[Treebase-guts] SF.net SVN: treebase:[55] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus

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

Revision: 55
          http://treebase.svn.sourceforge.net/treebase/?rev=55&view=rev
Author:   rvos
Date:     2009-06-18 09:32:34 +0000 (Thu, 18 Jun 2009)

Log Message:
-----------
Adding NeXML conversion classes.

Added Paths:
-----------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlConverter.java
    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/NexmlOTUConverter.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java

Added: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlConverter.java	                        (rev 0)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlConverter.java	2009-06-18 09:32:34 UTC (rev 55)
@@ -0,0 +1,72 @@
+package org.cipres.treebase.domain.nexus.nexml;
+
+import java.io.File;
+import java.util.Collection;
+
+import org.cipres.treebase.domain.matrix.Matrix;
+import org.cipres.treebase.domain.nexus.AbstractNexusConverter;
+import org.cipres.treebase.domain.nexus.NexusDataSet;
+import org.cipres.treebase.domain.nexus.NexusParserConverter;
+import org.cipres.treebase.domain.study.Study;
+import org.cipres.treebase.domain.tree.PhyloTree;
+import org.cipres.treebase.domain.tree.TreeBlock;
+import org.cipres.treebase.event.ProgressionListener;
+import org.nexml.model.Document;
+import org.nexml.model.DocumentFactory;
+import org.nexml.model.OTUs;
+
+public class NexmlConverter extends AbstractNexusConverter implements
+		NexusParserConverter {
+
+	/**
+	 * 
+	 */
+	public void processLoadFile(Collection<File> nexusFiles, Study study,
+			NexusDataSet dataSet, ProgressionListener listener) {
+		// TODO Auto-generated method stub
+
+	}
+	
+	/**
+	 * 
+	 * @param pFile
+	 * @param pStudy
+	 * @param pDataSet
+	 */
+	public void parseOneFile(File pFile, Study pStudy, NexusDataSet pDataSet) {
+		Document document = null;
+		try {
+			document = DocumentFactory.parse(pFile);
+		} catch (Exception e) {
+			e.printStackTrace();
+		}
+		
+		// Taxa
+		NexmlOTUConverter noc = new NexmlOTUConverter(pStudy,getTaxonLabelHome(),document);
+		for ( OTUs xmlOTUs : document.getOTUsList() ) {
+			pDataSet.addTaxonLabelSet(xmlOTUs, noc.fromXmlToTreeBase(xmlOTUs));
+		}
+	
+		// Matrices
+		NexmlMatrixConverter nmc = new NexmlMatrixConverter(pStudy,getTaxonLabelHome(),document);
+		for ( org.nexml.model.Matrix<?> xmlMatrix : document.getMatrices() ) {
+			Matrix tbMatrix = nmc.fromXmlToTreeBase(xmlMatrix);
+			tbMatrix.setNexusFileName(pFile.getName());
+			pDataSet.getMatrices().add(tbMatrix);
+		}		
+		
+		// Trees
+		NexmlTreeBlockConverter ntbc = new NexmlTreeBlockConverter(pStudy,getTaxonLabelHome(),document);
+		for ( org.nexml.model.TreeBlock xmlTreeBlock : document.getTreeBlockList() ) {
+			TreeBlock tbTreeBlock = ntbc.fromXmlToTreeBase(xmlTreeBlock);
+			for ( PhyloTree phyloTree : tbTreeBlock.getTreeList() ) {
+				phyloTree.setNexusFileName(pFile.getName());
+			}
+			pDataSet.getTreeBlocks().add(tbTreeBlock);
+		}	
+		
+		// Store document
+		pDataSet.setNexmlProject(document);
+	}
+	
+}

