/images/logWindow.jpg
trunk/treebase-core/lib/docs/mesquite/images/logo_cipres.gif
trunk/treebase-core/lib/docs/mesquite/images/maintainTargetMatch.jpg
trunk/treebase-core/lib/docs/mesquite/images/manual.jpg
trunk/treebase-core/lib/docs/mesquite/images/matrix.gif
trunk/treebase-core/lib/docs/mesquite/images/mesquiteIcon.gif
trunk/treebase-core/lib/docs/mesquite/images/mesquiteLower.gif
trunk/treebase-core/lib/docs/mesquite/images/mesquiteLowerManual.GIF
trunk/treebase-core/lib/docs/mesquite/images/mesquitePlain.gif
trunk/treebase-core/lib/docs/mesquite/images/mesquitesmall.gif
trunk/treebase-core/lib/docs/mesquite/images/miniScroll.jpg
trunk/treebase-core/lib/docs/mesquite/images/miniscrollHoriz.gif
trunk/treebase-core/lib/docs/mesquite/images/miniscrollVert.gif
trunk/treebase-core/lib/docs/mesquite/images/notesTool.gif
trunk/treebase-core/lib/docs/mesquite/images/nsf4c.jpg
trunk/treebase-core/lib/docs/mesquite/images/objects.gif
trunk/treebase-core/lib/docs/mesquite/images/pFWindow.jpg
trunk/treebase-core/lib/docs/mesquite/images/paintBucket.gif
trunk/treebase-core/lib/docs/mesquite/images/pixel.gif
trunk/treebase-core/lib/docs/mesquite/images/popIn.jpg
trunk/treebase-core/lib/docs/mesquite/images/popOut.jpg
trunk/treebase-core/lib/docs/mesquite/images/prerelease.gif
trunk/treebase-core/lib/docs/mesquite/images/projFilesWindow.jpg
trunk/treebase-core/lib/docs/mesquite/images/project1.gif
trunk/treebase-core/lib/docs/mesquite/images/projector.gif
trunk/treebase-core/lib/docs/mesquite/images/projectsFiles.gif
trunk/treebase-core/lib/docs/mesquite/images/release.gif
trunk/treebase-core/lib/docs/mesquite/images/searchData.jpg
trunk/treebase-core/lib/docs/mesquite/images/searchDicon.jpg
trunk/treebase-core/lib/docs/mesquite/images/searchFeaturesAND.jpg
trunk/treebase-core/lib/docs/mesquite/images/searchFeaturesOR.jpg
trunk/treebase-core/lib/docs/mesquite/images/searchWindow.jpg
trunk/treebase-core/lib/docs/mesquite/images/selectTaxa.gif
trunk/treebase-core/lib/docs/mesquite/images/showPicture.gif
trunk/treebase-core/lib/docs/mesquite/images/small.top.arrow.gif
trunk/treebase-core/lib/docs/mesquite/images/sortTool.gif
trunk/treebase-core/lib/docs/mesquite/images/stepsVsHydro.jpg
trunk/treebase-core/lib/docs/mesquite/images/submenu.gif
trunk/treebase-core/lib/docs/mesquite/images/tabLeft.gif
trunk/treebase-core/lib/docs/mesquite/images/tabRight.gif
trunk/treebase-core/lib/docs/mesquite/images/tabs.jpg
trunk/treebase-core/lib/docs/mesquite/images/taxWand.gif
trunk/treebase-core/lib/docs/mesquite/images/thassus.jpg
trunk/treebase-core/lib/docs/mesquite/images/toc.GIF
trunk/treebase-core/lib/docs/mesquite/images/toolPalette.gif
trunk/treebase-core/lib/docs/mesquite/images/treeScroll.jpg
trunk/treebase-core/lib/docs/mesquite/images/treeTools/
trunk/treebase-core/lib/docs/mesquite/images/treeTools/adjustBranchLength.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/adjustNodePosition.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/annotateNode.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/assignLineageWidth.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/branchInfo.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/collapseAllBranches.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/collapseBranch.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/colorBranch.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/drawAsTriangle.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/hyperlink.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/insertUnbranchedNode.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/interchangeBranches.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/ladderizeClade.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/magnifyClade.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/nameNode.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/pruneClade.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/rerootAtBranch.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/searchBetterTool.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/searchTaxonInDBTool.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/selectBranch.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/selectBranchesInClade.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/selectTaxaInClade.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/showPicture.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/stretchBranch.gif
trunk/treebase-core/lib/docs/mesquite/images/treeValues.jpg
trunk/treebase-core/lib/docs/mesquite/images/treeWindow.gif
trunk/treebase-core/lib/docs/mesquite/images/ubc_blue.gif
trunk/treebase-core/lib/docs/mesquite/images/using.gif
trunk/treebase-core/lib/docs/mesquite/images/wand.gif
trunk/treebase-core/lib/docs/mesquite/images/wiko_logo_grau.gif
trunk/treebase-core/lib/docs/mesquite/images/window.gif
trunk/treebase-core/lib/docs/mesquite/installation/
trunk/treebase-core/lib/docs/mesquite/installation/images/
trunk/treebase-core/lib/docs/mesquite/installation/images/installWin1.gif
trunk/treebase-core/lib/docs/mesquite/installation/images/installWin2.gif
trunk/treebase-core/lib/docs/mesquite/installation/images/installWin3.GIF
trunk/treebase-core/lib/docs/mesquite/installation/images/osXinstall.jpg
trunk/treebase-core/lib/docs/mesquite/installation/images/wc.gif
trunk/treebase-core/lib/docs/mesquite/installation/installation.html
trunk/treebase-core/lib/docs/mesquite/installation/installationMacOS.html
trunk/treebase-core/lib/docs/mesquite/installation/installationUNIX.html
trunk/treebase-core/lib/docs/mesquite/installation/installationWindows.html
trunk/treebase-core/lib/docs/mesquite/managingFiles.html
trunk/treebase-core/lib/docs/mesquite/manual.html
trunk/treebase-core/lib/docs/mesquite/menus.html
trunk/treebase-core/lib/docs/mesquite/moduleIndex.html
trunk/treebase-core/lib/docs/mesquite/modules.html
trunk/treebase-core/lib/docs/mesquite/molecular/
trunk/treebase-core/lib/docs/mesquite/molecular/images/
trunk/treebase-core/lib/docs/mesquite/molecular/images/aahydroColorMatrix.jpg
trunk/treebase-core/lib/docs/mesquite/molecular/images/assocBeforeFusedExport.gif
trunk/treebase-core/lib/docs/mesquite/molecular/images/becomesArrow.gif
trunk/treebase-core/lib/docs/mesquite/molecular/images/consensus.gif
trunk/treebase-core/lib/docs/mesquite/molecular/images/consensusAA.gif
trunk/treebase-core/lib/docs/mesquite/molecular/images/cytStructure.jpg
trunk/treebase-core/lib/docs/mesquite/molecular/images/gcBiasColorMatrix.jpg
trunk/treebase-core/lib/docs/mesquite/molecular/images/gcBiasTaxa.jpg
trunk/treebase-core/lib/docs/mesquite/molecular/images/gene1beforeConcat.jpg
trunk/treebase-core/lib/docs/mesquite/molecular/images/gene1beforeConcat2.jpg
trunk/treebase-core/lib/docs/mesquite/molecular/images/gene2beforeConcat.jpg
trunk/treebase-core/lib/docs/mesquite/molecular/images/gene2beforeInclude.jpg
trunk/treebase-core/lib/docs/mesquite/molecular/images/genePQRBeforeInclude.jpg
trunk/treebase-core/lib/docs/mesquite/molecular/images/genesAfterConcat.jpg
trunk/treebase-core/lib/docs/mesquite/molecular/images/genesAfterInclude.jpg
trunk/treebase-core/lib/docs/mesquite/molecular/molecular.html
trunk/treebase-core/lib/docs/mesquite/otherPrograms.html
