From ac5f3842d7230ae9761f2330b86e515efab29ee5 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 4 Apr 2007 13:10:57 +0000
Subject: [PATCH] flag for dasCoordSysFound added

---
 src/jalview/io/DasSequenceFeatureFetcher.java |   49 ++++++++++++++++---------
 1 file changed, 31 insertions(+), 18 deletions(-)

diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
index a4dc777..33791ad 100755
--- a/src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/src/jalview/io/DasSequenceFeatureFetcher.java
@@ -258,29 +258,42 @@ public class DasSequenceFeatureFetcher
         //  jalview.datamodel.DBRefSource.EMBL - not tested on any EMBL coord sys sources
       });
 // TODO: minimal list of DAS queries to make by querying with untyped ID if distinct from any typed IDs
-        if (uprefs != null)
+
+      boolean dasCoordSysFound = false;
+
+      if (uprefs != null)
         {
           // do any of these ids match the source's coordinate system ?
           for (int j = 0; j < uprefs.length; j++)
           {
             DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
-            
-            if(cs.length>0  && jalview.util.DBRefUtils
-                    .isDasCoordinateSystem(cs[0].getName(), uprefs[j]))
+
+            for(int csIndex=0; csIndex<cs.length; csIndex++)
             {
-              Cache.log.debug("Launched fetcher for coordinate system " +
-                  cs[0].getName());
-              //  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
-                  
-              createFeatureFetcher(seq,
-                                       dasSource,
-                                       uprefs[j]);
-              break; // only do this for one reference - assume same source will send same features for all IDs
+              if (cs.length > 0 && jalview.util.DBRefUtils
+                  .isDasCoordinateSystem(cs[csIndex].getName(), uprefs[j]))
+              {
+                Cache.log.debug("Launched fetcher for coordinate system " +
+                                cs[0].getName());
+                //  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
+
+                System.out.println(seq.getName() + " " + (seq.getDatasetSequence() == null)
+                                   + " " + dasSource.getUrl());
+
+                dasCoordSysFound = false;
+                createFeatureFetcher(seq,
+                                     dasSource,
+                                     uprefs[j]);
+                break; // only do this for one reference - assume same source will send same features for all IDs
+              }
+              else
+                System.out.println("IGNORE " + cs[csIndex].getName());
             }
           }
         }
-        else
+
+        if(!dasCoordSysFound)
         {
           String id = null;
           // try and use the name as the sequence id
@@ -312,16 +325,16 @@ public class DasSequenceFeatureFetcher
  * @param seq
  * @param SourceUrl
  * @param dbref
- */  
+ */
   protected void createFeatureFetcher(final SequenceI seq, final DasSource dasSource,
         final DBRefEntry dbref) {
-    
+
     //////////////
     /// fetch DAS features
     final Das1Source source = new Das1Source();
     source.setUrl(dasSource.getUrl());
     source.setNickname(dasSource.getNickname());
-    if (dbref==null || dbref.getAccessionId()==null || dbref.getAccessionId().length()<1) 
+    if (dbref==null || dbref.getAccessionId()==null || dbref.getAccessionId().length()<1)
     {
       return;
     }
@@ -361,7 +374,7 @@ public class DasSequenceFeatureFetcher
                 Cache.log.debug("mapping from "+f.getBegin()+" - "+f.getEnd());
                 SequenceFeature vf[] = dbref.getMap().locateFeature(f);
                 if (vf!=null) {
-                  for (int v=0;v<vf.length;v++) 
+                  for (int v=0;v<vf.length;v++)
                   {
                     Cache.log.debug("mapping to "+v+": "+vf[v].getBegin()+" - "+vf[v].getEnd());
                     seq.addSequenceFeature(vf[v]);
-- 
1.7.10.2