Added: 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	                        (rev 0)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java	2009-06-18 09:32:34 UTC (rev 55)
@@ -0,0 +1,162 @@
+package org.cipres.treebase.domain.nexus.nexml;
+
+import java.util.ArrayList;
+import java.util.List;
+import org.cipres.treebase.dao.jdbc.ContinuousMatrixElementJDBC;
+import org.cipres.treebase.dao.jdbc.ContinuousMatrixJDBC;
+import org.cipres.treebase.dao.jdbc.DiscreteMatrixElementJDBC;
+import org.cipres.treebase.dao.jdbc.DiscreteMatrixJDBC;
+import org.cipres.treebase.dao.jdbc.MatrixColumnJDBC;
+import org.cipres.treebase.domain.matrix.ContinuousChar;
+import org.cipres.treebase.domain.matrix.DiscreteChar;
+import org.cipres.treebase.domain.matrix.DiscreteMatrix;
+import org.cipres.treebase.domain.matrix.Matrix;
+import org.cipres.treebase.domain.study.Study;
+import org.cipres.treebase.domain.taxon.TaxonLabelHome;
+import org.cipres.treebase.domain.taxon.TaxonLabelSet;
+import org.nexml.model.Annotatable;
+import org.nexml.model.CategoricalMatrix;
+import org.nexml.model.CharacterState;
+import org.nexml.model.ContinuousMatrix;
+import org.nexml.model.Document;
+import org.nexml.model.MatrixCell;
+import org.nexml.model.OTUs;
+import org.nexml.model.OTU;
+
+public class NexmlMatrixConverter extends NexmlObjectConverter {
+
+	/**
+	 * 
+	 * @param study
+	 * @param taxonLabelHome
+	 */
+	public NexmlMatrixConverter(Study study,TaxonLabelHome taxonLabelHome,Document document) {
+		super(study,taxonLabelHome,document);	
+	}	
+	
+	/**
+	 * 
+	 * @param xmlMatrix
+	 * @return
+	 */
+	public Matrix fromXmlToTreeBase(CategoricalMatrix xmlMatrix) {
+		DiscreteMatrix tbMatrix = new DiscreteMatrix();
+		DiscreteMatrixJDBC matrixJDBC = new DiscreteMatrixJDBC(tbMatrix, xmlMatrix, this);
+		List<MatrixColumnJDBC> columnJDBCs = new ArrayList<MatrixColumnJDBC>();
+		long[] colIds = matrixJDBC.getColIDs();
+		long[] rowIds = matrixJDBC.getRowIDs();		
+		List<DiscreteMatrixElementJDBC> elements = new ArrayList<DiscreteMatrixElementJDBC>();
+		int colIndex = 0;
+		for ( org.nexml.model.Character xmlCharacter : xmlMatrix.getCharacters() ) {
+			String charName = xmlCharacter.getLabel();
+			DiscreteChar tbChar = new DiscreteChar();
+			tbChar.setDescription(charName);
+			MatrixColumnJDBC aColumnJDBC = new MatrixColumnJDBC();
+			aColumnJDBC.setPhyloChar(tbChar);			
+			columnJDBCs.add(aColumnJDBC);
+			int rowIndex = 0;
+			for ( OTU xmlOTU : xmlMatrix.getOTUs().getAllOTUs() ) {
+				MatrixCell<CharacterState> xmlCell = xmlMatrix.getCell(xmlOTU, xmlCharacter);
+				DiscreteMatrixElementJDBC element = new DiscreteMatrixElementJDBC();
+				//element.setValue(xmlCell.getValue()); // XXX nested stateset lookup song & dance here
+				element.setElementOrder(colIndex);				
+				element.setMatrixRowID(rowIds[rowIndex]);
+				element.setMatrixColID(colIds[colIndex]);
+				elements.add(element);
+				rowIndex++;
+			}			
+			colIndex++;
+		}
+		DiscreteMatrixElementJDBC.batchDiscreteElements(elements, getTaxonLabelHome().getConnection());		
+		return tbMatrix;		
+	}
+	
+	/**
+	 * 
+	 * @param xmlMatrix
+	 * @return
