merge from 2_4_Release branch

[jalview.git] / src / org / biojava / dasobert / das2 / io / DAS2SourceHandler.java

diff --git a/src/org/biojava/dasobert/das2/io/DAS2SourceHandler.java b/src/org/biojava/dasobert/das2/io/DAS2SourceHandler.java
index d8c61fa..0ee0b5e 100755 (executable)
--- a/src/org/biojava/dasobert/das2/io/DAS2SourceHandler.java
+++ b/src/org/biojava/dasobert/das2/io/DAS2SourceHandler.java
@@ -29,20 +29,24 @@ import org.biojava.dasobert.dasregistry.*;
 import org.xml.sax.*;
 import org.xml.sax.helpers.*;
 
-/** a parser for the DAS2 sources response
- *
+/**
+ * a parser for the DAS2 sources response
+ * 
  * @author Andreas Prlic
  * @since 6:53:45 PM
  * @version %I% %G%
  */
-public class DAS2SourceHandler
-    extends DefaultHandler
+public class DAS2SourceHandler extends DefaultHandler
 {
 
   List sources;
+
   Das2Source currentSource;
+
   List coordinates;
+
   List capabilities;
+
   List labels;
 
   public static final String LABELPROPERTY = "label";
@@ -59,7 +63,7 @@ public class DAS2SourceHandler
   }
 
   private void startSource(String uri, String name, String qName,
-                           Attributes atts)
+          Attributes atts)
   {
 
     String id = atts.getValue("uri");
@@ -75,7 +79,7 @@ public class DAS2SourceHandler
   }
 
   private DasCoordinateSystem getCoordinateSystem(String uri, String name,
-                                                  String qname, Attributes atts)
+          String qname, Attributes atts)
   {
     // e.g. uri="http://das.sanger.ac.uk/dasregistry/coordsys/CS_LOCAL6"
     // source="Protein Sequence" authority="UniProt" test_range="P06213" />
@@ -97,9 +101,9 @@ public class DAS2SourceHandler
       String taxidstr = atts.getValue("taxid");
       int taxid = Integer.parseInt(taxidstr);
       dcs.setNCBITaxId(taxid);
+    } catch (Exception e)
+    {
     }
-    catch (Exception e)
-    {}
 
     String version = atts.getValue("version");
     if (version != null)
@@ -111,13 +115,13 @@ public class DAS2SourceHandler
   }
 
   public void startElement(String uri, String name, String qName,
-                           Attributes atts)
+          Attributes atts)
   {
-    //System.out.println("new element "+qName);
+    // System.out.println("new element "+qName);
 
     if (qName.equals("SOURCE"))
     {
-      //System.out.println("new Source " + atts.getValue(uri));
+      // System.out.println("new Source " + atts.getValue(uri));
       currentSource = new Das2SourceImpl();
       coordinates = new ArrayList();
       capabilities = new ArrayList();
@@ -147,10 +151,11 @@ public class DAS2SourceHandler
     }
   }
 
-  private Das2Capability getCapability(String uri, String name, String qName,
-                                       Attributes atts)
+  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" />
+    // 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");
@@ -162,7 +167,7 @@ public class DAS2SourceHandler
   }
 
   private void addProperty(String uri, String name, String qName,
-                           Attributes atts)
+          Attributes atts)
   {
     String pname = atts.getValue("name");
     String label = atts.getValue("value");
@@ -183,19 +188,20 @@ public class DAS2SourceHandler
   {
     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()]));
+      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());
+      // 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();
     }
@@ -203,7 +209,7 @@ public class DAS2SourceHandler
 
   public DasSource[] getSources()
   {
-    //System.out.println("Das2SourceHandler: source size: " + sources.size());
+    // System.out.println("Das2SourceHandler: source size: " + sources.size());
     return (DasSource[]) sources.toArray(new DasSource[sources.size()]);
   }