trunk/treebase-core/lib/docs/mesquite/popGen/
trunk/treebase-core/lib/docs/mesquite/popGen/images/
trunk/treebase-core/lib/docs/mesquite/popGen/images/assoc.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/assoc2.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/assocEditing.jpg
trunk/treebase-core/lib/docs/mesquite/popGen/images/assocEst.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/assocList.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/createNewPop.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/depths.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/depths10000.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/geneTree.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/mbfChart.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/mbfFiles.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/mbfFiles2.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/mbfMBF.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/mbfModel.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/mbfTree.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/sDivergence.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/tree.gif
trunk/treebase-core/lib/docs/mesquite/popGen/popGen.html
trunk/treebase-core/lib/docs/mesquite/publication.html
trunk/treebase-core/lib/docs/mesquite/scripting.html
trunk/treebase-core/lib/docs/mesquite/studies/
trunk/treebase-core/lib/docs/mesquite/studies/index.html
trunk/treebase-core/lib/docs/mesquite/studies/study001/
trunk/treebase-core/lib/docs/mesquite/studies/study001/images/
trunk/treebase-core/lib/docs/mesquite/studies/study001/images/barValue.gif
trunk/treebase-core/lib/docs/mesquite/studies/study001/images/boundaryLeft.gif
trunk/treebase-core/lib/docs/mesquite/studies/study001/images/boundaryRight.gif
trunk/treebase-core/lib/docs/mesquite/studies/study001/images/histogramAsText.gif
trunk/treebase-core/lib/docs/mesquite/studies/study001/images/noterid.jpg
trunk/treebase-core/lib/docs/mesquite/studies/study001/images/showPercentile.gif
trunk/treebase-core/lib/docs/mesquite/studies/study001/images/showPercentileText.gif
trunk/treebase-core/lib/docs/mesquite/studies/study001/images/tdtree.gif
trunk/treebase-core/lib/docs/mesquite/studies/study001/images/templateEditor1.gif
trunk/treebase-core/lib/docs/mesquite/studies/study001/images/testStructure1.gif
trunk/treebase-core/lib/docs/mesquite/studies/study001/images/trachypachid.jpg
trunk/treebase-core/lib/docs/mesquite/studies/study001/images/treeTestDialog.gif
trunk/treebase-core/lib/docs/mesquite/studies/study001/index.html
trunk/treebase-core/lib/docs/mesquite/studies/study001/study001.nex
trunk/treebase-core/lib/docs/mesquite/studies/study002/
trunk/treebase-core/lib/docs/mesquite/studies/study002/images/
trunk/treebase-core/lib/docs/mesquite/studies/study002/images/embf.gif
trunk/treebase-core/lib/docs/mesquite/studies/study002/images/gamma.gif
trunk/treebase-core/lib/docs/mesquite/studies/study002/images/model.gif
trunk/treebase-core/lib/docs/mesquite/studies/study002/images/modelTree.gif
trunk/treebase-core/lib/docs/mesquite/studies/study002/images/modelTreePlain.gif
trunk/treebase-core/lib/docs/mesquite/studies/study002/images/parsimony.gif
trunk/treebase-core/lib/docs/mesquite/studies/study002/images/parsimonyLB.gif
trunk/treebase-core/lib/docs/mesquite/studies/study002/images/paupEnd.gif
trunk/treebase-core/lib/docs/mesquite/studies/study002/images/paupStart.gif
trunk/treebase-core/lib/docs/mesquite/studies/study002/images/result.gif
trunk/treebase-core/lib/docs/mesquite/studies/study002/images/titv.gif
trunk/treebase-core/lib/docs/mesquite/studies/study002/index.html
trunk/treebase-core/lib/docs/mesquite/studies/study002/study002.nex
trunk/treebase-core/lib/docs/mesquite/support.html
trunk/treebase-core/lib/docs/mesquite/taxa.html
trunk/treebase-core/lib/docs/mesquite/toc.html
trunk/treebase-core/lib/docs/mesquite/trees.html
trunk/treebase-core/lib/docs/mesquite/whyMesquite.html
trunk/treebase-core/lib/docs/mesquite/windows.html
Added: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/BeanTree.class
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Property changes on: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/BeanTree.class
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+ *
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+ application/octet-stream
Added: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/BeanTreeControls.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/BeanTreeControls.class
___________________________________________________________________
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+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/Branch.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/Branch.class
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/TreeCanvas.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/TreeCanvas.class
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/TreeClass.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/TreeClass.class
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/com/metrowerks/AppletFrame.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/com/metrowerks/AppletFrame.class
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.html
===================================================================
--- trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.html (rev 0)
+++ trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.html 2009-12-15 17:16:33 UTC (rev 356)
@@ -0,0 +1,9 @@
+<title>BeanTree</title>
+<h2>BeanTree</h2>
+It all started yesterday because I thought that perhaps I should try out some object oriented programming in case I wanted to teach an object oriented language to the students in my class next spring....
+<p>Much faster as stand alone application.
+<p>Taxon names must be one character only (actually, they can all be the same character).
+<hr>
+<applet codebase="BeanTree" code="BeanTree.class" width="500" height="400">
+</applet>
+<hr>
Property changes on: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.html
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.java
===================================================================
--- trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.java (rev 0)
+++ trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.java 2009-12-15 17:16:33 UTC (rev 356)
@@ -0,0 +1,492 @@
+//package wpm;
+
+import java.awt.*;
+import java.applet.Applet;
+
+
+public class BeanTree extends Applet
+{
+ static TreeCanvas TreeDisplay;
+ static BeanTreeControls controls;
+
+
+ public void init()
+ {
+ setLayout( new BorderLayout() );
+ resize(300, 300);
+ TreeDisplay = new TreeCanvas(10, 10, 400, 400);
+ add( "Center", TreeDisplay );
+ add("North", controls = new BeanTreeControls(TreeDisplay));
+ TreeDisplay.Tree = new TreeClass();
+ TreeDisplay.controls = controls;
+ TreeDisplay.Tree.SubRoot = new Branch(null, false);
+ TreeDisplay.Tree.Root = new Branch(TreeDisplay.Tree.SubRoot, false);
+ TreeDisplay.edgewidth = 10;
+ TreeDisplay.needsUpdating = false;
+ TreeDisplay.highlightedBranch = null;
+ TreeDisplay.Tree.exists = false;
+ repaint();
+ }
+
+ public void start() {
+ controls.enable();
+ }
+
+ public void stop() {
+ controls.disable();