+	 */
+	public Matrix fromXmlToTreeBase(ContinuousMatrix xmlMatrix) {		
+		org.cipres.treebase.domain.matrix.ContinuousMatrix tbMatrix = 
+			new org.cipres.treebase.domain.matrix.ContinuousMatrix();		
+		ContinuousMatrixJDBC matrixJDBC = new ContinuousMatrixJDBC(tbMatrix, xmlMatrix, this);		
+		List<MatrixColumnJDBC> columnJDBCs = new ArrayList<MatrixColumnJDBC>();
+		long[] colIds = matrixJDBC.getColIDs();
+		long[] rowIds = matrixJDBC.getRowIDs();
+		List<ContinuousMatrixElementJDBC> elements = new ArrayList<ContinuousMatrixElementJDBC>();
+		
+		int colIndex = 0;
+		for ( org.nexml.model.Character xmlCharacter : xmlMatrix.getCharacters() ) {
+			String charName = xmlCharacter.getLabel();
+			ContinuousChar tbChar = new ContinuousChar();
+			tbChar.setDescription(charName);
+			MatrixColumnJDBC aColumnJDBC = new MatrixColumnJDBC();
+			aColumnJDBC.setPhyloChar(tbChar);			
+			columnJDBCs.add(aColumnJDBC);
+			int rowIndex = 0;
+			for ( OTU xmlOTU : xmlMatrix.getOTUs().getAllOTUs() ) {
+				MatrixCell<Double> xmlCell = xmlMatrix.getCell(xmlOTU, xmlCharacter);
+				ContinuousMatrixElementJDBC element = new ContinuousMatrixElementJDBC();
+				element.setValue(xmlCell.getValue());
+				element.setElementOrder(colIndex);				
+				element.setMatrixRowID(rowIds[rowIndex]);
+				element.setMatrixColID(colIds[colIndex]);
+				elements.add(element);
+				rowIndex++;
+			}
+			colIndex++;
+		}	
+		ContinuousMatrixElementJDBC.batchContinuousElements(elements, getTaxonLabelHome().getConnection());
+		return tbMatrix;
+	}
+
+	/**
+	 * 
+	 * @param xmlMatrix
+	 * @return
+	 */
+	public Matrix fromXmlToTreeBase(org.nexml.model.Matrix<?> xmlMatrix) {
+		OTUs xmlOTUs = xmlMatrix.getOTUs();
+		Matrix tbMatrix = null;
+		TaxonLabelSet tbTaxa = null;
+		Long tbTaxonLabelSetID = readTreeBaseID((Annotatable) xmlOTUs,TaxonLabelSet.class);
+		if ( null != tbTaxonLabelSetID ) {
+			tbTaxa = getTaxonLabelHome()
+				.findPersistedObjectByID(TaxonLabelSet.class, tbTaxonLabelSetID);
+		}		
+		if ( xmlMatrix instanceof CategoricalMatrix ) {
+			tbMatrix = fromXmlToTreeBase((CategoricalMatrix) xmlMatrix);
+		}
+		else if ( xmlMatrix instanceof ContinuousMatrix ) {
+			tbMatrix = fromXmlToTreeBase((ContinuousMatrix) xmlMatrix);
+		}
+		if ( null != tbMatrix ) {
+			attachTreeBaseID((Annotatable) xmlMatrix, tbMatrix);
+			if ( null != tbTaxa ) {
+				tbMatrix.setTaxa(tbTaxa);
+			}
+			tbMatrix.setStudy(getStudy());
+			tbMatrix.setTitle(xmlMatrix.getLabel());
+			tbMatrix.setPublished(false);			
+		}
+		return tbMatrix;		
+	}
+	
+	public org.nexml.model.Matrix<?> fromTreeBaseToXml(Matrix tbMatrix) {
+		TaxonLabelSet taxonLabelSet = tbMatrix.getTaxa();
+		Long taxonLabelSetId = taxonLabelSet.getId();
+		OTUs xmlOTUs = null;
+		for ( OTUs otus : getDocument().getOTUsList() ) {
+			Long annotatedID = readTreeBaseID(otus, TaxonLabelSet.class);
+			if ( taxonLabelSetId == annotatedID ) {
+				xmlOTUs = otus;
+				break;
+			}
+		}
+		org.nexml.model.Matrix<?> xmlMatrix = getDocument().createCategoricalMatrix(xmlOTUs);
+		xmlMatrix.setLabel(tbMatrix.getTitle());
+		attachTreeBaseID((Annotatable)xmlMatrix, tbMatrix);
