DBRefs now array

[jalview.git] / src / jalview / io / DasSequenceFeatureFetcher.java

diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
index b4dd1f6..1d63e5b 100755 (executable)
--- a/src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/src/jalview/io/DasSequenceFeatureFetcher.java
@@ -95,15 +95,14 @@ public class DasSequenceFeatureFetcher implements Runnable
     int refCount = 0;\r
     for(int i=0; i<sequences.length; i++)\r
     {\r
-      Vector dbref = sequences[i].getDBRef();\r
+      DBRefEntry [] dbref = sequences[i].getDBRef();\r
       if(dbref!=null)\r
       {\r
-        for(int j=0; j<dbref.size(); j++)\r
+        for(int j=0; j<dbref.length; j++)\r
         {\r
-          DBRefEntry entry = (DBRefEntry)dbref.elementAt(j);\r
-          System.out.println(entry.getSource()\r
+          System.out.println(dbref[j].getSource()\r
                              +" "+jalview.datamodel.DBRefSource.UNIPROT);\r
-          if(entry.getSource()\r
+          if(dbref[j].getSource()\r
              .equals(jalview.datamodel.DBRefSource.UNIPROT))\r
           {\r
             System.out.println("got a match");\r
@@ -344,7 +343,7 @@ public class DasSequenceFeatureFetcher implements Runnable
       int seqIndex = 0;\r
       while (seqIndex < sequences.length)\r
       {\r
-          Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequences[seqIndex].getDBRef(),\r
+          DBRefEntry [] uprefs = jalview.util.DBRefUtils.selectRefs(sequences[seqIndex].getDBRef(),\r
               new String[]  {\r
               jalview.datamodel.DBRefSource.PDB,\r
               jalview.datamodel.DBRefSource.UNIPROT});\r
@@ -356,15 +355,14 @@ public class DasSequenceFeatureFetcher implements Runnable
             if (uprefs != null)\r
             {\r
               // we know the id for this entry, so don't note its ID in the unknownSequences list\r
-              for (int j = 0;  j < uprefs.size(); j++)\r
+              for (int j = 0;  j < uprefs.length; j++)\r
               {\r
 \r
                 // Will have to pass any mapping information to the fetcher - the start/end for the DBRefEntry may not be the same as the sequence's start/end\r
                 org.biojava.dasobert.dasregistry.DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();\r
                 for (int l=0; l<cs.length; l++)\r
                 {\r
-                  if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), (DBRefEntry)\r
-                      uprefs.get(j)))\r
+                  if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), uprefs[j]))\r
                   {\r
                     Cache.log.debug("Launched fetcher for coordinate system " +\r
                                     cs[l].getName());\r
@@ -372,8 +370,7 @@ public class DasSequenceFeatureFetcher implements Runnable
 \r
                     createFeatureFetcher(sequences[seqIndex],\r
                                          dasSource.getUrl(),\r
-                                         ( (DBRefEntry) uprefs.get(j)).\r
-                                         getAccessionId(),\r
+                                          uprefs[j].getAccessionId(),\r
                                          dasSource.getNickname());\r
                   }\r
                 }\r