Dasobert updates, labels and prefix changes

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

diff --git a/src/org/biojava/dasobert/das2/DasSourceConverter.java b/src/org/biojava/dasobert/das2/DasSourceConverter.java
index 4fb294a..513ba3f 100755 (executable)
--- a/src/org/biojava/dasobert/das2/DasSourceConverter.java
+++ b/src/org/biojava/dasobert/das2/DasSourceConverter.java
@@ -22,6 +22,7 @@
  */
 package org.biojava.dasobert.das2;
 
+//import org.biojava.bio.program.das.dasalignment.DASException;
 import org.biojava.dasobert.dasregistry.Das1Source;
 
 public class DasSourceConverter {
@@ -36,7 +37,9 @@ public class DasSourceConverter {
      * This only will work if is passes the Das2Source.isDas1Source() test
      * i.e. this is really a das1 server there
      *
-     * @return
+     * @param das2source a DAS2Source to be converted
+     * @return a Das1Source
+     * @throws DASException
      */
     public static Das1Source toDas1Source (Das2Source das2source) throws Exception{
         if ( ! das2source.hasDas1Capabilities())
@@ -52,16 +55,20 @@ public class DasSourceConverter {
         ds.setCoordinateSystem(das2source.getCoordinateSystem());
         ds.setNickname(das2source.getNickname());
         ds.setId(das2source.getId());
+        ds.setLabels(das2source.getLabels());
 
         // convert the capabilitites to das1 capabiltities and get the url
         Das2Capability[] caps = das2source.getDas2Capabilities();
         String[] das1capabilitites = new String[caps.length];
-        int DASPREFIXLENGTH = 4;
+        int DASPREFIXLENGTH = Das2CapabilityImpl.DAS1_CAPABILITY_PREFIX.length();
+
         for ( int i = 0 ; i< caps.length;i++){
             Das2Capability cap = caps[i];
 
             String c = cap.getCapability();
-            das1capabilitites[i] = c.substring(4,c.length());
+
+            das1capabilitites[i] = c.substring(DASPREFIXLENGTH,c.length());
+
             String query_uri = cap.getQueryUri();
 
             String url = query_uri.substring(0,(query_uri.length() - c.length() + DASPREFIXLENGTH));