[Treebase-guts] SF.net SVN: treebase:[468] trunk/treebase-core/src/main/java/org/cipres/ treebase

[<yo...@us...>]

Revision: 468
          http://treebase.svn.sourceforge.net/treebase/?rev=468&view=rev
Author:   youjun
Date:     2010-01-19 14:29:50 +0000 (Tue, 19 Jan 2010)

Log Message:
-----------
delete cipres framework delete ncl stuffs

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

Removed Paths:
-------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/ncl/
    trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNCL.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/NexusParserFinder.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/NexusParserFinder.java	2010-01-15 18:47:28 UTC (rev 467)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/NexusParserFinder.java	2010-01-19 14:29:50 UTC (rev 468)
@@ -7,7 +7,7 @@
 import org.cipres.treebase.domain.matrix.MatrixDataTypeHome;
 import org.cipres.treebase.domain.taxon.TaxonLabelHome;
 import org.cipres.treebase.service.nexus.NexusServiceMesquite;
-import org.cipres.treebase.service.nexus.NexusServiceNCL;
+//import org.cipres.treebase.service.nexus.NexusServiceNCL;
 
 /**
  * NexusParserFinder.java
@@ -43,14 +43,14 @@
 	 */
 	private NexusService getNexusServiceImpl() {
 		if (mNexusServiceImpl == null) {
-			if (PARSER_NCL.compareToIgnoreCase(getNexusParserStr()) == 0) {
-				NexusServiceNCL serviceNCL = new NexusServiceNCL();
+			//if (PARSER_NCL.compareToIgnoreCase(getNexusParserStr()) == 0) {
+				//NexusServiceNCL serviceNCL = new NexusServiceNCL();
 				
-				serviceNCL.setMatrixDataTypeHome(getMatrixDataTypeHome());
-				serviceNCL.setTaxonLabelHome(getTaxonLabelHome());
+				//serviceNCL.setMatrixDataTypeHome(getMatrixDataTypeHome());
+				//serviceNCL.setTaxonLabelHome(getTaxonLabelHome());
 				
-				mNexusServiceImpl = serviceNCL;
-			} else {
+				//mNexusServiceImpl = serviceNCL;
+			//} else {
 				NexusServiceMesquite serviceMesquite = new NexusServiceMesquite();
 				
 				serviceMesquite.setItemDefinitionHome(getItemDefinitionHome());
@@ -59,7 +59,7 @@
 				
 				mNexusServiceImpl = serviceMesquite;
 				
-			}
+			//}
 		}
 		return mNexusServiceImpl;
 	}

Deleted: trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNCL.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNCL.java	2010-01-15 18:47:28 UTC (rev 467)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNCL.java	2010-01-19 14:29:50 UTC (rev 468)
@@ -1,169 +0,0 @@
-
-package org.cipres.treebase.service.nexus;
-
-import java.io.File;
-import java.util.Collection;
-import java.util.Properties;
-
-import org.apache.log4j.Logger;
-
-import org.cipres.treebase.domain.DomainHome;
-import org.cipres.treebase.domain.matrix.MatrixDataTypeHome;
-import org.cipres.treebase.domain.nexus.NexusDataSet;
-import org.cipres.treebase.domain.nexus.NexusService;
-import org.cipres.treebase.domain.nexus.ncl.NCLNexusConverter;
-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;
-
-/**
- * NexusServiceNCL.java
- * 
- * Created on Apr 21, 2006
- * 
- * @author Jin Ruan
- * 
- */
-public class NexusServiceNCL extends AbstractServiceImpl implements NexusService {
-	private static final Logger LOGGER = Logger.getLogger(NexusServiceNCL.class);
-
-	private TaxonLabelHome mTaxonLabelHome;
-	private MatrixDataTypeHome mMatrixDataTypeHome;
-
-	/**
-	 * Constructor.
-	 */
-	public NexusServiceNCL() {
-		super();
-	}
-
-	/**
-	 * Return the TaxonLabelHome field.
-	 * 
-	 * @return TaxonLabelHome mTaxonLabelHome
-	 */
-	private TaxonLabelHome getTaxonLabelHome() {
-		return mTaxonLabelHome;
-	}
-
-	/**
-	 * Set the TaxonLabelHome field.
-	 */
-	public void setTaxonLabelHome(TaxonLabelHome pNewTaxonLabelHome) {
-		mTaxonLabelHome = pNewTaxonLabelHome;
-	}
-
-	/**
-	 * Return the MatrixDataTypeHome field.
-	 * 
-	 * @return MatrixDataTypeHome mMatrixDataTypeHome
-	 */
-	private MatrixDataTypeHome getMatrixDataTypeHome() {
-		return mMatrixDataTypeHome;
-	}
-
-	/**
-	 * Set the MatrixDataTypeHome field.
-	 */
-	public void setMatrixDataTypeHome(MatrixDataTypeHome pNewMatrixDataTypeHome) {
-		mMatrixDataTypeHome = pNewMatrixDataTypeHome;
-	}
-
-	/**
-	 * 
-	 * @see org.cipres.treebase.service.AbstractServiceImpl#getDomainHome()
-	 */
-	@Override
-	protected DomainHome getDomainHome() {
-		return null; // do not need persistence service.
-	}
-
-	/**
-	 * Returns true only if all files exist.
-	 * 
-	 * @param pNexusFiles
-	 * @return
-	 */
-	private boolean checkFiles(Collection<File> pNexusFiles) {
-		if (pNexusFiles == null) {
-			return false;
-		}
-
-		boolean hasError = false;
-		for (File file : pNexusFiles) {
-			if (!file.exists()) {
-				if (LOGGER.isInfoEnabled()) {
-					LOGGER.info(" input file does not exist:" + file.getAbsolutePath()); //$NON-NLS-1$
-				}
-				hasError = true;
-			}
-		}
-
-		return !hasError;
-	}
-
-	/** 
-	 * 
-	 * @see org.cipres.treebase.domain.nexus.NexusService#parseNexus(org.cipres.treebase.domain.study.Study, java.util.Collection, org.cipres.treebase.event.ProgressionListener)
-	 */
-	public NexusDataSet parseNexus(Study pStudy, Collection<File> pNexusFiles, ProgressionListener pListener) {
-		
-		if (pStudy == null) {
-			if (LOGGER.isInfoEnabled()) {
-				LOGGER
-					.info("parseNexus - Study is null"); //$NON-NLS-1$
-			}
-			return null;
-		}
-
-		if (!checkFiles(pNexusFiles)) {
-			return null;
-		}
-
-		NexusDataSet data = new NexusDataSet();
-		
-		NCLNexusConverter converter = new NCLNexusConverter();
-		converter.setMatrixDataTypeHome(getMatrixDataTypeHome());
-		converter.setTaxonLabelHome(getTaxonLabelHome());
-		
-		converter.processLoadFile(pNexusFiles, pStudy, data, pListener);
-		
-		return data;
-	}
-
-	/** 
-	 * 
-	 * @see org.cipres.treebase.domain.nexus.NexusService#parseNexus(org.cipres.treebase.domain.study.Study, java.io.File)
-	 */
-	public NexusDataSet parseNexus(Study pStudy, File pNexusFile) {
-		//TODO: parseNexus
-		return null;
-	}
-
-	@Override
-	public Class defaultResultClass() {
-		return null;
-	}
-
-	public String serialize(NexusDataSet nexusDataSet) {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	public String serialize(Study study) {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	public String serialize(NexusDataSet nexusDataSet, Properties properties) {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	public String serialize(Study study, Properties properties) {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-}


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