+		return xmlMatrix;
+	}
+
+}

Added: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java	                        (rev 0)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java	2009-06-18 09:32:34 UTC (rev 55)
@@ -0,0 +1,80 @@
+package org.cipres.treebase.domain.nexus.nexml;
+
+import org.cipres.treebase.domain.study.Study;
+import org.cipres.treebase.domain.taxon.TaxonLabel;
+import org.cipres.treebase.domain.taxon.TaxonLabelHome;
+import org.cipres.treebase.domain.taxon.TaxonLabelSet;
+import org.nexml.model.Document;
+import org.nexml.model.OTU;
+import org.nexml.model.OTUs;
+
+public class NexmlOTUConverter extends NexmlObjectConverter {
+	
+	/**
+	 * 
+	 * @param study
+	 * @param taxonLabelHome
+	 */
+	public NexmlOTUConverter(Study study,TaxonLabelHome taxonLabelHome,Document document) {
+		super(study,taxonLabelHome,document);	
+	}
+	
+	/**
+	 * 
+	 * @param xmlOTUs
+	 * @return
+	 */
+	public TaxonLabelSet fromXmlToTreeBase (OTUs xmlOTUs) {
+		TaxonLabelSet labelSet = new TaxonLabelSet();
+		attachTreeBaseID(xmlOTUs,labelSet);
+		labelSet.setStudy(getStudy());
+		labelSet.setTitle(xmlOTUs.getLabel());
+		labelSet.setTaxa(true);
+		for ( OTU xmlOTU : xmlOTUs.getAllOTUs() ) {
+			TaxonLabel taxonLabel = fromXmlToTreeBase(xmlOTU);
+			labelSet.addPhyloTaxonLabel(taxonLabel);
+		}	
+		return labelSet;
+	}
+	
+	/**
+	 * 
+	 * @param taxonLabelSet
+	 * @return
+	 */
+	public OTUs fromTreeBaseToXml(TaxonLabelSet taxonLabelSet) {
+		OTUs xmlOTUs = getDocument().createOTUs();
+		xmlOTUs.setLabel(taxonLabelSet.getTitle());
+		attachTreeBaseID(xmlOTUs,taxonLabelSet);
+		for ( TaxonLabel taxonLabel : taxonLabelSet.getTaxonLabelsReadOnly() ) {
+			fromTreeBaseToXml(taxonLabel,xmlOTUs);
+		}
+		return xmlOTUs;
+	}
+	
+	/**
+	 * 
+	 * @param xmlOTU
+	 * @return
+	 */
+	public TaxonLabel fromXmlToTreeBase(OTU xmlOTU) {
+		TaxonLabel taxonLabel = getTaxonLabelHome().getByDescriptionAndStudy(xmlOTU.getLabel(), getStudy());
+		taxonLabel.setStudy(getStudy());
+		attachTreeBaseID(xmlOTU,taxonLabel);
+		return taxonLabel;		
+	}
+	
+	/**
+	 * 
+	 * @param taxonLabel
+	 * @param xmlOTUs
+	 * @return
+	 */
+	public OTU fromTreeBaseToXml(TaxonLabel taxonLabel,OTUs xmlOTUs) {
+		OTU xmlOTU = xmlOTUs.createOTU();
+		xmlOTU.setLabel(taxonLabel.getTaxonLabel());
+		attachTreeBaseID(xmlOTU,taxonLabel);
+		return xmlOTU;
+	}
+
+}

Added: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java	                        (rev 0)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java	2009-06-18 09:32:34 UTC (rev 55)
@@ -0,0 +1,93 @@
+package org.cipres.treebase.domain.nexus.nexml;
+
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.util.Iterator;
+import java.util.Set;
+
+import org.cipres.treebase.TreebaseIDString;
+import org.cipres.treebase.domain.TBPersistable;
+import org.cipres.treebase.domain.nexus.AbstractNexusConverter;
+import org.cipres.treebase.domain.study.Study;
+import org.cipres.treebase.domain.taxon.TaxonLabelHome;
+import org.nexml.model.Annotatable;
+import org.nexml.model.Document;
+
+public class NexmlObjectConverter extends AbstractNexusConverter {
+	protected static URI mDCURI;