+ }
+ public static void main(String args[])
+ {
+ com.metrowerks.AppletFrame.startApplet("BeanTree", "BeanTree", args);
+ }
+
+}
+/** ======================================================================== */
+class TreeCanvas extends Canvas {
+ TreeClass Tree;
+
+ int x_max, y_max;
+ int edgewidth;
+ Branch highlightedBranch, branchFrom;
+ int xFrom, yFrom, xTo, yTo;
+ boolean needsUpdating;
+ String treeDescription;
+ BeanTreeControls controls;
+ private int lastleft;
+ private int taxspacing;
+ private Branch foundBranch;
+
+
+ public TreeCanvas( int x_max, int y_max, int x_size, int y_size )
+ {
+ this.x_max = x_max;
+ this.y_max = y_max;
+
+ resize( x_size, y_size );
+ repaint();
+ }
+
+
+ /*_________________________________________________*/
+ private void WriteTreeDescription(Branch N) {
+ if (N.left!=null)
+ {
+ treeDescription+='(';
+ WriteTreeDescription(N.left);
+ treeDescription+=',';
+ WriteTreeDescription(N.right);
+ treeDescription+=')';
+ }
+ else
+ {
+ treeDescription+='*';
+ }
+ }
+ public String Describe() {
+ treeDescription="";
+ WriteTreeDescription(Tree.Root);
+ treeDescription+=';';
+ return treeDescription;
+ }
+ /*_________________________________________________*/
+ private void CalcInternalLocs(Branch N)
+ {
+ if (N.left != null) //internal
+ {
+ CalcInternalLocs(N.left);
+ CalcInternalLocs(N.right);
+
+ N.y = (-N.left.x + N.right.x+N.left.y + N.right.y) / 2;
+ N.x =(N.left.x + N.right.x - N.left.y + N.right.y) / 2;
+ }
+ }
+
+ /*_________________________________________________*/
+ private void CalcTerminalLocs(Branch N)
+ {
+ if (N.left == null) //terminal
+ {
+ lastleft+= taxspacing;
+ N.y = 90;
+ N.x = lastleft;
+ }
+ else
+ {
+ CalcTerminalLocs(N.left);
+ CalcTerminalLocs(N.right);
+ }
+ }
+
+ /*_________________________________________________*/
+ private void CalcBranchPolys(Branch N)
+ {
+ if (N.left != null) //terminal
+ {
+ CalcBranchPolys(N.left);
+ CalcBranchPolys(N.right);
+ N.branchPoly.npoints=0;
+ N.branchPoly.addPoint(N.x, N.y);
+ N.branchPoly.addPoint(N.x+edgewidth/2, N.y-edgewidth/2);
+ N.branchPoly.addPoint(N.x+edgewidth, N.y);
+ N.branchPoly.addPoint(N.ancestor.x+edgewidth, N.ancestor.y);
+ N.branchPoly.addPoint(N.ancestor.x, N.ancestor.y);
+ N.branchPoly.npoints=5;
+ }
+ else
+ {
+ N.branchPoly.npoints=0;
+ N.branchPoly.addPoint(N.x, N.y);
+ N.branchPoly.addPoint(N.x+edgewidth, N.y);
+ N.branchPoly.addPoint(N.ancestor.x+edgewidth, N.ancestor.y);
+ N.branchPoly.addPoint(N.ancestor.x, N.ancestor.y);
+ N.branchPoly.npoints=4;
+ }
+ }
+ /*_________________________________________________*/
+ private void calcBranches() {
+ lastleft = 0;
+ taxspacing = (bounds().width - 10) / Tree.numTaxa;
+ CalcTerminalLocs(Tree.Root);
+ CalcInternalLocs(Tree.Root);
+ Tree.SubRoot.y = (Tree.Root.y)+20;
+ Tree.SubRoot.x = (Tree.Root.x)-20;
+ CalcBranchPolys(Tree.Root);
+ }
+
+ /*_________________________________________________*/
+ private void drawBranch(Graphics g, Branch N) {
+ g.setColor(N.color);
+ g.fillPolygon(N.branchPoly);
+ if (N.left != null)
+ drawBranch(g, N.left);
+ if (N.right != null)
+ drawBranch(g, N.right);
+ }
+ /*_________________________________________________*/
+ public void drawTree(Graphics g) {
+ if (Tree.exists)
+ {
+ calcBranches();
+ drawBranch(g, Tree.Root);
+ }
+ }
+ /*_________________________________________________*/
+ public void paint(Graphics g) {
+ drawTree(g);
+ needsUpdating = false;
+ }
+ /*_________________________________________________*/
+
+ public void InvertBranch(Graphics g, Branch N) {
+ // N.color=Color.white;
+ highlightedBranch=N;
+ g.setColor(Color.white);
+ g.fillPolygon(N.branchPoly);
+ // needsUpdating=true;
+ }
+
+ /*_________________________________________________*/
+ public void RevertBranch(Graphics g, Branch N) {
+ // N.color=Color.black;
+ highlightedBranch=null;
+ g.setColor(Color.black);
+ g.fillPolygon(N.branchPoly);
+ // needsUpdating=true;
+ }
+ /*_________________________________________________*/
+ private void ScanBranches(Branch N, int x, int y)
+ {
+ if (foundBranch==null) {
+ if (N.branchPoly.inside(x, y))
+ foundBranch = N;
+ if (N.left != null) //terminal
+ {
+ ScanBranches(N.left, x, y);
+ ScanBranches(N.right, x, y);
+ }
+ }
+ }
+ /*_________________________________________________*/
+ public Branch FindBranch(int x, int y) {
+ foundBranch=null;
+ ScanBranches(Tree.Root, x, y);
+ return foundBranch;
+ }
+
+ /*_________________________________________________*/
+ public void ScanTouch(Graphics g, int x, int y) {
+ Branch branchFound=FindBranch( x, y);
+ if (branchFound!=null)
+ {
+ branchFrom=branchFound;
+ xFrom=x;
+ yFrom=y;
+ xTo=x;
+ yTo=y;
+ g.setXORMode(Color.gray);
+ g.setColor(Color.black);
+ g.drawLine(xFrom,yFrom,xTo,yTo);
+ }
+
+ }
+ /*_________________________________________________*/
+ public void ScanFlash(Graphics g, int x, int y) {
+ Branch branchFound=FindBranch( x, y);
+ if (highlightedBranch != null)
+ {if (branchFound==null)
+ RevertBranch(g, highlightedBranch);
+ else if (branchFound!=highlightedBranch)
+ {
+ RevertBranch(g, highlightedBranch);
+ InvertBranch(g, branchFound);
+ }
+ }
+ else if (branchFound!=null)
+ InvertBranch(g, branchFound);
+ }
+ /*_________________________________________________*/
+ public void ScanDrop(Graphics g, int x, int y) {
+ Branch branchTo=FindBranch( x, y);
+ if (branchTo != null)
+ {if (branchFrom==branchTo)
+ {
+ }
+ else
+ {
+ Tree.MoveBranch(branchFrom, branchTo);
+ controls.RedescribeTree();
+ }
+ };
+ needsUpdating=true;
+ branchFrom = null;
+
+ }
+ /*_________________________________________________*/
+ public boolean mouseMove(Event e, int x, int y) {
+ Graphics g = getGraphics();
+ ScanFlash(g, x, y);
+ return true;
+ }
+ /*_________________________________________________*/
+ public boolean mouseDown(Event e, int x, int y) {
+ Graphics g = getGraphics();
+ ScanTouch(g, x, y);
+ if (needsUpdating)
+ repaint();
+ return true;
+ }
+
+ /*_________________________________________________*/
+ public boolean mouseDrag(Event e, int x, int y) {
+ if (branchFrom!=null)
+ {
+ Graphics g = getGraphics();
+ g.setColor(Color.black);
+ g.setXORMode(Color.gray);
+ g.drawLine(xFrom,yFrom,xTo,yTo);
+ xTo=x;
+ yTo=y;
+ g.drawLine(xFrom,yFrom,xTo,yTo);
+ }
+ return true;
+ }
+ /*_________________________________________________*/
+ public boolean mouseUp(Event e, int x, int y) {
+ Graphics g = getGraphics();
+ if (branchFrom!=null) {
+ ScanDrop( g, x, y);
+ repaint();
+ }
+ branchFrom=null;
+ g.setXORMode(g.getColor());
+ return true;
+ }
+ }
+
+
+
+/** ======================================================================== */
+public class TreeClass {
+ Branch Root, SubRoot;
+ int numTaxa;
+ boolean exists;
+
+ private int stringloc;
+
+ /** ________________ read tree ________________ */
+ private void ParseTreeDescription(String TreeDescription, Branch Ancestor) {
+ if (TreeDescription.charAt(stringloc) == '(')
+ {
+ stringloc++;
+ Ancestor.sprout();
+ ParseTreeDescription(TreeDescription, Ancestor.left);
+ stringloc++; //skip comma
+ ParseTreeDescription(TreeDescription, Ancestor.right);
+ stringloc++; //skip parensu
+ }
+ else
+ {
+ stringloc++; //skip tt name
+ numTaxa++;
+ }
+ }
+ public void ReadTree(String TreeDescription) {
+ stringloc=0;
+ numTaxa=0;
