X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=191e8fe167c223aafc5e9afd792ffa079d94dcfe;hb=d9b79c023346253c10dc907d1e75f509823266c4;hp=6a0c712793feef0db17d7ff9cf1e0e0f2ac319a7;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 6a0c712..191e8fe 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -20,7 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
@@ -116,6 +115,7 @@ public class SequenceFetcher extends JPanel implements Runnable
   private static Thread initingThread = null;
 
   int debounceTrap = 0;
+
   /**
    * Blocking method that initialises and returns the shared instance of the
    * SequenceFetcher client
@@ -131,9 +131,11 @@ public class SequenceFetcher extends JPanel implements Runnable
     {
       if (guiWindow != null)
       {
-        guiWindow.setProgressBar(
-                MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
-                Thread.currentThread().hashCode());
+        guiWindow
+                .setProgressBar(
+                        MessageManager
+                                .getString("status.waiting_sequence_database_fetchers_init"),
+                        Thread.currentThread().hashCode());
       }
       // initting happening on another thread - so wait around to see if it
       // finishes.
@@ -150,9 +152,11 @@ public class SequenceFetcher extends JPanel implements Runnable
       }
       if (guiWindow != null)
       {
-        guiWindow.setProgressBar(
-        		MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
-                Thread.currentThread().hashCode());
+        guiWindow
+                .setProgressBar(
+                        MessageManager
+                                .getString("status.waiting_sequence_database_fetchers_init"),
+                        Thread.currentThread().hashCode());
       }
     }
     if (sfetch == null
@@ -169,7 +173,8 @@ public class SequenceFetcher extends JPanel implements Runnable
        */
       if (guiWindow != null)
       {
-        guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"),
+        guiWindow.setProgressBar(MessageManager
+                .getString("status.init_sequence_database_fetchers"),
                 Thread.currentThread().hashCode());
       }
       dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
@@ -178,8 +183,7 @@ public class SequenceFetcher extends JPanel implements Runnable
       jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
       if (guiWindow != null)
       {
-        guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"),
-                Thread.currentThread().hashCode());
+        guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
       }
       lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
               .getLocalSourceString()).hashCode();
@@ -191,6 +195,7 @@ public class SequenceFetcher extends JPanel implements Runnable
   }
 
   private IProgressIndicator progressIndicator;
+
   public SequenceFetcher(IProgressIndicator guiIndic)
   {
     this.progressIndicator = guiIndic;
@@ -216,8 +221,10 @@ public class SequenceFetcher extends JPanel implements Runnable
               JOptionPane
                       .showInternalMessageDialog(
                               Desktop.desktop,
-                              MessageManager.getString("warn.couldnt_create_sequence_fetcher_client"),
-                              MessageManager.getString("label.couldnt_create_sequence_fetcher"),
+                              MessageManager
+                                      .getString("warn.couldnt_create_sequence_fetcher_client"),
+                              MessageManager
+                                      .getString("label.couldnt_create_sequence_fetcher"),
                               JOptionPane.ERROR_MESSAGE);
             }
           });
@@ -274,7 +281,9 @@ public class SequenceFetcher extends JPanel implements Runnable
 
   private String getFrameTitle()
   {
-    return ((alignFrame == null) ? MessageManager.getString("label.new_sequence_fetcher") : MessageManager.getString("label.additional_sequence_fetcher"));
+    return ((alignFrame == null) ? MessageManager
+            .getString("label.new_sequence_fetcher") : MessageManager
+            .getString("label.additional_sequence_fetcher"));
   }
 
   private void jbInit() throws Exception
@@ -360,18 +369,19 @@ public class SequenceFetcher extends JPanel implements Runnable
       {
         debounceTrap++;
         String currentSelection = database.getSelectedItem();
-
         if (!currentSelection.equalsIgnoreCase("pdb"))
         {
-            otherSourceAction();
+          otherSourceAction();
         }
-        if (currentSelection.equalsIgnoreCase("pdb") && ((debounceTrap % 2) == 0))
+        if (currentSelection.equalsIgnoreCase("pdb")
+                && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
         {
           pdbSourceAction();
         }
-
+        database.action = -1;
       }
     });
+
     dbeg.setText("");
     jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
     jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
@@ -405,8 +415,7 @@ public class SequenceFetcher extends JPanel implements Runnable
                       : ""));
       String eq = database.getExampleQueries();
       dbeg.setText(MessageManager.formatMessage(
-              "label.example_query_param", new String[]
-              { eq }));
+              "label.example_query_param", new String[] { eq }));
       boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
       for (DbSourceProxy dbs : database.getSelectedSources())
       {
@@ -444,8 +453,6 @@ public class SequenceFetcher extends JPanel implements Runnable
     jPanel3.repaint();
   }
 
-
-
   public void close_actionPerformed(ActionEvent e)
   {
     try
@@ -538,8 +545,13 @@ public class SequenceFetcher extends JPanel implements Runnable
       try
       {
         // update status
-        guiWindow.setProgressBar(MessageManager.formatMessage("status.fetching_sequence_queries_from", new String[]{Integer.valueOf(nqueries).toString(),proxy.getDbName()}), Thread
-                .currentThread().hashCode());
+        guiWindow
+                .setProgressBar(MessageManager.formatMessage(
+                        "status.fetching_sequence_queries_from",
+                        new String[] {
+                            Integer.valueOf(nqueries).toString(),
+                            proxy.getDbName() }), Thread.currentThread()
+                        .hashCode());
         isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
         if (proxy.getAccessionSeparator() == null)
         {
@@ -649,7 +661,7 @@ public class SequenceFetcher extends JPanel implements Runnable
                 {
                   if (rs[r] != null
                           && (found = DBRefUtils.searchRefs(
-                                  rs[r].getDBRef(), dbr)) != null
+                                  rs[r].getDBRefs(), dbr)) != null
                           && found.length > 0)
                   {
                     rfound = true;
@@ -736,11 +748,15 @@ public class SequenceFetcher extends JPanel implements Runnable
           presultTitle.add(titl);
         }
       }
-      guiWindow.setProgressBar(MessageManager.getString("status.finshed_querying"), Thread.currentThread()
+      guiWindow.setProgressBar(MessageManager
+              .getString("status.finshed_querying"), Thread.currentThread()
               .hashCode());
     }
-    guiWindow.setProgressBar((presult.size() > 0) ? MessageManager.getString("status.parsing_results")
-            : MessageManager.getString("status.processing"), Thread.currentThread().hashCode());
+    guiWindow.setProgressBar(
+            (presult.size() > 0) ? MessageManager
+                    .getString("status.parsing_results") : MessageManager
+                    .getString("status.processing"), Thread.currentThread()
+                    .hashCode());
     // process results
     while (presult.size() > 0)
     {
@@ -775,7 +791,7 @@ public class SequenceFetcher extends JPanel implements Runnable
   AlignmentI parseResult(String result, String title)
   {
     String format = new IdentifyFile().Identify(result, "Paste");
-    Alignment sequences = null;
+    AlignmentI sequences = null;
     if (FormatAdapter.isValidFormat(format))
     {
       sequences = null;