Takes AlignFrame as arg, to update progressbar

diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
index 5bfb861..d0bc92d 100755 (executable)
--- a/src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/src/jalview/io/DasSequenceFeatureFetcher.java
@@ -51,7 +51,7 @@ import jalview.bin.Cache;
 public class DasSequenceFeatureFetcher implements Runnable\r
 {\r
   final AlignmentI dataset;\r
-  final AlignmentPanel ap;\r
+  final AlignFrame af;\r
   StringBuffer sbuffer = new StringBuffer();\r
 \r
 \r
@@ -62,10 +62,11 @@ public class DasSequenceFeatureFetcher implements Runnable
    * @param align DOCUMENT ME!\r
    * @param ap DOCUMENT ME!\r
    */\r
-  public DasSequenceFeatureFetcher(AlignmentI align, AlignmentPanel ap)\r
+  public DasSequenceFeatureFetcher(AlignmentI align,\r
+                                   AlignFrame af)\r
   {\r
     this.dataset = align.getDataset();\r
-    this.ap = ap;\r
+    this.af = af;\r
 \r
     Thread thread = new Thread(this);\r
     thread.start();\r
@@ -154,7 +155,7 @@ public class DasSequenceFeatureFetcher implements Runnable
           if (id != null && id.length() > 0)\r
           {\r
             FeatureThread fetcher = new FeatureThread(id\r
-               +  ":" + seq.getStart() + "," +seq.getEnd()\r
+            //   +  ":" + seq.getStart() + "," +seq.getEnd()\r
                  , source);\r
 \r
             fetcher.addFeatureListener(new FeatureListener()\r
@@ -186,14 +187,13 @@ public class DasSequenceFeatureFetcher implements Runnable
                   }\r
                 }\r
               }\r
-\r
             }\r
 \r
             );\r
 \r
             //NOTE alignPanel listener will be called after the previous\r
             //anonymous listener!!!\r
-            fetcher.addFeatureListener(ap);\r
+            fetcher.addFeatureListener(af);\r
 \r
             fetcher.start();\r
          }\r
@@ -203,6 +203,9 @@ public class DasSequenceFeatureFetcher implements Runnable
    */\r
   public void run()\r
   {\r
+    long startTime = System.currentTimeMillis();\r
+    af.setProgressBar("Fetching DAS Sequence Features", startTime);\r
+\r
     DasSource [] sources = new jalview.gui.DasSourceBrowser().getDASSource();\r
 \r
     String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");\r
@@ -226,6 +229,7 @@ public class DasSequenceFeatureFetcher implements Runnable
     if(selectedSources == null || selectedSources.size()==0)\r
     {\r
       System.out.println("No DAS Sources active");\r
+      af.setProgressBar("No DAS Sources Active", startTime);\r
       return;\r
     }\r
 \r
@@ -248,16 +252,20 @@ 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, k = uprefs.size(); j < k; j++)\r
+              for (int j = 0;  j < uprefs.size(); 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
+                for (int l=0; l<cs.length; l++)\r
+                {\r
                   if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), (DBRefEntry)\r
                       uprefs.get(j)))\r
                   {\r
                     Cache.log.debug("Launched fetcher for coordinate system " +\r
                                     cs[l].getName());\r
+\r
+\r
                     createFeatureFetcher(sequence,\r
                                          dasSource.getUrl(),\r
                                          ( (DBRefEntry) uprefs.get(j)).\r
@@ -298,6 +306,8 @@ public class DasSequenceFeatureFetcher implements Runnable
     {\r
       ex.printStackTrace();\r
     }\r
+\r
+    af.setProgressBar("DAS Feature Fetching Complete", startTime);\r
   }\r
 \r
 \r