+	private static String mDCURIString = "http://purl.org/dc/elements/1.1/";
+	private static String mDCIdentifier = "dc:identifier";	
+	public static String TreeBASE2Prefix = "TreeBASE2";
+	private Document mDocument;
+		
+	/**
+	 * 
+	 * @param study
+	 * @param taxonLabelHome
+	 */
+	public NexmlObjectConverter(Study study, TaxonLabelHome taxonLabelHome, Document document) {
+		try {
+			mDCURI = new URI(mDCURIString);
+		} catch (URISyntaxException e) {
+			e.printStackTrace();
+		}	
+		setTaxonLabelHome(taxonLabelHome);
+		setStudy(study);
+		setDocument(document);
+	}	
+	
+	/**
+	 * 
+	 * @param tbPersistable
+	 * @return
+	 */
+	public String makeNamespacedID (TBPersistable tbPersistable) {
+		StringBuilder sb = new StringBuilder();
+		sb
+			.append(TreeBASE2Prefix)
+			.append(':')
+			.append(TreebaseIDString.getPrefixForClass(tbPersistable.getClass()))
+			.append(tbPersistable.getId());
+		return sb.toString();
+	}
+	
+	/**
+	 * 
+	 * @param annotatable
+	 * @param tbPersistable
+	 */
+	protected void attachTreeBaseID(Annotatable annotatable,TBPersistable tbPersistable) {
+		annotatable.addAnnotationValue(mDCIdentifier, mDCURI, makeNamespacedID(tbPersistable));
+	}
+	
+	/**
+	 * 
+	 * @param annotatable
+	 * @param persistableClass
+	 * @return
+	 */
+	protected Long readTreeBaseID(Annotatable annotatable, Class<? extends TBPersistable> persistableClass) {
+		Set<Object> values = annotatable.getAnnotationValues(mDCIdentifier);
+		Iterator<Object> objectIterator = values.iterator();
+		while ( objectIterator.hasNext() ) {
+			String namespacedId = objectIterator.next().toString();
+			StringBuffer prefix = new StringBuffer();
+			prefix
+				.append(TreeBASE2Prefix)
+				.append(':')
+				.append(TreebaseIDString.getPrefixForClass(persistableClass));
+			if ( namespacedId.startsWith(prefix.toString()) ) {
+				return Long.parseLong(namespacedId.substring(prefix.length()));
+			}
+		}
+		return null;
+	}
+
+	public Document getDocument() {
+		return mDocument;
+	}
+
+	public void setDocument(Document document) {
+		mDocument = document;
+	}
+}

Added: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java	                        (rev 0)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java	2009-06-18 09:32:34 UTC (rev 55)
@@ -0,0 +1,226 @@
+package org.cipres.treebase.domain.nexus.nexml;
+
+import java.util.Iterator;
+import java.util.Set;
+
+import org.cipres.treebase.domain.study.Study;
+import org.cipres.treebase.domain.taxon.TaxonLabel;
+import org.cipres.treebase.domain.taxon.TaxonLabelHome;
+import org.cipres.treebase.domain.taxon.TaxonLabelSet;
+import org.cipres.treebase.domain.tree.PhyloTree;
+import org.cipres.treebase.domain.tree.PhyloTreeNode;
+import org.cipres.treebase.domain.tree.TreeBlock;
+import org.nexml.model.Annotatable;
+import org.nexml.model.Document;
+import org.nexml.model.Edge;
+import org.nexml.model.FloatEdge;
+import org.nexml.model.IntEdge;
+import org.nexml.model.Network;
+import org.nexml.model.Node;
+import org.nexml.model.OTUs;
+import org.nexml.model.Tree;
+
+public class NexmlTreeBlockConverter extends NexmlObjectConverter {
+	
+	/**
