From fa089b1e2ac2acf8940d89d8b717eafc88aaeaa2 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 30 Apr 2007 15:36:20 +0000
Subject: [PATCH] 'no sources selected' calls method on feature settings
 dialog to prompt user. fixed never-ending das feature
 retrieval bug.

---
 src/jalview/io/DasSequenceFeatureFetcher.java |   17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
index c8b5d3e..58ae580 100755
--- a/src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/src/jalview/io/DasSequenceFeatureFetcher.java
@@ -172,6 +172,8 @@ public class DasSequenceFeatureFetcher
      {
        System.out.println("No DAS Sources active");
        af.setProgressBar("No DAS Sources Active", startTime);
+       cancelled = true;
+       fsettings.noDasSourceActive();
        return;
      }
 
@@ -249,7 +251,9 @@ public class DasSequenceFeatureFetcher
 
   void nextSequence(DasSource dasSource, SequenceI seq)
   {
-      DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(),
+    if (cancelled)
+      return;
+    DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(),
           new String[]
           {
         //  jalview.datamodel.DBRefSource.PDB,
@@ -263,11 +267,11 @@ public class DasSequenceFeatureFetcher
       if (uprefs != null)
         {
           // do any of these ids match the source's coordinate system ?
-          for (int j = 0; j < uprefs.length; j++)
+          for (int j = 0; !dasCoordSysFound && j < uprefs.length; j++)
           {
             DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
 
-            for(int csIndex=0; csIndex<cs.length; csIndex++)
+            for(int csIndex=0; csIndex<cs.length && !dasCoordSysFound; csIndex++)
             {
               if (cs.length > 0 && jalview.util.DBRefUtils
                   .isDasCoordinateSystem(cs[csIndex].getName(), uprefs[j]))
@@ -280,11 +284,10 @@ public class DasSequenceFeatureFetcher
                 System.out.println(seq.getName() + " " + (seq.getDatasetSequence() == null)
                                    + " " + dasSource.getUrl());
 
-                dasCoordSysFound = false;
+                dasCoordSysFound = true; // break's out of the loop
                 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());
@@ -474,6 +477,10 @@ public class DasSequenceFeatureFetcher
    */
   SequenceFeature newSequenceFeature(Map dasfeature, String nickname)
   {
+    if (dasfeature==null)
+    {
+      return null;
+    }
     try
     {
       /**
-- 
1.7.10.2