From 6853e551dad73c21f52fefa6bf619443f09107ab Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 19 Jul 2006 10:39:38 +0000
Subject: [PATCH] Use Selection group to define sequence range to fetch
 features

---
 src/jalview/io/DasSequenceFeatureFetcher.java |   30 +++++++++++++++++++------
 1 file changed, 23 insertions(+), 7 deletions(-)

diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
index 70af276..20ae27c 100755
--- a/src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/src/jalview/io/DasSequenceFeatureFetcher.java
@@ -94,13 +94,14 @@ public class DasSequenceFeatureFetcher implements Runnable
     int refCount = 0;
     for(int i=0; i<sequences.length; i++)
     {
-      if(sequences[i].getDBRef()!=null)
+      Vector dbref = sequences[i].getDBRef();
+      if(dbref!=null)
       {
-        for(int j=0; j<sequences[i].getDBRef().size(); j++)
+        for(int j=0; j<dbref.size(); j++)
         {
-          System.out.println(sequences[i].getDBRef().elementAt(j)
+          System.out.println(dbref.elementAt(j)
                              +" "+jalview.datamodel.DBRefSource.UNIPROT);
-          if(sequences[i].getDBRef().elementAt(j)
+          if(dbref.elementAt(j)
              .equals(jalview.datamodel.DBRefSource.UNIPROT))
           {
             System.out.println("got a match");
@@ -210,7 +211,8 @@ public class DasSequenceFeatureFetcher implements Runnable
   protected void createFeatureFetcher(final SequenceI seq,
                                       final String sourceUrl,
                                       String id,
-                                      String nickname)  {
+                                      String nickname)
+  {
 	  //////////////
 	  /// fetch DAS features
           final Das1Source source = new Das1Source();
@@ -220,13 +222,27 @@ public class DasSequenceFeatureFetcher implements Runnable
 
           Cache.log.debug("new Das Feature Fetcher for " + id + " querying " +
                           sourceUrl);
+
           if (id != null && id.length() > 0)
           {
             setThreadsRunning(+1);
 
+            int start=seq.getStart(), end = seq.getEnd();
+
+            if(af.getViewport().getSelectionGroup()!=null)
+            {
+              SequenceI tmp = af.getViewport().getAlignment().findName(seq.getName());
+              start = tmp.findPosition(
+              af.getViewport().getSelectionGroup().getStartRes()
+                  );
+
+              end = tmp.findPosition(
+                 af.getViewport().getSelectionGroup().getEndRes()
+                 );
+            }
+
             FeatureThread fetcher = new FeatureThread(id
-               +  ":" + seq.getStart() + "," +seq.getEnd()
-                 , source);
+               +  ":" + start + "," + end, source);
 
             fetcher.addFeatureListener(new FeatureListener()
             {
-- 
1.7.10.2