* at:
*
* http://www.biojava.org/
- *
+ *
* Created on Mar 15, 2006
*
*/
package org.biojava.dasobert.das2.io;
-import java.util.ArrayList;
-import java.util.List;
+import java.util.*;
-import org.biojava.dasobert.das2.Das2Capability;
-import org.biojava.dasobert.das2.Das2CapabilityImpl;
-import org.biojava.dasobert.das2.Das2Source;
-import org.biojava.dasobert.das2.Das2SourceImpl;
-import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
-import org.biojava.dasobert.dasregistry.DasSource;
-import org.xml.sax.Attributes;
-import org.xml.sax.helpers.DefaultHandler;
+import org.biojava.dasobert.das2.*;
+import org.biojava.dasobert.dasregistry.*;
+import org.xml.sax.*;
+import org.xml.sax.helpers.*;
/** a parser for the DAS2 sources response
- *
+ *
* @author Andreas Prlic
* @since 6:53:45 PM
* @version %I% %G%
*/
-public class DAS2SourceHandler extends DefaultHandler{
-
- List sources;
- Das2Source currentSource;
- List coordinates;
- List capabilities;
- List labels;
-
- public static final String LABELPROPERTY = "label";
-
- public DAS2SourceHandler() {
- super();
-
- sources = new ArrayList();
- currentSource = new Das2SourceImpl();
- coordinates = new ArrayList();
- capabilities = new ArrayList();
- labels = new ArrayList();
+public class DAS2SourceHandler
+ extends DefaultHandler
+{
+
+ List sources;
+ Das2Source currentSource;
+ List coordinates;
+ List capabilities;
+ List labels;
+
+ public static final String LABELPROPERTY = "label";
+
+ public DAS2SourceHandler()
+ {
+ super();
+
+ sources = new ArrayList();
+ currentSource = new Das2SourceImpl();
+ coordinates = new ArrayList();
+ capabilities = new ArrayList();
+ labels = new ArrayList();
+ }
+
+ private void startSource(String uri, String name, String qName,
+ Attributes atts)
+ {
+
+ String id = atts.getValue("uri");
+ String title = atts.getValue("title");
+ String doc_ref = atts.getValue("doc_href");
+ String description = atts.getValue("description");
+
+ currentSource.setId(id);
+ currentSource.setNickname(title);
+ currentSource.setHelperurl(doc_ref);
+ currentSource.setDescription(description);
+
+ }
+
+ private DasCoordinateSystem getCoordinateSystem(String uri, String name,
+ String qname, Attributes atts)
+ {
+ // e.g. uri="http://das.sanger.ac.uk/dasregistry/coordsys/CS_LOCAL6"
+ // source="Protein Sequence" authority="UniProt" test_range="P06213" />
+ DasCoordinateSystem dcs = new DasCoordinateSystem();
+ String id = atts.getValue("uri");
+ dcs.setUniqueId(id);
+
+ String source = atts.getValue("source");
+ dcs.setCategory(source);
+
+ String authority = atts.getValue("authority");
+ dcs.setName(authority);
+
+ String test_range = atts.getValue("test_range");
+ dcs.setTestCode(test_range);
+
+ try
+ {
+ String taxidstr = atts.getValue("taxid");
+ int taxid = Integer.parseInt(taxidstr);
+ dcs.setNCBITaxId(taxid);
}
-
- private void startSource (String uri, String name, String qName, Attributes atts){
-
- String id = atts.getValue("uri");
- String title = atts.getValue("title");
- String doc_ref = atts.getValue("doc_href");
- String description = atts.getValue("description");
-
-
- currentSource.setId(id);
- currentSource.setNickname(title);
- currentSource.setHelperurl(doc_ref);
- currentSource.setDescription(description);
-
+ catch (Exception e)
+ {}
+
+ String version = atts.getValue("version");
+ if (version != null)
+ {
+ dcs.setVersion(version);
}
-
- private DasCoordinateSystem getCoordinateSystem(String uri, String name, String qname, Attributes atts){
- // e.g. uri="http://das.sanger.ac.uk/dasregistry/coordsys/CS_LOCAL6"
- // source="Protein Sequence" authority="UniProt" test_range="P06213" />
- DasCoordinateSystem dcs = new DasCoordinateSystem();
- String id = atts.getValue("uri");
- dcs.setUniqueId(id);
-
- String source = atts.getValue("source");
- dcs.setCategory(source);
-
- String authority = atts.getValue("authority");
- dcs.setName(authority);
-
- String test_range = atts.getValue("test_range");
- dcs.setTestCode(test_range);
-
- try {
- String taxidstr = atts.getValue("taxid");
- int taxid = Integer.parseInt(taxidstr);
- dcs.setNCBITaxId(taxid);
- } catch (Exception e){}
-
- String version = atts.getValue("version");
- if ( version != null)
- dcs.setVersion(version);
-
- return dcs;
+
+ return dcs;
+ }
+
+ public void startElement(String uri, String name, String qName,
+ Attributes atts)
+ {
+ //System.out.println("new element "+qName);
+
+ if (qName.equals("SOURCE"))
+ {
+ //System.out.println("new Source " + atts.getValue(uri));
+ currentSource = new Das2SourceImpl();
+ coordinates = new ArrayList();
+ capabilities = new ArrayList();
+
+ startSource(uri, name, qName, atts);
+
}
-
- public void startElement (String uri, String name, String qName, Attributes atts){
- //System.out.println("new element "+qName);