+ ParseTreeDescription(TreeDescription, Root);
+ exists=true;
+ }
+
+ /** ______________________________________________ */
+
+ private boolean DescendantOf(Branch branchD, Branch branchA) {
+ return false;
+ }
+
+ private boolean NodeSlantsRight(Branch N) {
+ if (N.ancestor.right==N)
+ return true;
+ else
+ return false;
+ }
+ private Branch Sister(Branch N) {
+ if (N.ancestor.right==N)
+ return N.ancestor.left;
+ else
+ return N.ancestor.right;
+ }
+ /** ______________________________________________ */
+ public void MoveBranch(Branch branchFrom, Branch branchTo) {
+
+ Branch sideN,C, G, F, H, NCAnc;
+ boolean fromancslantRight, fromslantRight, toslantRight, NCslantRight, fromroot, toroot;
+
+ if ((branchFrom.ancestor.ancestor == branchTo) & (branchTo == Root))
+ {
+ branchFrom = Sister(branchFrom);
+ branchTo = Sister(branchFrom.ancestor);
+ }
+ if ((branchFrom.ancestor == Root) & (branchTo.ancestor.ancestor == Root))
+ {
+ sideN = branchFrom;
+ branchFrom = branchTo;
+ branchTo = sideN;
+ }
+
+ fromroot = false;
+ toroot = false;
+ fromslantRight = NodeSlantsRight(branchFrom);
+ fromancslantRight = NodeSlantsRight(branchFrom.ancestor);
+ toslantRight = NodeSlantsRight(branchTo);
+ G = Sister(branchFrom);
+ H = branchFrom.ancestor.ancestor;
+ C = branchTo.ancestor;
+ F = branchFrom.ancestor;
+
+ if (F == Root)
+ fromroot = true;
+ else if (branchTo == Root )
+ toroot = true;
+
+ if (fromslantRight == toslantRight)
+ {
+ sideN = F.left;
+ F.left = F.right;
+ F.right = sideN;
+ }
+
+ G.ancestor = H;
+ F.ancestor = C;
+ branchTo.ancestor = F;
+ if (fromancslantRight)
+ H.right = G;
+ else
+ H.left = G;
+ if (toslantRight)
+ {
+ F.right = branchTo;
+ C.right = F;
+ }
+ else
+ {
+ F.left = branchTo;
+ C.left = F;
+ }
+ sideN = Sister(G);
+
+ if (fromroot)
+ {
+ sideN = Root;
+ Root = G;
+ G = sideN;
+ }
+ if (toroot)
+ {
+ sideN = Root;
+ Root = F;
+ F = sideN;
+ }
+ if (!NodeSlantsRight(Root))
+ {
+ SubRoot.right = Root;
+ }
+
+ }
+
+}
+/** ======================================================================== */
+public class Branch {
+ Branch left, right, ancestor;
+ int x;
+ int y;
+ Polygon branchPoly;
+ Color color;
+
+ Branch(Branch Ancestor, boolean isFirstDescendant) {
+ this.ancestor = Ancestor;
+ this.color=Color.black;
+ branchPoly= new Polygon();
+ branchPoly.xpoints = new int[5];
+ branchPoly.ypoints = new int[5];
+ branchPoly.npoints=5;
+ }
+
+ public boolean sprout() {
+ this.left = new Branch(this, true);
+ this.right = new Branch(this, false);
+ return true;
+ }
+}
+
+class BeanTreeControls extends Panel {
+ TextField tf;
+ TreeCanvas TreeDisplay;
+
+ public BeanTreeControls(TreeCanvas TreeDisplay) {
+ this.TreeDisplay = TreeDisplay;
+ add(tf = new TextField("(((*,*),(*,*)),(((*,*),*),*));", 40));
+ add(new Button("Show"));
+ }
+
+ public boolean action(Event ev, Object arg) {
+ if (ev.target instanceof Button) {
+ /* destroy current tree if present */
+ /*Display.startApplet("BeanTree.html", "BeanTree.html", args);*/
+
+
+ TreeDisplay.treeDescription=tf.getText();
+ TreeDisplay.Tree.ReadTree(TreeDisplay.treeDescription);
+ TreeDisplay.repaint();
+ return true;
+ }
+ return false;
+ }
+
+ public void RedescribeTree() {
+ TreeDisplay.treeDescription = TreeDisplay.Describe();
+ tf.setText(TreeDisplay.treeDescription);
+ repaint();
+ }
+
+}
+
Property changes on: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.java
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/AncestralStates.html
===================================================================
--- trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/AncestralStates.html (rev 0)
+++ trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/AncestralStates.html 2009-12-15 17:16:33 UTC (rev 356)
@@ -0,0 +1,802 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><!-- #BeginTemplate "/Templates/Template.dwt" --><!-- DW6 -->
+<head>
+<!--LINK REL="SHORTCUT ICON" HREF="images/mesq.ico"-->
+<!-- #BeginEditable "doctitle" -->
+<title>Ancestral States</title>
+<!-- #EndEditable -->
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+</head>
+
+<body bgcolor="#FFFFFF">
+<div id="Page" style="position:absolute; left:0px; top:0px; z-index:1; visibility: visible; width: 100%; height: 100%">
+ <table border="0" cellspacing="0" cellpadding="0" width="100%">
+ <tr>
+ <td align="left" valign="top" height="60">
+ <table border="0" cellspacing="0" cellpadding="0" height="60" width="300">
+ <tr>
+ <td width="10" height="60" align="left" valign="top"> <font face="Trebuchet MS"><img src="../images/pixel.gif" width="1" height="1" alt=" " border="0"></font></td>
+ <td bgcolor="#FFFFFF">
+ <div align="left"><font face="Trebuchet MS"><a href="../manual.html"><img src="../images/mesquitesmall.gif" width="268" height="92" border="0" alt="Mesquite"></a></font></div>
+ </td>
+ </tr>
+ <tr>
+ <td height="42" align="left" valign="top"></td>
+ <td height="42" align="left" valign="top"><font face="Trebuchet MS"><a href="../manual.html"><img src="../images/mesquiteLowerManual.gif" border="0"></a></font></td>
+ </tr>
+<!-- <tr>
+ <td colspan="2" height="10"></td>
+ </tr>
+ <tr>
+ <td colspan="2" height="15" align="center" valign="middle">
+ <!-- Google CSE Search Box Begins
+ <form id="searchbox_016202157087875381635:khljhzi-ps8" action="http://www.google.com/cse">
+ <input type="hidden" name="cx" value="016202157087875381635:khljhzi-ps8" />
+ <input type="hidden" name="cof" value="FORID:0" />
+ <input name="q" type="text" size="20" />
+ <input type="submit" name="sa" value="Search Mesquite" />
+ <!--<img src="http://www.google.com/coop/images/google_custom_search_smnar.gif" alt="Google Custom Search" />
+ </form>
+ <!-- Google CSE Search Box Ends
+ </td>
+ </tr> -->
+ </table>
+ </td>
+ <td>
+ <table border="0" cellspacing="0" cellpadding="0" height="134" width="550">
+ <tr valign="top" height="92">
+ <td width="72" align="center" height="92" valign="top" bgcolor="#FFFFFF"><font face="Trebuchet MS"><img src="../images/fadeRight.gif" width="72" height="160"></font></td>
+ <td bgcolor="#99FF99"><img src="../images/introduction.gif" valign="bottom"></td>
+ <td align="left" valign="top" height="92" width = "160" bgcolor="#99FF99">
+ <p><font face="Trebuchet MS"><span class="smallplain"><a href="../manual.html">
+ Introduction</a><br>
+ </span><a href="../whyMesquite.html">Why?</a><br>
+ <a href="../publication.html#howToCite">How to Cite</a> <br>
+ <a href="../publication.html">Publication</a><br>
+ <a href="../support.html">Support</a><br>
+ <a href="../credits.html">Credits</a> </font><br>
+ <font face="Trebuchet MS"><span class="smallplain"><a href="../help.html">Help</a></span></font><br>
+ <a href="../Help/MesquiteFAQ.html"><font face="Trebuchet MS">FAQ</font></a><br>
+ <a href="http://mesquiteproject.org"><font face="Trebuchet MS">Web Site</font></a><br>
+ </td>
+ <td bgcolor="#99FF99"><img src="../images/basics.gif" valign="bottom"></td>
+ <td align="left" valign="top" height="92" width="220" bgcolor="#99FF99">
+ <p><font face="Trebuchet MS"><span class="smallplain"><a href="../help.html"></a>
+ <a href="../managingFiles.html">Files</a></span> <br>
+ <span class="smallplain"><a href="../menus.html">Menus</a><br>
+ <a href="../windows.html">Windows</a><br>
