Author: kono
Date: 2010-02-02 13:39:08 -0800 (Tue, 02 Feb 2010)
New Revision: 19146
Added:
coreplugins/trunk/BioMartClient/
Removed:
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/utils/BiomartXMLQuery.java
Modified:
coreplugins/trunk/BioMartClient/build.xml
Log:
BioMartPlugin moved to core.
Copied: coreplugins/trunk/BioMartClient (from rev 19144,
csplugins/trunk/ucsd/kono/BiomartClient)
Modified: coreplugins/trunk/BioMartClient/build.xml
===================================================================
--- csplugins/trunk/ucsd/kono/BiomartClient/build.xml 2010-02-02 21:15:22 UTC
(rev 19144)
+++ coreplugins/trunk/BioMartClient/build.xml 2010-02-02 21:39:08 UTC (rev
19146)
@@ -26,7 +26,7 @@
<property name="biomartClient.root.dir" value="." />
<!-- You need to modify this line to point to Cytoscape
directory. -->
- <property name="cytoscape.dir"
value="${biomartClient.root.dir}/../FRESH4" />
+ <property name="cytoscape.dir"
value="${biomartClient.root.dir}/../cytoscape" />
<property name="cytoscape.lib.dir" value="${cytoscape.dir}/lib"
/>
<property name="cytoscape.plugin.dir"
value="${cytoscape.dir}/plugins" />
Deleted:
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/utils/BiomartXMLQuery.java
===================================================================
---
csplugins/trunk/ucsd/kono/BiomartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/utils/BiomartXMLQuery.java
2010-02-02 21:15:22 UTC (rev 19144)
+++
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/utils/BiomartXMLQuery.java
2010-02-02 21:39:08 UTC (rev 19146)
@@ -1,55 +0,0 @@
-package edu.ucsd.bioeng.idekerlab.biomartclient.utils;
-
-import java.io.StringWriter;
-
-import javax.xml.transform.OutputKeys;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerConfigurationException;
-import javax.xml.transform.TransformerException;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.dom.DOMSource;
-import javax.xml.transform.stream.StreamResult;
-
-import com.sun.org.apache.xerces.internal.impl.xs.opti.DefaultDocument;
-
-public class BiomartXMLQuery extends DefaultDocument {
-
- private enum Format {
- XSL, HTML, TSV;
- }
-
-
- private static final String ENCODING = "UTF-8";
-
- private String virtualSchemaName;
- private String formatter;
-
-
- public String getQueryString() {
- final TransformerFactory tff = TransformerFactory.newInstance();
- final Transformer tf;
-
- String result = null;
- try {
- tf = tff.newTransformer();
- tf.setOutputProperty(OutputKeys.ENCODING, ENCODING);
-
- StringWriter strWtr = new StringWriter();
- StreamResult strResult = new StreamResult(strWtr);
-
-
- tf.transform(new DOMSource(this.getDocumentElement()),
strResult);
-
- result = strResult.getWriter().toString();
-
- } catch (TransformerConfigurationException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- } catch (TransformerException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
-
- return result;
- }
-}
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