[Treebase-guts] SF.net SVN: treebase:[67] trunk/treebase-core/src/main/java/org/cipres/ treebase/service/nexus/NexusServiceNexml.java

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

Revision: 67
          http://treebase.svn.sourceforge.net/treebase/?rev=67&view=rev
Author:   rvos
Date:     2009-06-19 02:17:12 +0000 (Fri, 19 Jun 2009)

Log Message:
-----------
Implemented serialize() methods.

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java	2009-06-19 02:16:12 UTC (rev 66)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java	2009-06-19 02:17:12 UTC (rev 67)
@@ -3,18 +3,25 @@
 import java.io.File;
 import java.util.Collection;
 
+import javax.xml.parsers.ParserConfigurationException;
+
 import org.apache.log4j.Logger;
 import org.cipres.treebase.domain.DomainHome;
 import org.cipres.treebase.domain.nexus.NexusDataSet;
 import org.cipres.treebase.domain.nexus.NexusService;
 import org.cipres.treebase.domain.nexus.nexml.NexmlConverter;
+import org.cipres.treebase.domain.nexus.nexml.NexmlDocumentConverter;
 import org.cipres.treebase.domain.study.Study;
+import org.cipres.treebase.domain.taxon.TaxonLabelHome;
 import org.cipres.treebase.event.ProgressionListener;
 import org.cipres.treebase.service.AbstractServiceImpl;
+import org.nexml.model.Document;
+import org.nexml.model.DocumentFactory;
 
 public class NexusServiceNexml extends AbstractServiceImpl implements NexusService {
 	private static final Logger LOGGER = Logger.getLogger(NexusServiceNexml.class);
 	private DomainHome mDomainHome;
+	private TaxonLabelHome mTaxonLabelHome;
 
 	@Override
 	public Class defaultResultClass() {
@@ -32,8 +39,12 @@
 
 	public NexusDataSet parseNexus(Study study, Collection<File> nexusFiles,
 			ProgressionListener listener) {
-		// TODO Auto-generated method stub
-		return null;
+		NexusDataSet data = new NexusDataSet();
+		NexmlConverter converter = new NexmlConverter();
+		for ( File nexusFile : nexusFiles ) {
+			converter.parseOneFile(nexusFile, study, data);
+		}
+		return data;
 	}
 
 	public NexusDataSet parseNexus(Study study, File nexusFile) {
@@ -49,4 +60,34 @@
 		return data;
 	}
 
+	public String serialize(NexusDataSet nexusDataSet) {
+		Document document = null;
+		try {
+			document = DocumentFactory.createDocument();
+		} catch (ParserConfigurationException e) {
+			e.printStackTrace();
+		}
+		NexmlDocumentConverter ndc = new NexmlDocumentConverter(null,getTaxonLabelHome(),document);
+		return ndc.fromTreeBaseToXml(nexusDataSet).getXmlString();
+	}
+
+	public String serialize(Study study) {
+		Document document = null;
+		try {
+			document = DocumentFactory.createDocument();
+		} catch (ParserConfigurationException e) {
+			e.printStackTrace();
+		}
+		NexmlDocumentConverter ndc = new NexmlDocumentConverter(study,getTaxonLabelHome(),document);
+		return ndc.fromTreeBaseToXml(study).getXmlString();
+	}
+
+	public TaxonLabelHome getTaxonLabelHome() {
+		return mTaxonLabelHome;
+	}
+
+	public void setTaxonLabelHome(TaxonLabelHome taxonLabelHome) {
+		mTaxonLabelHome = taxonLabelHome;
+	}
+
 }


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