+ <a href="../charts.html">Charts</a><br>
+ <a href="../scripting.html">Scripts/Macros</a> <br>
+ <a href="../modules.html">Modules</a><br>
+ <a href="../howMesquiteWorks.html">How</a></span></font>
+ </td>
+ <td bgcolor="#99FF99"><img src="../images/objects.gif" valign="bottom"></td>
+ <td align="left" valign="top" height="92" width="260" bgcolor="#99FF99">
+ <p><font face="Trebuchet MS">
+ <span class="smallplain"><a href="../characters.html">Characters</a></span></font><font face="Trebuchet MS"><span class="smallplain"><a href="../Taxa.html"><br>
+ Taxa<br>
+ </a></span></font><font face="Trebuchet MS"><a href="../trees.html">Trees</a><br>
+ <a href="../glossary.html">Glossary</a> </font></p>
+ <p><font face="Trebuchet MS"><em><font face="Trebuchet MS"><a href="../changes.html">New</a><br>
+ <a href="../changes.html">Features</a></font></em></font></p>
+ </td>
+ <td align="left" valign="top" height="92" width="92"><font face="Trebuchet MS"><img src="../images/fadeLeft.gif" width="92" height="160"></font></td>
+ </tr>
+ <tr>
+ <td width="72" height="20"></td>
+ <td></td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+ </table>
+ </td>
+ </tr>
+ </table>
+ <table border="0" cellspacing="0" cellpadding="0" width="100%" height="100%">
+ <tr>
+ <td valign="top" align="left" width="110" height="100%">
+ <table border="0" cellspacing="0" cellpadding="0" width="142">
+ <tr>
+ <td colspan="3" bgcolor="#99FF99"><p><font face="Trebuchet MS"><img src="../images/fadeDown.gif" width="100%" height="95" valign "top" border="0" alt=" "></font></p></td>
+ </tr>
+ <tr>
+ <td width="6" bgcolor="#99FF99" height="35"></td>
+ <td colspan="2" bgcolor="99FF99" valign="top" height="35"><p><font face="Trebuchet MS"><a href="../toc.html">Table of</a><br>
+ <a href="../toc.html">Contents</a></font></p></td>
+ </tr>
+ <tr>
+ <td width="6" bgcolor="#99FF99" height="35"></td>
+ <td colspan="2" bgcolor="#99FF99" height="35"><p><font face="Trebuchet MS"><img src="../images/analyses.gif"></font></p>
+ </td>
+ </tr>
+ <tr bgcolor="#99FF99">
+ <td height="35" align="left" valign="middle" bgcolor="#99FF99"> </td>
+ <td width="131" height="35" align="left" valign="middle"><p>
+ <font face="Trebuchet MS">
+ <a href="charEvolution.html">Character</a><br>
+ <a href="charEvolution.html">Evolution</a> <br> <br>
+ <a href="../Diversification/diversification.html">Diversification</a><br><br>
+ <a href="../molecular/molecular.html">Molecular</a><br>
+ <a href="../molecular/molecular.html">Data</a><br><br>
+ <a href="../popGen/popGen.html">Gene trees</a> <br> <br>
+ <a href="../RandomSimul/RandomSimul.html">Simulations &</a><br>
+ <a href="../RandomSimul/RandomSimul.html">Randomizations</a> <br> <br>
+ <a href="../continuous/continuous.html">Continuous</a><br>
+ <a href="../continuous/continuous.html">Characters</a><br> <br>
+ <a href="../otherPrograms.html">Use with</a><br>
+ <a href="../otherPrograms.html">Other Programs</a> <br><br>
+ <a href="../studies/index.html">Studies</a> </font></p></td>
+ <td width="5" height="35" align="left" valign="middle"> </td>
+ </tr>
+ <tr bgcolor="#99FF99">
+ <td height="35" align="left" valign="middle"> </td>
+ <td height="35" align="left" valign="middle"> </td>
+ <td height="35" align="left" valign="middle"> </td>
+ </tr>
+ <tr>
+ <td height="35" align="left" valign="middle"><font face="Trebuchet MS"><img src="../images/fadeUp.gif" width="5" height="92"></font></td>
+ <td height="35" align="left" valign="middle" colspan="2"><font face="Trebuchet MS"><img src="../images/fadeUp.gif" width="100%" height="92"></font></td>
+ </tr>
+ </table>
+ </td>
+ <td valign="top" width="100%" height="100%">
+ <table width="700" border="0" cellpadding="10" cellspacing="0">
+ <tr>
+ <td><font face="Trebuchet MS"><!-- #BeginEditable "body" -->
+ <h2><font face="Trebuchet MS">Studying the History of Character
+ Evolution</font></h2>
+ <p><font face="Trebuchet MS">With a phylogenetic tree and a distribution
+ of character states in the observed (terminal) taxa, Mesquite
+ can attempt to reconstruct the character states at ancestral nodes.
+ Two separate issues to consider are the method by which the reconstruction
+ is done, and how its results are displayed to the user. Mesquite
+ currently can use either parsimony, likelihood or Bayesian methods
+ to reconstruct ancestral states, and has several display methods,
+ including "Trace Character History" which paints the
+ branches of the tree to show the reconstruction. </font></p>
+ <p><font face="Trebuchet MS">We recommend highly that you examine
+ the <strong>example files</strong> provided in the folder "Ancestral
+ State Examples". The minimal configuration to use with these
+ examples is "Ancestral States" (indicate this configuration
+ under <u><font size="-1">File>Activate/Deactivate Packages>Choose
+ Configuration</font></u>), but you can also leave Mesquite in
+ its default All Installed Modules mode.</font></p>
+ <p align="center"><font face="Trebuchet MS"><img src="images/ancStates.gif"></font></p>
+ <h3><font face="Trebuchet MS"><a name="tch"></a>Trace Character
+ History</font></h3>
+ <p><font face="Trebuchet MS">The Trace Character History facility
+ graphically represents a history of character evolution on the
+ tree. It is available under the Analysis menu of a tree window
+ (e.g., the basic Tree Window, Dependent Tree Window, Mirror Tree
+ Window, Multitree Window). If you select this you will probably
+ be asked for a <strong>source of characters</strong> (e.g., stored
+ characters) and a <strong>reconstruction method</strong> (e.g.,
+ <a href="#parsimony">parsimony</a>, <a href="#likelihood">likelihood</a>,
+ <a href="#scm">stochastic character mapping</a>). (If you have "Use Stored Characters/Matrices by Default" turned on in the Defaults submenu if the File menu, Mesquite won't ask you and will simply use Stored Characters.) The tree will
+ be painted to show ancestral states, and a trace legend will appear.
+ The <strong>Trace Legend</strong> contains an important text area
+ that gives details of the current ancestral state tracing. You
+ can also see details of the reconstruction by switching the window
+ to Text mode using the tabs at its top.</font></p>
+ <p>For categorical and molecular data, you can <strong>change the
+ colors</strong> used in Trace Character by double clicking on
+ the color rectangle in the Trace Legend. Revert to Default Colors
+ is available in the Trace menu.</p>
+ <p>For parsimony reconstructions, any tree drawing style will suffice.
+ For likelihood reconstructions, we recommend the Balls&Sticks
+ style (Drawing menu, Tree Form) with Line Style "Square".
+ This permits you to see the relative likelihoods and branch lengths.
+ For stochastic character mapping, we recommend the Square Tree
+ style in order to display the changes within a branch.</p>
+ <p><font face="Trebuchet MS">The Trace menu gives menu items to
+ control the character history and its display. Some important
+ ones are:</font></p>
+ <p><font face="Trebuchet MS"><strong>Character history source</strong>:
+ Typically you may use Trace Character History to reconstruct the
+ ancestral states of an observed character. Alternatively, you
+ can trace a simulated history ("Simulate Ancestral States").
