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From: <rv...@us...> - 2009-06-19 02:15:56
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Revision: 65
http://treebase.svn.sourceforge.net/treebase/?rev=65&view=rev
Author: rvos
Date: 2009-06-19 02:15:55 +0000 (Fri, 19 Jun 2009)
Log Message:
-----------
Added serialize() stubs.
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 2009-06-19 02:15:10 UTC (rev 64)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java 2009-06-19 02:15:55 UTC (rev 65)
@@ -212,4 +212,14 @@
return null;
}
+ public String serialize(NexusDataSet nexusDataSet) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ public String serialize(Study study) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
}
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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: <rv...@us...> - 2009-12-16 17:57:23
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Revision: 398
http://treebase.svn.sourceforge.net/treebase/?rev=398&view=rev
Author: rvos
Date: 2009-12-16 17:57:12 +0000 (Wed, 16 Dec 2009)
Log Message:
-----------
Added assignments to MesquiteModule.mesquiteDirectory and MesquiteModule.mesquiteDirectoryPath, as per Wayne Maddison's suggestion. This solves the issue where mesquite can't find where it lives and so can't start up.
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 2009-12-16 17:14:59 UTC (rev 397)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java 2009-12-16 17:57:12 UTC (rev 398)
@@ -5,6 +5,8 @@
import java.util.Collection;
import java.util.Properties;
+import mesquite.lib.MesquiteModule;
+
import org.apache.log4j.Logger;
import org.cipres.treebase.domain.DomainHome;
@@ -191,6 +193,8 @@
*/
public void setMesquiteFolderDir(String pMesquiteFolderDir) {
System.setProperty(MESQUITE_FOLDER_DIR_KEY, pMesquiteFolderDir);
+ MesquiteModule.mesquiteDirectory = new File(pMesquiteFolderDir);
+ MesquiteModule.mesquiteDirectoryPath = pMesquiteFolderDir;
}
@Override
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From: <vga...@us...> - 2010-03-31 14:49:07
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Revision: 662
http://treebase.svn.sourceforge.net/treebase/?rev=662&view=rev
Author: vgapeyev
Date: 2010-03-31 14:49:01 +0000 (Wed, 31 Mar 2010)
Log Message:
-----------
Fixed a typo in a log message.
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 2010-03-31 13:54:49 UTC (rev 661)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java 2010-03-31 14:49:01 UTC (rev 662)
@@ -132,7 +132,7 @@
InitialContext ic = new InitialContext();
mJndiMesquiteFolder = (String) ic.lookup("java:comp/env/tb2/MesquiteFolder");
} catch (NamingException e) {
- LOGGER.info("Failure looking up tb/MesquiteFolder via JNDI");
+ LOGGER.info("Failure looking up tb2/MesquiteFolder via JNDI");
}
String mesquiteFolder;
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From: <rv...@us...> - 2011-05-12 20:37:03
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Revision: 862
http://treebase.svn.sourceforge.net/treebase/?rev=862&view=rev
Author: rvos
Date: 2011-05-12 20:36:56 +0000 (Thu, 12 May 2011)
Log Message:
-----------
Added empty stub for the overloaded case where we both have a nexus data set (generated de novo, perhaps) and a containing study. It seems we need this instead of the one without the study but with the nexus data set: looks like we're getting NPEs that way.
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 2011-05-12 20:36:03 UTC (rev 861)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java 2011-05-12 20:36:56 UTC (rev 862)
@@ -262,4 +262,10 @@
return null;
}
+ public String serialize(NexusDataSet pNexusDataSet, Properties pProperties,
+ Study study) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
}
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