+	 * 
+	 * @param study
+	 * @param taxonLabelHome
+	 */
+	public NexmlTreeBlockConverter(Study study,TaxonLabelHome taxonLabelHome,Document document) {
+		super(study,taxonLabelHome,document);
+	}
+	
+	/**
+	 * 
+	 * @param xmlTreeBlock
+	 * @return
+	 */
+	public TreeBlock fromXmlToTreeBase(org.nexml.model.TreeBlock xmlTreeBlock) {
+		OTUs xmlOTUs = xmlTreeBlock.getOTUs();
+		Long tbTaxonLabelSetId = readTreeBaseID(xmlOTUs,TaxonLabelSet.class);
+		TreeBlock tbTreeBlock = new TreeBlock();
+		tbTreeBlock.setTitle(xmlTreeBlock.getLabel());
+		if ( null != tbTaxonLabelSetId ) {
+			TaxonLabelSet tbTaxonLabelSet = getTaxonLabelHome()
+				.findPersistedObjectByID(TaxonLabelSet.class, tbTaxonLabelSetId);
+			tbTreeBlock.setTaxonLabelSet(tbTaxonLabelSet);
+		}
+		Iterator<Network<?>> xmlNetworkIterator = xmlTreeBlock.iterator();
+		while ( xmlNetworkIterator.hasNext() ) {
+			Network<?> xmlNetwork = xmlNetworkIterator.next();
+			if ( xmlNetwork instanceof Tree ) {
+				PhyloTree tbPhyloTree = fromXmlToTreeBase((Tree<?>) xmlNetwork); 
+				tbPhyloTree.setStudy(getStudy());
+				tbTreeBlock.addPhyloTree(tbPhyloTree);
+			}				
+		}		
+		return tbTreeBlock;
+	}
+	
+	/**
+	 * 
+	 * @param xmlTree
+	 * @return
+	 */
+	public PhyloTree fromXmlToTreeBase(Tree<?> xmlTree) {
+		PhyloTree tbPhyloTree = new PhyloTree();
+		tbPhyloTree.setLabel(xmlTree.getLabel());
+		tbPhyloTree.setPublished(false);
+		tbPhyloTree.setRootedTree(((Node)xmlTree.getRoot()).isRoot());
+		copyXmlTree(xmlTree, tbPhyloTree);		
+		tbPhyloTree.updateSubtreeBounds();		
+		return tbPhyloTree;		
+	}
+	
+	/**
+	 * 
+	 * @param phyloTree
+	 * @return
+	 */
+	public Tree<?> fromTreeBaseToXml(PhyloTree phyloTree,org.nexml.model.TreeBlock xmlTreeBlock) {
+		Tree<FloatEdge> xmlTree = xmlTreeBlock.createFloatTree();
+		xmlTree.setLabel(phyloTree.getLabel());
+		attachTreeBaseID(xmlTree, phyloTree);
+		copyTreeBaseTree(phyloTree, xmlTree);
+		return xmlTree;
+	}
+	
+	/**
+	 * 
+	 * @param treeBlock
+	 * @return
+	 */
+	public org.nexml.model.TreeBlock fromTreeBaseToXML(TreeBlock treeBlock) {
+		TaxonLabelSet taxonLabelSet = treeBlock.getTaxonLabelSet();
+		OTUs xmlOTUs = null;
+		Long taxonLabelSetId = taxonLabelSet.getId();
+		for ( OTUs otus : getDocument().getOTUsList() ) {
+			Long otusId = readTreeBaseID(otus, TaxonLabelSet.class);
+			if ( taxonLabelSetId == otusId ) {
+				xmlOTUs = otus;
+				break;
+			}
+		}
+		org.nexml.model.TreeBlock xmlTreeBlock = getDocument().createTreeBlock(xmlOTUs);
+		xmlTreeBlock.setLabel(treeBlock.getTitle());
+		attachTreeBaseID((Annotatable)xmlTreeBlock,treeBlock);
+		for ( PhyloTree phyloTree : treeBlock.getTreeList() ) {
+			fromTreeBaseToXml(phyloTree,xmlTreeBlock);
+		}
+		return xmlTreeBlock;
+	}
+	
+	/**
+	 * 
+	 * @param phyloTree
+	 * @param xmlTree
+	 */
+	private void copyTreeBaseTree(PhyloTree phyloTree,Tree<FloatEdge> xmlTree) {
+		traverseTreeBaseTree(phyloTree,phyloTree.getRootNode(),xmlTree.createNode(),xmlTree);
+	}
+	
+	/**
+	 * 
+	 * @param tbTree
+	 * @param tbNode
+	 * @param xmlNode
+	 * @param xmlTree
+	 */
+	private void traverseTreeBaseTree(PhyloTree tbTree,PhyloTreeNode tbNode,Node xmlNode,Tree<FloatEdge> xmlTree) {