+ The reconstructed states need not be based on actual data, but
+ could be based on simulated data. "Simulate Ancestral States"
+ shows the "actual" history of character evolution branch
+ by branch as it occured in the <a href="../RandomSimul/RandomSimul.html">simulation</a>,
+ not as it was reconstructed, and thus may show ancestral states
+ that would be unreconstructable, obliterated by subsequent changes.</font></p>
+ <p><font face="Trebuchet MS"><strong>Next, Previous, Choose Character
+ History</strong>: Usually, this will allow you to choose which
+ character to view. You can also scroll through characters using
+ the blue arrows in the trace legend.</font></p>
+ <p><font face="Trebuchet MS"><strong>Trace Display Mode</strong>:
+ With <u><font size="-1">Trace>Trace Display Mode>Shade States</font></u>
+ and <u><font size="-1">Trace>Trace Display Mode>Label States</font></u>
+ you choose whether to see the branches painted, or have the states
+ indicated in labels. If painted, you can also ask that states
+ be indicated by labels by choosing <u><font size="-1">Trace>Label
+ States</font></u>. </font></p>
+ <p><font face="Trebuchet MS">You can also see details of the reconstruction
+ at a node by holding the cursor over the branch. A description
+ of the reconstructed states will appear at the bottom part of
+ the Trace Character Legend. Another method is to use the Text
+ view of the window (touch on the Text tab at the top of the tree
+ window) and scroll down — a text version of the trace should
+ appear.</font></p>
+ <p><strong>Reconstruction Method</strong>: For more details on reconstruction
+ methods, see the sections on <a href="#parsimony">parsimony</a>,
+ <a href="#likelihood">likelihood</a>, and <a href="#scm">stochastic
+ character mapping</a>.</p>
+ <h3><a name="tac"></a>Trace All Characters</h3>
+ <p>Trace All Characters summarizes ancestral state reconstructions
+ of many characters simultaneously. To request it, choose Choose
+ <u><font size="-1">(Tree Window)Analysis>Trace All Characters</font></u>.
+ A text window like that shown below will appear, listing the ancestral
+ states reconstructed at each node for each character. Node numbers
+ show up in red on the tree. (Alternatively, spots showing node
+ numbers in the figure below can be turned on in the Tree Window's
+ Drawing menu by selecting Show Node Numbers.)</p>
+ <p align="center"><img src="images/traceAll.gif" width="630" height="299"></p>
+ <p align="left">By default only the selected nodes are listed. (Nodes
+ can be selected using tools in the Tree Window.) You can request
+ to show all nodes by turning off Show Selected Nodes Only in the
+ Trace_All menu. By default all characters are listed; this can
+ be changed using the Show Selected Characters Only menu item.</p>
+ <p align="left">The ancestral state reconstruction can be controlled
+ in the Trace_All menu of the tree window.</p>
+ <p align="left">The table is either listed by characters or by nodes;
+ you can switch from one to the other using the Rows are Characters
+ menu item</p>
+ <p align="left">Columns in the table in the text window may not
+ appear perfectly aligned, but it is presented as a tab-delimited
+ table, so you should be able to copy the text and paste it in
+ to a text file to read in to your favorite spreadsheet program.</p>
+ <h3><font face="Trebuchet MS"><a name="tcot"></a>Trace Character
+ Over Trees</font></h3>
+ <p>The Trace Character Over Trees facility summarizes<font face="Trebuchet MS">
+ ancestral state reconstructions over a series of trees. This is
+ useful to understand how ancestral state reconstructions vary
+ over a series of trees, for instance if there is uncertainty in
+ the tree. It works for <strong>categorical characters</strong>
+ only. Also, Trace Character Over Trees <strong>does NOT calculate
+ a consensus tree</strong> for you. As with all other analyses
+ in the Tree Window, it works with the tree that is given to it
+ by the Tree Window. If you want to make your summary on a consensus
+ tree, then you need to put the consensus tree into the Tree Window
+ first and then request Trace Character Over Trees.</font></p>
+ <p><font face="Trebuchet MS">Choose <u><font size="-1">(Tree Window)Analysis>Trace
+ Character Over Trees</font></u>. This examines a series of trees,
+ and for each examines a character's ancestral states on that tree.
+ For each node in the tree in the tree window, it attempts to summarize
+ what ancestral states are reconstructed for that same clade in
+ the series of trees (as long as the same clade exists in the other
+ trees). For example, imagine the tree in the tree window includes
+ the clade Tetrapoda. Each of the series of trees is examined,
+ and if that tree includes the clade Tetrapoda, then its reconstructed
+ ancestral states are examined. If the tree doesn't include Tetrapoda,
+ then it is ignored for the sake of summarizing the tetrapod ancestral
+ states. The tree in the tree window is then decorated to summarize
+ what ancestral states are reconstructed for each of the clades.</font></p>
+ <p>Here is an example of Trace Character Over Trees in action:</p>
+ <p align="center"><img src="images/tcot.gif" width="433" height="421"></p>
+ <p>The cursor is over a node (the most recent common ancestor of
+ carinatum and coxendix), and thus the legend shows a summary.
+ The node (i.e., the clade it
+ represents)
+ is
+ present
+ in only 445
+ of the 545 trees examined. For this reason, 100/545 or 18.3%
+ of the pie chart for that node is shown in red, as the node is
+ not present in that fraction of the trees. In addition, 100 of
+ the trees with that node have an equivocal reconstruction at
+ that node; those trees are shown in gray
+ in the pie chart.
+ Of the 345 trees with the node and an unequivocal reconstruction,
+ 321 trees have "isodiametric" reconstructed at the node (shown
+ in white), and in 24 trees have state "slightly trans." at that
+ node (shown as a very thin sliver of green). In this example,
+ "Count Trees with Un...
