From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 13 Jul 2006 17:00:47 +0000 (+0000)
Subject: Selected DAS sources may differ from default
X-Git-Tag: Release_2_1~286
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=062dc2bf3f9a188f2797c4133da4474f79704185;p=jalview.git

Selected DAS sources may differ from default
---

diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
index 7dbb183..dc51617 100755
--- a/src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/src/jalview/io/DasSequenceFeatureFetcher.java
@@ -53,18 +53,24 @@ public class DasSequenceFeatureFetcher implements Runnable
   final AlignmentI dataset;
   final AlignFrame af;
   StringBuffer sbuffer = new StringBuffer();
+  Vector selectedSources;
 
+  long startTime;
+  int threadsRunning = 0;
 
 
   /**
    * Creates a new SequenceFeatureFetcher object.
+   * Uses default
    *
    * @param align DOCUMENT ME!
    * @param ap DOCUMENT ME!
    */
   public DasSequenceFeatureFetcher(AlignmentI align,
-                                   AlignFrame af)
+                                   AlignFrame af,
+                                   Vector selectedSources)
   {
+    this.selectedSources = selectedSources;
     this.dataset = align.getDataset();
     this.af = af;
 
@@ -154,6 +160,8 @@ public class DasSequenceFeatureFetcher implements Runnable
                           sourceUrl);
           if (id != null && id.length() > 0)
           {
+            setThreadsRunning(+1);
+
             FeatureThread fetcher = new FeatureThread(id
                +  ":" + seq.getStart() + "," +seq.getEnd()
                  , source);
@@ -162,6 +170,7 @@ public class DasSequenceFeatureFetcher implements Runnable
             {
               public void comeBackLater(FeatureEvent e)
               {
+                setThreadsRunning(-1);
                 Cache.log.debug("das source " + e.getDasSource().getNickname() +
                                 " asked us to come back in " + e.getComeBackLater() +
                                 " secs.");
@@ -169,6 +178,7 @@ public class DasSequenceFeatureFetcher implements Runnable
 
               public void newFeatures(FeatureEvent e)
               {
+                setThreadsRunning(-1);
                 Das1Source ds = e.getDasSource();
 
                 Map[] features = e.getFeatures();
@@ -204,34 +214,44 @@ public class DasSequenceFeatureFetcher implements Runnable
             fetcher.start();
 	  }
   }
+
+  synchronized void setThreadsRunning(int i)
+  {
+    threadsRunning += i;
+    if(threadsRunning<1)
+      af.setProgressBar("DAS Feature Fetching Complete", startTime);
+  }
+
   /**
    * Spawns a number of dasobert Fetcher threads to add features to sequences in the dataset
    */
   public void run()
   {
-    long startTime = System.currentTimeMillis();
+    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");
-    StringTokenizer st = new StringTokenizer(active, "\t");
-    Vector selectedSources = new Vector();
-    String token;
-    while (st.hasMoreTokens())
+    if(selectedSources==null || selectedSources.size()==0)
     {
-      token = st.nextToken();
-      for(int i=0; i<sources.length; i++)
+      String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");
+      StringTokenizer st = new StringTokenizer(active, "\t");
+      Vector selectedSources = new Vector();
+      String token;
+      while (st.hasMoreTokens())
       {
-        if(sources[i].getNickname().equals(token))
+        token = st.nextToken();
+        for (int i = 0; i < sources.length; i++)
         {
-          selectedSources.addElement(sources[i]);
-          break;
+          if (sources[i].getNickname().equals(token))
+          {
+            selectedSources.addElement(sources[i]);
+            break;
+          }
         }
       }
     }
 
-
     if(selectedSources == null || selectedSources.size()==0)
     {
       System.out.println("No DAS Sources active");
@@ -312,8 +332,6 @@ public class DasSequenceFeatureFetcher implements Runnable
     {
       ex.printStackTrace();
     }
-
-    af.setProgressBar("DAS Feature Fetching Complete", startTime);
   }