[Treebase-guts] SF.net SVN: treebase:[581] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/tree/PhyloTree.java

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

Revision: 581
          http://treebase.svn.sourceforge.net/treebase/?rev=581&view=rev
Author:   rvos
Date:     2010-03-15 01:16:43 +0000 (Mon, 15 Mar 2010)

Log Message:
-----------
Added getAnnotations() for nexml and rdf serialization.

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

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java	2010-03-15 01:15:19 UTC (rev 580)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java	2010-03-15 01:16:43 UTC (rev 581)
@@ -4,6 +4,7 @@
 import java.util.Collections;
 import java.util.HashSet;
 import java.util.Iterator;
+import java.util.List;
 import java.util.Set;
 
 import javax.persistence.AttributeOverride;
@@ -25,9 +26,11 @@
 import mesquite.lib.MesquiteDouble;
 import mesquite.lib.StringUtil;
 
+import org.cipres.treebase.Constants;
 import org.cipres.treebase.TreebaseIDString;
 import org.cipres.treebase.TreebaseUtil;
 import org.cipres.treebase.domain.AbstractPersistedObject;
+import org.cipres.treebase.domain.Annotation;
 import org.cipres.treebase.domain.TBPersistable;
 import org.cipres.treebase.domain.study.Study;
 import org.cipres.treebase.domain.taxon.TaxonLabel;
@@ -227,6 +230,7 @@
 	 * 
 	 * @return String
 	 */
+	@Override
 	@Column(name = "Label", length = TBPersistable.COLUMN_LENGTH_STRING)
 	public String getLabel() {
 		return mLabel;
@@ -778,4 +782,26 @@
 		setRootNode(null);
 		setNewickString(null);
 	}
+	
+	@Transient
+	public List<Annotation> getAnnotations() {
+		List<Annotation> annotations = super.getAnnotations();
+		if ( null != getId() ) { 
+			annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.tree", getId()));
+		}
+		if ( null != getKindDescription() ) {
+			annotations.add(new Annotation(Constants.TBTermsURI, "tb:kind.tree", getKindDescription()));
+		}
+		if ( null != getTypeDescription() ) {
+			annotations.add(new Annotation(Constants.TBTermsURI, "tb:type.tree", getTypeDescription()));
+		}
+		if ( null != getQualityDescription() ) {
+			annotations.add(new Annotation(Constants.TBTermsURI, "tb:quality.tree", getQualityDescription()));
+		}
+		if ( null != getnTax() ) {
+			annotations.add(new Annotation(Constants.TBTermsURI, "tb:ntax.tree", getnTax()));
+		}		
+		return annotations;
+	}
+
 }


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