[truncated message content] |
|
From: <rv...@us...> - 2009-12-15 17:11:11
|
Revision: 355
http://treebase.svn.sourceforge.net/treebase/?rev=355&view=rev
Author: rvos
Date: 2009-12-15 17:11:05 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/corejava/
trunk/treebase-core/lib/corejava/Format.class
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This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-12-15 17:10:50
|
Revision: 354
http://treebase.svn.sourceforge.net/treebase/?rev=354&view=rev
Author: rvos
Date: 2009-12-15 17:10:40 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/com/
trunk/treebase-core/lib/com/apple/
trunk/treebase-core/lib/com/apple/eawt/
trunk/treebase-core/lib/com/apple/eawt/Application.class
trunk/treebase-core/lib/com/apple/eawt/ApplicationAdapter.class
trunk/treebase-core/lib/com/apple/eawt/ApplicationBeanInfo.class
trunk/treebase-core/lib/com/apple/eawt/ApplicationEvent.class
trunk/treebase-core/lib/com/apple/eawt/ApplicationListener.class
trunk/treebase-core/lib/com/apple/eawt/CocoaComponent.class
trunk/treebase-core/lib/com/apple/eio/
trunk/treebase-core/lib/com/apple/eio/FileManager.class
trunk/treebase-core/lib/com/apple/mrj/
trunk/treebase-core/lib/com/apple/mrj/MRJAboutHandler.class
trunk/treebase-core/lib/com/apple/mrj/MRJApplicationUtils.class
trunk/treebase-core/lib/com/apple/mrj/MRJCoercionHandler.class
trunk/treebase-core/lib/com/apple/mrj/MRJFileUtils.class
trunk/treebase-core/lib/com/apple/mrj/MRJMenuUtils.class
trunk/treebase-core/lib/com/apple/mrj/MRJOSType.class
trunk/treebase-core/lib/com/apple/mrj/MRJOpenApplicationHandler.class
trunk/treebase-core/lib/com/apple/mrj/MRJOpenDocumentHandler.class
trunk/treebase-core/lib/com/apple/mrj/MRJPrefsHandler.class
trunk/treebase-core/lib/com/apple/mrj/MRJPrintDocumentHandler.class
trunk/treebase-core/lib/com/apple/mrj/MRJPriv.class
trunk/treebase-core/lib/com/apple/mrj/MRJQuitHandler.class
trunk/treebase-core/lib/com/apple/mrj/datatransfer/
trunk/treebase-core/lib/com/apple/mrj/datatransfer/FlaggedTransferable.class
trunk/treebase-core/lib/com/apple/mrj/datatransfer/OSTypeFlavor.class
trunk/treebase-core/lib/com/apple/mrj/datatransfer/Transfer.class
trunk/treebase-core/lib/com/apple/mrj/dnd/
trunk/treebase-core/lib/com/apple/mrj/dnd/DragAdapter.class
trunk/treebase-core/lib/com/apple/mrj/dnd/DragInitiatorAdapter.class
trunk/treebase-core/lib/com/apple/mrj/dnd/DragInitiatorListener.class
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|
|
From: <rv...@us...> - 2009-12-15 15:53:02
|
Revision: 353
http://treebase.svn.sourceforge.net/treebase/?rev=353&view=rev
Author: rvos
Date: 2009-12-15 15:52:55 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Reverted to 2.01tb behaviour
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/mesquite/MesquiteMatrixConverter.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/mesquite/MesquiteMatrixConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/mesquite/MesquiteMatrixConverter.java 2009-12-15 10:14:32 UTC (rev 352)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/mesquite/MesquiteMatrixConverter.java 2009-12-15 15:52:55 UTC (rev 353)
@@ -821,8 +821,6 @@
int continuing = 0;
for (int ic = 0; ic < pNumChar; ic++) {
-
- //
if (pBitsSpecsSet.isSelected(ic)) {
if (continuing == 0) {
// discontinue
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-12-15 10:14:41
|
Revision: 352
http://treebase.svn.sourceforge.net/treebase/?rev=352&view=rev
Author: rvos
Date: 2009-12-15 10:14:32 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Downgraded postgres jdbc driver dependency to jdbc3
Modified Paths:
--------------
trunk/pom.xml
Modified: trunk/pom.xml
===================================================================
--- trunk/pom.xml 2009-12-11 14:35:56 UTC (rev 351)
+++ trunk/pom.xml 2009-12-15 10:14:32 UTC (rev 352)
@@ -109,7 +109,7 @@
<dependency>
<groupId>postgresql</groupId>
<artifactId>postgresql</artifactId>
- <version>8.2-507.jdbc4</version>
+ <version>8.3-603.jdbc3</version>
</dependency>
</dependencies>
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From: SourceForge.net <no...@so...> - 2009-12-14 19:01:57
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Bugs item #2825363, was opened at 2009-07-22 09:23 Message generated for change (Settings changed) made by youjun You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2825363&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 7 Private: No Submitted By: William Piel (sfrgpiel) >Assigned to: youjun guo (youjun) Summary: Analysis falsely reports taxon mismatch when tree in+out Initial Comment: when creating an analysis step that has trees as input and trees as output, software reports that the taxon labels among the input objects do not match with those in the output objects, when in fact they do. example is here: http://8ball.sdsc.edu:6666/treebase-web/user/summary.html?id=2383 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2825363&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-12-14 16:46:51
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Bugs item #2854768, was opened at 2009-09-08 19:07 Message generated for change (Settings changed) made by youjun You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2854768&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Priority: 7 Private: No Submitted By: William Piel (sfrgpiel) >Assigned to: youjun guo (youjun) Summary: Editors and Administrators Cannot Edit Ready Submissions Initial Comment: When an Associate Editor or Administrator is examining a submission with the status of "Ready", the submission should be editable to the Associate Editor or Administrator but not to the User. Currently, it is editable by nobody, except that an Associate Editor or Administrator can toggle it to "Published" status. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2854768&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-12-14 16:42:03
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Bugs item #2902650, was opened at 2009-11-23 13:31 Message generated for change (Comment added) made by youjun You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2902650&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Closed Priority: 7 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: youjun guo (youjun) Summary: Book titles don't appear under study tab Initial Comment: When searching on a study, under the study tab there is a column called "Title" which lists the titles for publications. Journal article titles are fine, but this column ought to also list the title of books, but it does not (that column is blank for books). In the event of book sections, this column should show the title of the chapter in the book. For example, see study_id 253 or tb_study_id S9x6x96c10c10c17 for a book title that does not appear in the column. However, if you look at the study details (e.g. http://treebasedb-dev.nescent.org:6666/treebase-web/search/study/summary.html?id=253) the citation is written properly. The book title is also missing from the BibTeX and RIS output. ---------------------------------------------------------------------- >Comment By: youjun guo (youjun) Date: 2009-12-14 11:42 Message: solved with #2903172 ---------------------------------------------------------------------- Comment By: youjun guo (youjun) Date: 2009-12-14 11:39 Message: solved with #2903172 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2902650&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-12-14 16:39:01
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Bugs item #2902650, was opened at 2009-11-23 13:31 Message generated for change (Settings changed) made by youjun You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2902650&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 7 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: youjun guo (youjun) Summary: Book titles don't appear under study tab Initial Comment: When searching on a study, under the study tab there is a column called "Title" which lists the titles for publications. Journal article titles are fine, but this column ought to also list the title of books, but it does not (that column is blank for books). In the event of book sections, this column should show the title of the chapter in the book. For example, see study_id 253 or tb_study_id S9x6x96c10c10c17 for a book title that does not appear in the column. However, if you look at the study details (e.g. http://treebasedb-dev.nescent.org:6666/treebase-web/search/study/summary.html?id=253) the citation is written properly. The book title is also missing from the BibTeX and RIS output. ---------------------------------------------------------------------- >Comment By: youjun guo (youjun) Date: 2009-12-14 11:39 Message: solved with #2903172 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2902650&group_id=248804 |
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From: <rv...@us...> - 2009-12-11 14:36:04
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Revision: 351
http://treebase.svn.sourceforge.net/treebase/?rev=351&view=rev
Author: rvos
Date: 2009-12-11 14:35:56 +0000 (Fri, 11 Dec 2009)
Log Message:
-----------
Added log line to check mesquite.folder_dir
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java 2009-12-10 20:28:52 UTC (rev 350)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java 2009-12-11 14:35:56 UTC (rev 351)
@@ -118,6 +118,10 @@
converter.setTaxonLabelHome(getTaxonLabelHome());
//converter.processLoadFile(pNexusFiles, pStudy, data, pListener);
+ if ( LOGGER.isInfoEnabled() ) {
+ LOGGER.info("Mesquite is located at: '"+System.getProperty(MESQUITE_FOLDER_DIR_KEY)+"'");
+ }
+
converter.parseOneFile(pNexusFile, pStudy, data);
return data;
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From: SourceForge.net <no...@so...> - 2009-12-11 00:37:49
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Bugs item #2826165, was opened at 2009-07-23 15:36 Message generated for change (Comment added) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2826165&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) >Assigned to: Vladimir Gapeyev (vgapeyev) Summary: Reviewer/Referee Access Initial Comment: I'm making this a priority of 9 only because it is needed before TreeBASE2 can be made public. We need to make sure that reviewers or referees can have access to datasets that are "in progress" and associated with a manuscript that is in the review process of a journal. Jin Ruan initially created a user role called "reviewer" which gives someone read-only access to the private sections of the database. We decided that this is a bad solution because it requires that each reviewer get a login name and password, which implies a huge amount of admin overhead. A better solution is to auto-generate a long random string which can be used in an URL to give someone a read-only access to the submission page. But however which way we do this, it is needed because some journals depend on this as part of their review process. ---------------------------------------------------------------------- >Comment By: William Piel (sfrgpiel) Date: 2009-12-10 19:37 Message: Here are some more comments on how I envision this feature -- but of course I'm open to input from everyone regarding this. The basic requirement is that the submitter gets either a PIN or an URL for each submission/study that s/he initiates. This should be provided to the submitter at the submission summary page. For example, here is the "summary" page that a submitter might see: http://treebasedb-dev.nescent.org:6666/treebase-web/user/summary.html?id=1937 ... in this case, the submission is "published" so it is visible to everyone -- but in the event that the submission was "in progress" or "ready," only the submitter or an administrator can view the submission. In the "Summary" box that you can see after following the url (above), we currently have the following items: (1) submission id (2) the date submission initiated (3) citation (4) abstract For submissions regardless of status, we should add the following: (a) the date last modified (b) the following statement: "To cite your data in a paper or other data resources, please use the following Universal Resource Identifier (URI): http://purl.org/phylo/treebase/phylows/study/TB2:S1936" For submissions that are "in progress" or "ready," we should add the following: (c) "Until your submission status is change to "published," your data will remain invisible to everyone except you, TreeBASE staff, and anyone who uses your URI together with a unique "x-reviewer_pin" parameter. To provide journal editors or reviewers of your paper with advanced access to your data, please email the following URL to them: http://purl.org/phylo/treebase/phylows/study/TB2:S1936?x-reviewer_pin=1234567890&format=html This URL contains the unique x-reviewer_pin parameter that provides read-only access to your data. It is recommended that you provide this to your editor or reviews only after your submission is complete." So... for this to work we need to modify Rutger's phylows code to read the extra parameter "x-reviewer_pin" and to use this to give anonymous access to the corresponding submission even though its status is "in progress" or "ready." My guess is that this would involve generating a cookie so that once the user's browser resolves the phylows + x-reviewer_pin URL, the reviewer can continue clicking on the related analysis, matrix, tree, and taxa tabs. Additionally, the cookie allows the reviewer to download matrices and trees for this study. How should we generate the PIN? One way is to add a new field to the study table to store a randomly-generated PIN. But that means modifying the schema, which is probably not ideal. Another way is to generate an md5 on, for example, a concatenation of the study_id and the date that the submission was first created. The other thing that would be good is that when the reviewer first follows the phylows + x-reviewer_pin URL, he/she is confronted with an "agreement" page or pop-up. This "agreement" page or popup contains an "Accept" and a "Cancel" button. The Cancel button closes out the browser page. The "Accept" button continues to the submission. The verbiage for this "agreement" page is written below. regards, Bill ===================== Reviewer/Referee Access Agreement You have reached this page using a PIN that is intended to be used by journal editors and reviewers or referees of a paper that is under consideration for publication. This PIN gives you access to the submitted data and metadata associated with analyses and results presented in the paper under review. Please carefully examine the data paying special attention to the following: - The citation data (authors, year, citation, abstract) should be complete, except for information that is not yet known (e.g. volume or page numbers). - Verify that nexus files are error-free and executable by software programs (e.g. PAUP, Mesquite, MacClade, etc). Please make sure that the taxon labels for trees are identical, or a subset of, the taxon labels in data matrices connected by way of an analysis. If taxon labels in trees do not match with taxon labels in associated data matrices, the data will not be useful to the scientific community. - Verify that data are not missing and that opportunities to supply valuable metadata are not overlooked. For example, TreeBASE can store Genbank accession numbers, museum voucher IDs, latitude and longitudes for specimen localities, character names and character state names for morphological data, etc. Including these metadata are sometimes overlooked by submitting authors, yet sharing this metadata is extremely valuable to the scientific community. Please use your power as a reviewer to encourage the sharing of richly-annotated metadata. - Verify that analyses are not missing and that, where possible, analysis entries include software commands (e.g. the contents of a PAUP block or MrBayes block) so that analyses can be replicated easily (e.g. commands that describe substitution models, data partitions, and heuristic search parameters). - Verify that taxon labels are mapped against TreeBASE's taxonomic dictionary. Data in TreeBASE can only be found using a taxon name search if the taxon labels are properly mapped. By clicking the "Accept" button below, you agree to keep these data confidential; you agree not retain these data after completing your report to the journal editor; you agree not use these data or knowledge of these data for the purposes of your research until and unless the paper under review has been published and the data have been made available to the general public; you agree to keep the PIN confidential. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2826165&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-12-10 22:29:37
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Bugs item #2912290, was opened at 2009-12-10 17:27 Message generated for change (Comment added) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2912290&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 5 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Nobody/Anonymous (nobody) Summary: Data on an in-progress study returns exception Initial Comment: If an anonymous user tries to look at a study which is not yet released (i.e. it's a "in progress" or "ready") the result is an Uncaught Exception Encountered. The result ought to be something more elegant, such as "These data are not yet available to the public" OR "These data are unknown" (if there is no study by that id). Here is an example of an "in progress" study that produces this error: http://treebasedb-dev.nescent.org:6666/treebase-web/search/study/summary.html?id=9920 ---------------------------------------------------------------------- >Comment By: William Piel (sfrgpiel) Date: 2009-12-10 17:29 Message: Here's the error verbiage, by the way: Uncaught Exception Encountered org.cipres.treebase.web.controllers.SearchSummaryController$UnknownStudyError at org.cipres.treebase.web.controllers.SearchSummaryController.formBackingObject(S earchSummaryController.java:91) at org.cipres.treebase.web.controllers.SearchSum maryController.formBackingObject(SearchSummaryController.java:60) at org.springf ramework.web.servlet.mvc.AbstractFormController.getErrorsForNewForm(AbstractForm Controller.java:358) at org.springframework.web.servlet.mvc.AbstractFormControll er.showNewForm(AbstractFormController.java:338) at org.springframework.web.servl et.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java: 278) at org.springframework.web.servlet.mvc.AbstractController.handleRequest(Abs tractController.java:153) at org.springframework.web.servlet.mvc.SimpleControlle rHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) at org.springfram ework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) at or g.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java :792) at org.springframework.web.servlet.FrameworkServlet.processRequest(Framewo rkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doGet(Fr ameworkServlet.java:431) at javax.servlet.http.HttpServlet.service(HttpServlet.j ava:627) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org. apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterCh ain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(Applic ationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFil ter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilt erChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.sp ringframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(Op enSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequest Filter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.Applic ationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache .catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java: 119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.j ava:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Appl icationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain. doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainP roxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity .intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:1 07) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(Filter SecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualF ilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.Exception TranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecu rity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274 ) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter( SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.Filte rChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegis ecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterCha inProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilt er.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.u til.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at o rg.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at or g.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at or g.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilter Chain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(Appl icationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.in voke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextV alve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardH ostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorR eportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.Standar dEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connect or.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Htt p11Processor.process(Http11Processor.java:873) at org.apache.coyote.http11.Http1 1BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java: 665) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint .java:528) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(Leader FollowerWorkerThread.java:81) at org.apache.tomcat.util.threads.ThreadPool$Contr olRunnable.run(ThreadPool.java:689) at java.lang.Thread.run(Thread.java:636) Coo kies: JSESSIONID=[C0036217D51F8124936C87BBA883D514] __utma=[53240375.1924499357. 1236724314.1257296380.1257360601.37] __utmz=[53240375.1252007373.35.5.utmccn] ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2912290&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-12-10 22:27:22
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Bugs item #2912290, was opened at 2009-12-10 17:27 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2912290&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 5 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Nobody/Anonymous (nobody) Summary: Data on an in-progress study returns exception Initial Comment: If an anonymous user tries to look at a study which is not yet released (i.e. it's a "in progress" or "ready") the result is an Uncaught Exception Encountered. The result ought to be something more elegant, such as "These data are not yet available to the public" OR "These data are unknown" (if there is no study by that id). Here is an example of an "in progress" study that produces this error: http://treebasedb-dev.nescent.org:6666/treebase-web/search/study/summary.html?id=9920 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2912290&group_id=248804 |
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From: <vga...@us...> - 2009-12-10 20:28:59
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Revision: 350
http://treebase.svn.sourceforge.net/treebase/?rev=350&view=rev
Author: vgapeyev
Date: 2009-12-10 20:28:52 +0000 (Thu, 10 Dec 2009)
Log Message:
-----------
removing the commit-test file
Removed Paths:
-------------
trunk/test-vg.txt
Deleted: trunk/test-vg.txt
===================================================================
--- trunk/test-vg.txt 2009-12-10 20:27:55 UTC (rev 349)
+++ trunk/test-vg.txt 2009-12-10 20:28:52 UTC (rev 350)
@@ -1 +0,0 @@
-vg test
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