+		xmlNode.setLabel(tbNode.getName());
+		attachTreeBaseID(xmlNode, tbNode);	
+		TaxonLabel taxonLabel = tbNode.getTaxonLabel();
+		if ( null != taxonLabel ) {
+			Long taxonId = taxonLabel.getId();
+			for ( OTUs xmlOTUs : getDocument().getOTUsList() ) {
+				for ( org.nexml.model.OTU xmlOTU : xmlOTUs.getAllOTUs() ) {
+					Long currentTaxonId = readTreeBaseID(xmlOTU, TaxonLabel.class);
+					if ( taxonId == currentTaxonId ) {
+						xmlNode.setOTU(xmlOTU);
+						break;
+					}
+				}
+			}
+		}
+		for ( PhyloTreeNode tbChildNode : tbNode.getChildNodes() ) {
+			Node xmlChildNode = xmlTree.createNode();
+			FloatEdge xmlEdge = xmlTree.createEdge(xmlNode, xmlChildNode);
+			xmlEdge.setLength(tbChildNode.getBranchLength());
+			traverseTreeBaseTree(tbTree, tbChildNode, xmlChildNode, xmlTree);
+		}
+	}
+	
+	/**
+	 * 
+	 * @param xmlTree
+	 * @param tbPhyloTree
+	 */
+	private void copyXmlTree(Tree<?> xmlTree, PhyloTree tbPhyloTree) {
+		StringBuilder sb = new StringBuilder();
+		PhyloTreeNode tbRoot = new PhyloTreeNode();		
+		traverseXmlTree(xmlTree,sb,xmlTree.getRoot(), tbRoot, tbPhyloTree);
+		tbPhyloTree.setRootNode(tbRoot);
+		sb.append(';');
+		tbPhyloTree.setNewickString(sb.toString());
+	}
+	
+	/**
+	 * 
+	 * @param xmlTree
+	 * @param sb
+	 * @param xmlNode
+	 * @param tbNode
+	 * @param tbTree
+	 */
+	private void traverseXmlTree(Tree<?> xmlTree, StringBuilder sb, Node xmlNode, PhyloTreeNode tbNode, PhyloTree tbTree) {
+		tbTree.addTreeNode(tbNode);
+		if ( null != xmlNode.getOTU() ) {
+			Long tbTaxonLabelId = readTreeBaseID(xmlNode.getOTU(),TaxonLabel.class);
+			if ( null != tbTaxonLabelId ) {
+				TaxonLabel tbTaxonLabel = getTaxonLabelHome()
+					.findPersistedObjectByID(TaxonLabel.class, tbTaxonLabelId);
+				tbNode.setTaxonLabel(tbTaxonLabel);
+			}
+		}
+		
+		Set<Node> xmlChildren = xmlTree.getOutNodes(xmlNode);			
+		if ( ! xmlChildren.isEmpty() ) {// xmlNode is internal
+			sb.append('(');
+		}
+		int currentChild = 1;
+		for ( Node child : xmlChildren ) {
+			PhyloTreeNode tbChild = new PhyloTreeNode();
+			tbNode.addChildNode(tbChild);
+			traverseXmlTree(xmlTree,sb,child,tbChild,tbTree);
+			if ( currentChild < xmlChildren.size() ) {
+				sb.append(',');
+			}
+			currentChild++;
+		}		
+		if ( ! xmlChildren.isEmpty() ) {// xmlNode is internal
+			sb.append(')');
+		}
+		String label = xmlNode.getLabel();
+		if ( null != label ) {
+			sb.append(label);
+			tbNode.setName(label);
+		}
+		
+		Set<Node> xmlParents = xmlTree.getInNodes(xmlNode);	
+		if ( ! xmlParents.isEmpty() ) { // xmlNode is not topological root
+			Edge xmlEdge = xmlTree.getEdge(xmlParents.iterator().next(), xmlNode);
+			if ( xmlEdge instanceof FloatEdge ) {
+				Double length = ((FloatEdge)xmlEdge).getLength();
+				sb.append(':').append(length);
+				tbNode.setBranchLength(length);
+			}
+			else if ( xmlEdge instanceof IntEdge ) {
+				Integer length = ((IntEdge)xmlEdge).getLength();
+				sb.append(':').append(length);
+				tbNode.setBranchLength(length.doubleValue());
+			}
+		}		
+	}
+
+}


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