-
- if (qName.equals("SOURCE")) {
- //System.out.println("new Source " + atts.getValue(uri));
- currentSource = new Das2SourceImpl();
- coordinates = new ArrayList();
- capabilities = new ArrayList();
-
- startSource(uri,name, qName, atts);
-
- } else if ( qName.equals("MAINTAINER")){
- String email = atts.getValue("email");
- currentSource.setAdminemail(email);
- } else if ( qName.equals("COORDINATES")){
- DasCoordinateSystem dcs = getCoordinateSystem(uri,name,qName,atts);
- coordinates.add(dcs);
-
- } else if ( qName.equals("CAPABILITY")){
- Das2Capability cap = getCapability(uri,name,qName,atts);
- capabilities.add(cap);
- } else if (qName.equals("PROPERTY")) {
- addProperty(uri,name,qName,atts);
- }
+ else if (qName.equals("MAINTAINER"))
+ {
+ String email = atts.getValue("email");
+ currentSource.setAdminemail(email);
}
-
- private Das2Capability getCapability(String uri, String name, String qName, Attributes atts){
- // e.g <CAPABILITY type="features" query_id="http://das.biopackages.net/das/genome/yeast/S228C/feature" />
- Das2Capability cap = new Das2CapabilityImpl();
-
- String type = atts.getValue("type");
- cap.setCapability(type);
- String query_uri = atts.getValue("query_uri");
- cap.setQueryUri(query_uri);
- return cap;
-
+ else if (qName.equals("COORDINATES"))
+ {
+ DasCoordinateSystem dcs = getCoordinateSystem(uri, name, qName, atts);
+ coordinates.add(dcs);
+
}
-
- private void addProperty(String uri, String name, String qName, Attributes atts){
- String pname = atts.getValue("name");
- String label = atts.getValue("value");
- if ( pname.equals(LABELPROPERTY) )
- labels.add(label);
+ else if (qName.equals("CAPABILITY"))
+ {
+ Das2Capability cap = getCapability(uri, name, qName, atts);
+ capabilities.add(cap);
}
-
- public void startDocument(){
- sources = new ArrayList();
- coordinates = new ArrayList();
- capabilities = new ArrayList();
+ else if (qName.equals("PROPERTY"))
+ {
+ addProperty(uri, name, qName, atts);
}
-
- public void endElement(String uri, String name, String qName) {
- if ( qName.equals("SOURCE")) {
- currentSource.setDas2Capabilities((Das2Capability[])capabilities.toArray(new Das2Capability[capabilities.size()]));
- //System.out.println("got coordinates " + coordinates.size());
- currentSource.setCoordinateSystem((DasCoordinateSystem[])coordinates.toArray(new DasCoordinateSystem[coordinates.size()]));
-
- currentSource.setLabels((String[])labels.toArray(new String[labels.size()]));
- labels.clear();
-
- //System.out.println("Das2SourceHandler endElement name " + name + " uri " + uri + " qName " + qName);
- //System.out.println("Das2SourceHandler adding to source: " + currentSource.getId());
- sources.add(currentSource);
- currentSource = new Das2SourceImpl();
- }
+ }
+
+ private Das2Capability getCapability(String uri, String name, String qName,
+ Attributes atts)
+ {
+ // e.g <CAPABILITY type="features" query_id="http://das.biopackages.net/das/genome/yeast/S228C/feature" />
+ Das2Capability cap = new Das2CapabilityImpl();
+
+ String type = atts.getValue("type");
+ cap.setCapability(type);
+ String query_uri = atts.getValue("query_uri");
+ cap.setQueryUri(query_uri);
+ return cap;
+
+ }
+
+ private void addProperty(String uri, String name, String qName,
+ Attributes atts)
+ {
+ String pname = atts.getValue("name");
+ String label = atts.getValue("value");
+ if (pname.equals(LABELPROPERTY))
+ {
+ labels.add(label);
}
-
- public DasSource[] getSources(){
- //System.out.println("Das2SourceHandler: source size: " + sources.size());
- return (DasSource[])sources.toArray(new DasSource[sources.size()]);
+ }
+
+ public void startDocument()
+ {
+ sources = new ArrayList();
+ coordinates = new ArrayList();
+ capabilities = new ArrayList();
+ }
+
+ public void endElement(String uri, String name, String qName)
+ {
+ if (qName.equals("SOURCE"))
+ {
+ currentSource.setDas2Capabilities( (Das2Capability[]) capabilities.
+ toArray(new Das2Capability[capabilities.
+ size()]));
+ //System.out.println("got coordinates " + coordinates.size());
+ currentSource.setCoordinateSystem( (DasCoordinateSystem[]) coordinates.
+ toArray(new DasCoordinateSystem[
+ coordinates.size()]));
+
+ currentSource.setLabels( (String[]) labels.toArray(new String[labels.size()]));
+ labels.clear();
+
+ //System.out.println("Das2SourceHandler endElement name " + name + " uri " + uri + " qName " + qName);
+ //System.out.println("Das2SourceHandler adding to source: " + currentSource.getId());
+ sources.add(currentSource);
+ currentSource = new Das2SourceImpl();
}
-
-
+ }
+
+ public DasSource[] getSources()
+ {
+ //System.out.println("Das2SourceHandler: source size: " + sources.size());
+ return (DasSource[]) sources.toArray(new DasSource[sources.size()]);
+ }
}
git://source.jalview.org / jalview.git / blobdiff