Menu
▾
▴
treebase-guts
|
From: <rv...@us...> - 2009-06-18 09:40:44
|
Revision: 59
http://treebase.svn.sourceforge.net/treebase/?rev=59&view=rev
Author: rvos
Date: 2009-06-18 09:40:42 +0000 (Thu, 18 Jun 2009)
Log Message:
-----------
Added NexusService for NeXML
Added Paths:
-----------
trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java
Added: 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 (rev 0)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java 2009-06-18 09:40:42 UTC (rev 59)
@@ -0,0 +1,52 @@
+package org.cipres.treebase.service.nexus;
+
+import java.io.File;
+import java.util.Collection;
+
+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.study.Study;
+import org.cipres.treebase.event.ProgressionListener;
+import org.cipres.treebase.service.AbstractServiceImpl;
+
+public class NexusServiceNexml extends AbstractServiceImpl implements NexusService {
+ private static final Logger LOGGER = Logger.getLogger(NexusServiceNexml.class);
+ private DomainHome mDomainHome;
+
+ @Override
+ public Class defaultResultClass() {
+ return null;
+ }
+
+ @Override
+ protected DomainHome getDomainHome() {
+ return mDomainHome;
+ }
+
+ public void setDomainHome(DomainHome domainHome) {
+ mDomainHome = domainHome;
+ }
+
+ public NexusDataSet parseNexus(Study study, Collection<File> nexusFiles,
+ ProgressionListener listener) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ public NexusDataSet parseNexus(Study study, File nexusFile) {
+ if (study == null) {
+ if (LOGGER.isInfoEnabled()) {
+ LOGGER.info("parseNexus - Study is null"); //$NON-NLS-1$
+ }
+ return null;
+ }
+ NexusDataSet data = new NexusDataSet();
+ NexmlConverter converter = new NexmlConverter();
+ converter.parseOneFile(nexusFile, study, data);
+ return data;
+ }
+
+}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-06-19 02:17:13
|
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;
+ }
+
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-06-23 10:59:29
|
Revision: 77
http://treebase.svn.sourceforge.net/treebase/?rev=77&view=rev
Author: rvos
Date: 2009-06-23 10:59:03 +0000 (Tue, 23 Jun 2009)
Log Message:
-----------
Commenting out DomainHome fields: we don't need persistence, but the interface wants us to have the 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 2009-06-23 10:57:15 UTC (rev 76)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java 2009-06-23 10:59:03 UTC (rev 77)
@@ -20,22 +20,24 @@
public class NexusServiceNexml extends AbstractServiceImpl implements NexusService {
private static final Logger LOGGER = Logger.getLogger(NexusServiceNexml.class);
- private DomainHome mDomainHome;
+// private DomainHome mDomainHome;
private TaxonLabelHome mTaxonLabelHome;
@Override
- public Class defaultResultClass() {
+ public Class<?> defaultResultClass() {
return null;
}
@Override
protected DomainHome getDomainHome() {
- return mDomainHome;
+ return null; // do not need persistence service.
}
+ /*
public void setDomainHome(DomainHome domainHome) {
mDomainHome = domainHome;
}
+ */
public NexusDataSet parseNexus(Study study, Collection<File> nexusFiles,
ProgressionListener listener) {
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2010-02-12 04:41:20
|
Revision: 495
http://treebase.svn.sourceforge.net/treebase/?rev=495&view=rev
Author: rvos
Date: 2010-02-12 04:41:13 +0000 (Fri, 12 Feb 2010)
Log Message:
-----------
Removed commented-out, redundant code
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 2010-02-12 04:37:30 UTC (rev 494)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java 2010-02-12 04:41:13 UTC (rev 495)
@@ -23,7 +23,6 @@
public class NexusServiceNexml extends AbstractServiceImpl implements NexusService {
private static final Logger LOGGER = Logger.getLogger(NexusServiceNexml.class);
-// private DomainHome mDomainHome;
private TaxonLabelHome mTaxonLabelHome;
@Override
@@ -35,12 +34,6 @@
protected DomainHome getDomainHome() {
return null; // do not need persistence service.
}
-
- /*
- public void setDomainHome(DomainHome domainHome) {
- mDomainHome = domainHome;
- }
- */
public NexusDataSet parseNexus(Study study, Collection<File> nexusFiles,
ProgressionListener listener) {
@@ -66,30 +59,10 @@
}
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();
- */
return serialize(nexusDataSet,null);
}
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();
- */
return serialize(study,null);
}
@@ -120,38 +93,12 @@
}
public String serialize(NexusDataSet nexusDataSet, Properties properties) {
- /*
- String baseURI = null;
- if ( null != properties ) {
- baseURI = properties.getProperty("nexml.uri.base");
- }
- Document document = null;
- try {
- document = DocumentFactory.createDocument();
- } catch (ParserConfigurationException e) {
- e.printStackTrace();
- }
- NexmlDocumentConverter ndc = new NexmlDocumentConverter(null,getTaxonLabelHome(),document,baseURI);
- */
- NexmlDocumentConverter ndc = this.getNexmlDocumentConverter(null, properties);
+ NexmlDocumentConverter ndc = getNexmlDocumentConverter(null, properties);
return ndc.fromTreeBaseToXml(nexusDataSet).getXmlString();
}
public String serialize(Study study, Properties properties) {
- /*
- String baseURI = null;
- if ( null != properties ) {
- baseURI = properties.getProperty("nexml.uri.base");
- }
- Document document = null;
- try {
- document = DocumentFactory.createDocument();
- } catch (ParserConfigurationException e) {
- e.printStackTrace();
- }
- NexmlDocumentConverter ndc = new NexmlDocumentConverter(study,getTaxonLabelHome(),document,baseURI);
- */
- NexmlDocumentConverter ndc = this.getNexmlDocumentConverter(study, properties);
+ NexmlDocumentConverter ndc = getNexmlDocumentConverter(study, properties);
return ndc.fromTreeBaseToXml(study).getXmlString();
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
Thanks for helping keep SourceForge clean.
X