[Treebase-guts] SF.net SVN: treebase:[494] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml/NexmlMatrixConverter.java

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

Revision: 494
          http://treebase.svn.sourceforge.net/treebase/?rev=494&view=rev
Author:   rvos
Date:     2010-02-12 04:37:30 +0000 (Fri, 12 Feb 2010)

Log Message:
-----------
Added DwC:DecimalLatitude and DwC:DecimalLongitude annotations

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

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java	2010-02-12 04:35:22 UTC (rev 493)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java	2010-02-12 04:37:30 UTC (rev 494)
@@ -2,6 +2,7 @@
 
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Set;
 
 import org.cipres.treebase.dao.jdbc.ContinuousMatrixElementJDBC;
 import org.cipres.treebase.dao.jdbc.ContinuousMatrixJDBC;
@@ -22,6 +23,7 @@
 import org.cipres.treebase.domain.matrix.MatrixElement;
 import org.cipres.treebase.domain.matrix.MatrixRow;
 import org.cipres.treebase.domain.matrix.PhyloChar;
+import org.cipres.treebase.domain.matrix.RowSegment;
 import org.cipres.treebase.domain.matrix.StandardMatrix;
 import org.cipres.treebase.domain.study.Study;
 import org.cipres.treebase.domain.taxon.TaxonLabelHome;
@@ -292,11 +294,12 @@
 			DiscreteMatrix tbMatrix) {	
 		OTUs xmlOTUs = xmlMatrix.getOTUs();
 		List<org.nexml.model.Character> characterList = xmlMatrix.getCharacters();
-		for ( MatrixRow row : tbMatrix.getRowsReadOnly() ) {
-			OTU xmlOTU = getOTUById(xmlOTUs, row.getTaxonLabel().getId());
+		for ( MatrixRow tbRow : tbMatrix.getRowsReadOnly() ) {
+			Set<RowSegment> tbSegments = tbRow.getSegmentsReadOnly();
+			OTU xmlOTU = getOTUById(xmlOTUs, tbRow.getTaxonLabel().getId());
 			int charIndex = 0;
 			if ( characterList.size() <= MAX_GRANULAR_NCHAR && xmlOTUs.getAllOTUs().size() <= MAX_GRANULAR_NTAX ) {
-				for ( MatrixElement tbCell : row.getElements() ) {
+				for ( MatrixElement tbCell : tbRow.getElements() ) {
 					org.nexml.model.Character xmlCharacter = characterList.get(charIndex);
 					MatrixCell<CharacterState> xmlCell = xmlMatrix.getCell(xmlOTU, xmlCharacter);				
 					DiscreteCharState tbState = ((DiscreteMatrixElement)tbCell).getCharState();
@@ -304,11 +307,21 @@
 					CharacterState xmlState = xmlCharacter.getCharacterStateSet().lookupCharacterStateBySymbol(tbSymbolString);								
 					xmlCell.setValue(xmlState);								
 					attachTreeBaseID((Annotatable)xmlCell,tbCell,DiscreteMatrixElement.class);
+					for ( RowSegment tbSegment : tbSegments ) {
+						if ( tbSegment.getStartIndex() <= charIndex && charIndex <= tbSegment.getEndIndex() ) {
+							if ( tbSegment.getSpecimenLabel().getLatitude() != null ) {
+								((Annotatable)xmlCell).addAnnotationValue("DwC:DecimalLatitude", mDwCURI, tbSegment.getSpecimenLabel().getLatitude());
+							}
+							if ( tbSegment.getSpecimenLabel().getLongitude() != null ) {
+								((Annotatable)xmlCell).addAnnotationValue("DwC:DecimalLongitude", mDwCURI, tbSegment.getSpecimenLabel().getLongitude());
+							}
+						}
+					}
 					charIndex++;
 				}
 			}
 			else {
-				String seq = row.buildElementAsString();
+				String seq = tbRow.buildElementAsString();
 				if ( tbMatrix.getDataType().getDescription().equals(MatrixDataType.MATRIX_DATATYPE_STANDARD) ) {
 					StringBuilder sb = new StringBuilder();
 					for ( int i = 0; i < seq.length(); i++ ) {


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.