treebase-guts

[Treebase-guts] SF.net SVN: treebase:[582] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/tree/PhyloTreeNode.java

[<rv...@us...>]

Revision: 582
          http://treebase.svn.sourceforge.net/treebase/?rev=582&view=rev
Author:   rvos
Date:     2010-03-15 01:17:38 +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/PhyloTreeNode.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTreeNode.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTreeNode.java	2010-03-15 01:16:43 UTC (rev 581)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTreeNode.java	2010-03-15 01:17:38 UTC (rev 582)
@@ -585,4 +585,10 @@
 	public boolean haveABCTopology(PhyloTreeNode n1, PhyloTreeNode n2) {
 		return ! n1.nearestCommonAncestor(n2).isAncestorOf(this);
 	}
+	
+	@Override
+	@Transient
+	public String getLabel() {
+		return getTaxonLabelAsString();
+	}
 }


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[Treebase-guts] SF.net SVN: treebase:[607] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/tree/PhyloTreeNode.java

[<rv...@us...>]

Revision: 607
          http://treebase.svn.sourceforge.net/treebase/?rev=607&view=rev
Author:   rvos
Date:     2010-03-16 16:57:25 +0000 (Tue, 16 Mar 2010)

Log Message:
-----------
Added implementation of getContext, which returns the containing phylogeny.

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTreeNode.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTreeNode.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTreeNode.java	2010-03-16 16:55:33 UTC (rev 606)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTreeNode.java	2010-03-16 16:57:25 UTC (rev 607)
@@ -591,4 +591,10 @@
 	public String getLabel() {
 		return getTaxonLabelAsString();
 	}
+	
+	@Override
+	@Transient
+	public PhyloTree getContext() {
+		return getTree();
+	}
 }


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[Treebase-guts] SF.net SVN: treebase:[790] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/tree/PhyloTreeNode.java

[<rv...@us...>]

Revision: 790
          http://treebase.svn.sourceforge.net/treebase/?rev=790&view=rev
Author:   rvos
Date:     2011-04-19 11:17:37 +0000 (Tue, 19 Apr 2011)

Log Message:
-----------
No longer returning the context (i.e. the defining tree) so that we don't emit rdfs:isDefinedBy annotations, which are not useful on tree nodes anyway - because they have no other annotations, so why turn them into RDF? Things are less verbose this way.

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTreeNode.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTreeNode.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTreeNode.java	2011-04-19 11:16:03 UTC (rev 789)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTreeNode.java	2011-04-19 11:17:37 UTC (rev 790)
@@ -595,9 +595,15 @@
 		return getTaxonLabelAsString();
 	}
 	
+	
+	/*
+	 * If there are no annotations on individual nodes there is no good reason to have them
+	 * be "seen" in the RDF anyway, which they would be if we state them as being defined by
+	 * their containing tree. So let's skip that for now.
 	@Override
 	@Transient
 	public PhyloTree getContext() {
 		return getTree();
 	}
+	*/
 }


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