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treebase-guts
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From: <rv...@us...> - 2009-06-23 10:56:33
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Revision: 75
http://treebase.svn.sourceforge.net/treebase/?rev=75&view=rev
Author: rvos
Date: 2009-06-23 10:56:13 +0000 (Tue, 23 Jun 2009)
Log Message:
-----------
Fix: now no longer returns TreeBlocknull as a default title. Instead, if getId() returns a value, return a TreebaseIDString, otherwise return null.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java 2009-06-23 10:54:08 UTC (rev 74)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java 2009-06-23 10:56:13 UTC (rev 75)
@@ -39,6 +39,7 @@
import mesquite.lib.StringUtil;
+import org.cipres.treebase.TreebaseIDString;
import org.cipres.treebase.TreebaseUtil;
import org.cipres.treebase.domain.AbstractPersistedObject;
import org.cipres.treebase.domain.TBPersistable;
@@ -88,8 +89,11 @@
if ( ! TreebaseUtil.isEmpty(mTitle) ) {
return mTitle;
}
+ else if ( null != getId() ){
+ return TreebaseIDString.getIDString(this);
+ }
else {
- return "TreeBlock" + getId();
+ return null;
}
}
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From: <rv...@us...> - 2010-03-15 01:20:44
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Revision: 583
http://treebase.svn.sourceforge.net/treebase/?rev=583&view=rev
Author: rvos
Date: 2010-03-15 01:20:38 +0000 (Mon, 15 Mar 2010)
Log Message:
-----------
Added getLabel() for nexml and rdf serialization.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java 2010-03-15 01:17:38 UTC (rev 582)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java 2010-03-15 01:20:38 UTC (rev 583)
@@ -276,5 +276,10 @@
return tlSet == null ? new ArrayList<TaxonLabel>()
: tlSet.getTaxonLabelsReadOnly();
}
+
+ @Transient
+ public String getLabel() {
+ return getTitle();
+ }
}
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From: <rv...@us...> - 2010-03-16 16:58:23
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Revision: 608
http://treebase.svn.sourceforge.net/treebase/?rev=608&view=rev
Author: rvos
Date: 2010-03-16 16:58:15 +0000 (Tue, 16 Mar 2010)
Log Message:
-----------
Added implementation of getContext, which provides the containing Study.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java 2010-03-16 16:57:25 UTC (rev 607)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java 2010-03-16 16:58:15 UTC (rev 608)
@@ -22,6 +22,7 @@
import org.cipres.treebase.TreebaseUtil;
import org.cipres.treebase.domain.AbstractPersistedObject;
import org.cipres.treebase.domain.TBPersistable;
+import org.cipres.treebase.domain.study.Study;
import org.cipres.treebase.domain.taxon.TaxonLabel;
import org.cipres.treebase.domain.taxon.TaxonLabelSet;
import org.hibernate.annotations.Cache;
@@ -281,5 +282,14 @@
public String getLabel() {
return getTitle();
}
+
+ @Transient
+ public Study getContext() {
+ PhyloTree firstTree = getTreeList().iterator().next();
+ if ( null != firstTree ) {
+ return firstTree.getContext();
+ }
+ return null;
+ }
}
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From: <hs...@us...> - 2011-05-10 19:34:32
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Revision: 831
http://treebase.svn.sourceforge.net/treebase/?rev=831&view=rev
Author: hshyket
Date: 2011-05-10 19:34:26 +0000 (Tue, 10 May 2011)
Log Message:
-----------
Adding in Link Taxa to Trees in Nexus file
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java 2011-05-05 20:31:14 UTC (rev 830)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java 2011-05-10 19:34:26 UTC (rev 831)
@@ -226,7 +226,7 @@
}
pBuilder.append("BEGIN TREES;\n");
pBuilder.append(" TITLE " + StringUtil.tokenize(getTitle()) + ";\n");
- //pBuilder.append(" LINK TAXA = " + StringUtil.tokenize(getTaxobLabelSetTitle()) + ";\n");
+ pBuilder.append(" LINK TAXA = " + StringUtil.tokenize(tlSet.getTitle().replaceAll("Input|Output", "")) + ";\n");
pBuilder.append(" TRANSLATE\n");
tlSet.buildTaxonWithLineNumber(pBuilder);
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From: <hs...@us...> - 2011-11-02 15:16:01
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Revision: 979
http://treebase.svn.sourceforge.net/treebase/?rev=979&view=rev
Author: hshyket
Date: 2011-11-02 15:15:55 +0000 (Wed, 02 Nov 2011)
Log Message:
-----------
Changing name of Tree in nexus file (for all tree download) to Tree ID instead of Tree Label
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java 2011-11-01 16:29:00 UTC (rev 978)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java 2011-11-02 15:15:55 UTC (rev 979)
@@ -280,7 +280,7 @@
for (PhyloTree atree : getTreeList()) {
- pBuilder.append(" TREE " + StringUtil.tokenize(atree.getLabel()) + " = ");
+ pBuilder.append(" TREE Tr" + atree.getId() + " = ");
if (atree.getRootedTree() != null) {
if (atree.getRootedTree().booleanValue()) {
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From: <hs...@us...> - 2011-11-02 17:48:24
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Revision: 980
http://treebase.svn.sourceforge.net/treebase/?rev=980&view=rev
Author: hshyket
Date: 2011-11-02 17:48:18 +0000 (Wed, 02 Nov 2011)
Log Message:
-----------
Adding TreeBase title of number of trees for all tree downloads
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java 2011-11-02 15:15:55 UTC (rev 979)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java 2011-11-02 17:48:18 UTC (rev 980)
@@ -275,7 +275,9 @@
//title = "List of Uploaded Tree Block";
}
pBuilder.append("BEGIN TREES;\n");
- pBuilder.append(" TITLE " + StringUtil.tokenize(getTitle()) + ";\n");
+ //pBuilder.append(" TITLE " + StringUtil.tokenize(getTitle()) + ";\n");
+
+ pBuilder.append(" TITLE " + StringUtil.tokenize(Integer.toString(getTreeList().size())) + "Trees;\n");
pBuilder.append(" LINK TAXA = " + StringUtil.tokenize(tlSet.getTitle().replaceAll("Input|Output", "")) + ";\n");
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