[Treebase-guts] SF.net SVN: treebase:[1055] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml/NexmlMatrixWriter.java

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

Revision: 1055
          http://treebase.svn.sourceforge.net/treebase/?rev=1055&view=rev
Author:   rvos
Date:     2012-02-05 15:23:09 +0000 (Sun, 05 Feb 2012)
Log Message:
-----------
Now uses org.nexml.model.MatrixRow objects to attach Darwin Core annotations

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixWriter.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixWriter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixWriter.java	2012-02-04 09:26:30 UTC (rev 1054)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixWriter.java	2012-02-05 15:23:09 UTC (rev 1055)
@@ -30,6 +30,7 @@
 import org.cipres.treebase.domain.taxon.SpecimenLabel;
 import org.cipres.treebase.domain.taxon.TaxonLabelHome;
 import org.nexml.model.Annotatable;
+import org.nexml.model.Annotation;
 import org.nexml.model.CategoricalMatrix;
 import org.nexml.model.CharacterState;
 import org.nexml.model.CharacterStateSet;
@@ -340,6 +341,8 @@
 			}
 			else {
 				String seq = tbRow.getNormalizedSymbolString();
+				
+				// In NeXML, 'standard' data needs to be space-separated
 				if ( tbMatrix.getDataType().getDescription().equals(MatrixDataType.MATRIX_DATATYPE_STANDARD) ) {
 					StringBuilder sb = new StringBuilder();
 					for ( int i = 0; i < seq.length(); i++ ) {
@@ -348,19 +351,23 @@
 							sb.append(' ');
 						}
 					}
-				}				
+				}
 				xmlMatrix.setSeq(seq,xmlOTU);
 				
 				// this often only happens once, when the row has only 1 segment
 				for ( RowSegment tbSegment : tbSegments ) {
-					copyDarwinCoreAnnotations(tbSegment, xmlOTU);
+					org.nexml.model.MatrixRow<CharacterState> xmlRow = xmlMatrix.getRowObject(xmlOTU);
+					Annotation xmlSegment = xmlRow.addAnnotationValue("tb:rowSegment", Constants.TBTermsURI, new String());
+					xmlSegment.addAnnotationValue("tb:startIndex", Constants.TBTermsURI, tbSegment.getStartIndex());
+					xmlSegment.addAnnotationValue("tb:endIndex", Constants.TBTermsURI, tbSegment.getEndIndex());
+					copyDarwinCoreAnnotations(tbSegment, xmlSegment);
 				}				
 			}
 		}	
 	}
 
 	/**
-	 * 
+	 * XXX this never executes, we always make compact matrices - RAV 5/2/2012
 	 * @param xmlMatrix
 	 * @param tbMatrix
 	 * @param xmlCharacterList
@@ -421,7 +428,11 @@
 			}
 			Set<RowSegment> tbSegments = tbRow.getSegmentsReadOnly();
 			for ( RowSegment tbSegment : tbSegments ) {
-				copyDarwinCoreAnnotations(tbSegment,xmlOTU);
+				org.nexml.model.MatrixRow<Double> xmlRow = xmlMatrix.getRowObject(xmlOTU);
+				Annotation xmlSegment = xmlRow.addAnnotationValue("tb:rowSegment", Constants.TBTermsURI, new String());
+				xmlSegment.addAnnotationValue("tb:startIndex", Constants.TBTermsURI, tbSegment.getStartIndex());
+				xmlSegment.addAnnotationValue("tb:endIndex", Constants.TBTermsURI, tbSegment.getEndIndex());				
+				copyDarwinCoreAnnotations(tbSegment,xmlSegment);
 			}
 		}		
 	}	

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