JAL-2154 always check dataset sequence for sequence instance exists in dataset before...

[jalview.git] / src / jalview / ws / DBRefFetcher.java

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 2e0197c..3ba0e34 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -55,9 +55,16 @@ import uk.ac.ebi.picr.model.UPEntry;
  */
 public class DBRefFetcher implements Runnable
 {
+  public interface FetchFinishedListenerI
+  {
+    void finished();
+  }
+
+  private List<FetchFinishedListenerI> listeners;
+
   SequenceI[] dataset;
 
-  IProgressIndicator af;
+  IProgressIndicator progressWindow;
 
   CutAndPasteTransfer output = new CutAndPasteTransfer();
 
@@ -86,10 +93,6 @@ public class DBRefFetcher implements Runnable
    */
   private boolean trimDsSeqs = true;
 
-  public DBRefFetcher()
-  {
-  }
-
   /**
    * Creates a new DBRefFetcher object and fetches from the currently selected
    * set of databases, if this is null then it fetches based on feature settings
@@ -109,7 +112,8 @@ public class DBRefFetcher implements Runnable
           IProgressIndicator progressIndicatorFrame,
           DbSourceProxy[] sources, FeatureSettings featureSettings, boolean isNucleotide)
   {
-    this.af = progressIndicatorFrame;
+    listeners = new ArrayList<FetchFinishedListenerI>();
+    this.progressWindow = progressIndicatorFrame;
     alseqs = new SequenceI[seqs.length];
     SequenceI[] ds = new SequenceI[seqs.length];
     for (int i = 0; i < seqs.length; i++)
@@ -137,7 +141,7 @@ public class DBRefFetcher implements Runnable
       String[] defdb = null, otherdb = sfetcher
               .getDbInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);
       List<DbSourceProxy> selsources = new ArrayList<DbSourceProxy>();
-      Vector dasselsrc = (featureSettings != null) ? featureSettings
+      Vector<jalviewSourceI> dasselsrc = (featureSettings != null) ? featureSettings
               .getSelectedSources() : new jalview.gui.DasSourceBrowser()
               .getSelectedSources();
       Enumeration<jalviewSourceI> en = dasselsrc.elements();
@@ -186,6 +190,26 @@ public class DBRefFetcher implements Runnable
   }
 
   /**
+   * Constructor with only sequences provided
+   * 
+   * @param sequences
+   */
+  public DBRefFetcher(SequenceI[] sequences)
+  {
+    this(sequences, null, null, null, false);
+  }
+
+  /**
+   * Add a listener to be notified when sequence fetching is complete
+   * 
+   * @param l
+   */
+  public void addListener(FetchFinishedListenerI l)
+  {
+    listeners.add(l);
+  }
+
+  /**
    * retrieve all the das sequence sources and add them to the list of db
    * sources to retrieve from
    */
@@ -286,8 +310,12 @@ public class DBRefFetcher implements Runnable
     }
     running = true;
     long startTime = System.currentTimeMillis();
-    af.setProgressBar(MessageManager.getString("status.fetching_db_refs"),
+    if (progressWindow != null)
+    {
+      progressWindow.setProgressBar(
+              MessageManager.getString("status.fetching_db_refs"),
             startTime);
+    }
     try
     {
       if (Cache.getDefault("DBREFFETCH_USEPICR", false))
@@ -328,16 +356,8 @@ public class DBRefFetcher implements Runnable
         // TODO: introduce multithread multisource queries and logic to remove a
         // query from other sources if any source for a database returns a
         // record
-        if (dbsource.getDbSourceProperties().containsKey(
-                DBRefSource.MULTIACC))
-        {
-          maxqlen = ((Integer) dbsource.getDbSourceProperties().get(
-                  DBRefSource.MULTIACC)).intValue();
-        }
-        else
-        {
-          maxqlen = 1;
-        }
+        maxqlen = dbsource.getMaximumQueryCount();
+
         while (queries.size() > 0 || seqIndex < currSeqs.length)
         {
           if (queries.size() > 0)
@@ -472,14 +492,18 @@ public class DBRefFetcher implements Runnable
       // of the viewed sequence
 
     }
+    if (progressWindow != null)
+    {
+      progressWindow.setProgressBar(
+              MessageManager.getString("label.dbref_search_completed"),
+              startTime);
+    }
 
-    af.setProgressBar(
-            MessageManager.getString("label.dbref_search_completed"),
-            startTime);
-    // promptBeforeBlast();
-
+    for (FetchFinishedListenerI listener : listeners)
+    {
+      listener.finished();
+    }
     running = false;
-
   }
 
   /**