From 3bdd4947c87108581abe34d05c878ee110b60f72 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 22 Jun 2006 08:52:25 +0000
Subject: [PATCH] Takes AlignFrame as arg, to update progressbar

---
 src/jalview/io/DasSequenceFeatureFetcher.java |   26 +++++++++++++++++--------
 1 file changed, 18 insertions(+), 8 deletions(-)

diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
index 5bfb861..d0bc92d 100755
--- 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
 {
   final AlignmentI dataset;
-  final AlignmentPanel ap;
+  final AlignFrame af;
   StringBuffer sbuffer = new StringBuffer();
 
 
@@ -62,10 +62,11 @@ public class DasSequenceFeatureFetcher implements Runnable
    * @param align DOCUMENT ME!
    * @param ap DOCUMENT ME!
    */
-  public DasSequenceFeatureFetcher(AlignmentI align, AlignmentPanel ap)
+  public DasSequenceFeatureFetcher(AlignmentI align,
+                                   AlignFrame af)
   {
     this.dataset = align.getDataset();
-    this.ap = ap;
+    this.af = af;
 
     Thread thread = new Thread(this);
     thread.start();
@@ -154,7 +155,7 @@ public class DasSequenceFeatureFetcher implements Runnable
           if (id != null && id.length() > 0)
           {
             FeatureThread fetcher = new FeatureThread(id
-               +  ":" + seq.getStart() + "," +seq.getEnd()
+            //   +  ":" + seq.getStart() + "," +seq.getEnd()
                  , source);
 
             fetcher.addFeatureListener(new FeatureListener()
@@ -186,14 +187,13 @@ public class DasSequenceFeatureFetcher implements Runnable
                   }
                 }
               }
-
             }
 
             );
 
             //NOTE alignPanel listener will be called after the previous
             //anonymous listener!!!
-            fetcher.addFeatureListener(ap);
+            fetcher.addFeatureListener(af);
 
             fetcher.start();
 	  }
@@ -203,6 +203,9 @@ public class DasSequenceFeatureFetcher implements Runnable
    */
   public void run()
   {
+    long startTime = System.currentTimeMillis();
+    af.setProgressBar("Fetching DAS Sequence Features", startTime);
+
     DasSource [] sources = new jalview.gui.DasSourceBrowser().getDASSource();
 
     String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");
@@ -226,6 +229,7 @@ public class DasSequenceFeatureFetcher implements Runnable
     if(selectedSources == null || selectedSources.size()==0)
     {
       System.out.println("No DAS Sources active");
+      af.setProgressBar("No DAS Sources Active", startTime);
       return;
     }
 
@@ -248,16 +252,20 @@ public class DasSequenceFeatureFetcher implements Runnable
             if (uprefs != null)
             {
               // we know the id for this entry, so don't note its ID in the unknownSequences list
-              for (int j = 0, k = uprefs.size(); j < k; j++)
+              for (int j = 0;  j < uprefs.size(); j++)
               {
+
                 // 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
                 org.biojava.dasobert.dasregistry.DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
-                for (int l=0; l<cs.length; l++) {
+                for (int l=0; l<cs.length; l++)
+                {
                   if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), (DBRefEntry)
                       uprefs.get(j)))
                   {
                     Cache.log.debug("Launched fetcher for coordinate system " +
                                     cs[l].getName());
+
+
                     createFeatureFetcher(sequence,
                                          dasSource.getUrl(),
                                          ( (DBRefEntry) uprefs.get(j)).
@@ -298,6 +306,8 @@ public class DasSequenceFeatureFetcher implements Runnable
     {
       ex.printStackTrace();
     }
+
+    af.setProgressBar("DAS Feature Fetching Complete", startTime);
   }
 
 
-- 
1.7.10.2