header updated

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

diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
index f8bd7e0..f78f943 100755 (executable)
--- a/src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/src/jalview/io/DasSequenceFeatureFetcher.java
@@ -1,6 +1,6 @@
 /*\r
 * Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
 *\r
 * This program is free software; you can redistribute it and/or\r
 * modify it under the terms of the GNU General Public License\r
@@ -27,7 +27,6 @@ import java.util.*;
 import java.net.URL;\r
 \r
 import org.biojava.dasobert.das.FeatureThread;\r
-import org.biojava.dasobert.dasregistry.Das1Source;\r
 import org.biojava.dasobert.eventmodel.FeatureEvent;\r
 import org.biojava.dasobert.eventmodel.FeatureListener;\r
 import org.biojava.dasobert.dasregistry.DasSource;\r
@@ -206,7 +205,6 @@ public class DasSequenceFeatureFetcher implements Runnable
                                //  null\r
                        // );\r
 \r
-                     // System.out.println(nickname+" "+f.getType()+" "+f.begin+" "+f.end);\r
          return f;\r
          }\r
          catch (Exception e) {\r
@@ -240,9 +238,8 @@ public class DasSequenceFeatureFetcher implements Runnable
           {\r
             setThreadsRunning(+1);\r
 \r
-            int start=seq.getStart(), end = seq.getEnd();\r
-\r
-            if(af.getViewport().getSelectionGroup()!=null)\r
+          //  int start=seq.getStart(), end = seq.getEnd();\r
+          /*  if(af.getViewport().getSelectionGroup()!=null)\r
             {\r
               SequenceI tmp = af.getViewport().getAlignment().findName(seq.getName());\r
               start = tmp.findPosition(\r
@@ -252,7 +249,7 @@ public class DasSequenceFeatureFetcher implements Runnable
               end = tmp.findPosition(\r
                  af.getViewport().getSelectionGroup().getEndRes()\r
                  );\r
-            }\r
+            }*/\r
 \r
             FeatureThread fetcher = new FeatureThread(id\r
                                                    //  +  ":" + start + "," + end,\r
@@ -312,7 +309,12 @@ public class DasSequenceFeatureFetcher implements Runnable
   {\r
     threadsRunning += i;\r
     if(threadsRunning<1)\r
+    {\r
       af.setProgressBar("DAS Feature Fetching Complete", startTime);\r
+\r
+      if(af.featureSettings!=null)\r
+        af.featureSettings.setTableData();\r
+    }\r
   }\r
 \r
   /**\r
@@ -373,7 +375,7 @@ public class DasSequenceFeatureFetcher implements Runnable
               {\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
+                DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();\r
                 for (int l=0; l<cs.length; l++)\r
                 {\r
                   if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), uprefs[j]))\r