JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

[jalview.git] / src / jalview / gui / SequenceFetcher.java

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 56b4b87..9f92c42 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -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();
@@ -190,9 +194,11 @@ public class SequenceFetcher extends JPanel implements Runnable
     return sfetch;
   }
 
+  private IProgressIndicator progressIndicator;
+
   public SequenceFetcher(IProgressIndicator guiIndic)
   {
-    final IProgressIndicator guiWindow = guiIndic;
+    this.progressIndicator = guiIndic;
     final SequenceFetcher us = this;
     // launch initialiser thread
     Thread sf = new Thread(new Runnable()
@@ -201,9 +207,9 @@ public class SequenceFetcher extends JPanel implements Runnable
       @Override
       public void run()
       {
-        if (getSequenceFetcherSingleton(guiWindow) != null)
+        if (getSequenceFetcherSingleton(progressIndicator) != null)
         {
-          us.initGui(guiWindow);
+          us.initGui(progressIndicator);
         }
         else
         {
@@ -215,8 +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);
             }
           });
@@ -273,7 +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
@@ -359,18 +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);
@@ -390,7 +401,7 @@ public class SequenceFetcher extends JPanel implements Runnable
   private void pdbSourceAction()
   {
     databaseButt.setText(database.getSelectedItem());
-    new PDBFetchPanel(this);
+    new PDBSearchPanel(this);
     frame.dispose();
   }
 
@@ -404,8 +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())
       {
@@ -443,8 +453,6 @@ public class SequenceFetcher extends JPanel implements Runnable
     jPanel3.repaint();
   }
 
-
-
   public void close_actionPerformed(ActionEvent e)
   {
     try
@@ -537,8 +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)
         {
@@ -735,11 +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)
     {
@@ -774,7 +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;
@@ -816,6 +833,10 @@ public class SequenceFetcher extends JPanel implements Runnable
 
     if (al != null && al.getHeight() > 0)
     {
+      if (title == null)
+      {
+        title = getDefaultRetrievalTitle();
+      }
       if (alignFrame == null)
       {
         AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
@@ -828,10 +849,6 @@ public class SequenceFetcher extends JPanel implements Runnable
           // Alignments?
         }
 
-        if (title == null)
-        {
-          title = getDefaultRetrievalTitle();
-        }
         SequenceFeature[] sfs = null;
         List<SequenceI> alsqs;
         synchronized (alsqs = al.getSequences())
@@ -865,21 +882,7 @@ public class SequenceFetcher extends JPanel implements Runnable
       }
       else
       {
-        for (int i = 0; i < al.getHeight(); i++)
-        {
-          alignFrame.viewport.getAlignment().addSequence(
-                  al.getSequenceAt(i)); // this
-          // also
-          // creates
-          // dataset
-          // sequence
-          // entries
-        }
-        alignFrame.viewport.setEndSeq(alignFrame.viewport.getAlignment()
-                .getHeight());
-        alignFrame.viewport.getAlignment().getWidth();
-        alignFrame.viewport.firePropertyChange("alignment", null,
-                alignFrame.viewport.getAlignment().getSequences());
+        alignFrame.viewport.addAlignment(al, title);
       }
     }
     return al;
@@ -899,4 +902,14 @@ public class SequenceFetcher extends JPanel implements Runnable
       }
     });
   }
+
+  public IProgressIndicator getProgressIndicator()
+  {
+    return progressIndicator;
+  }
+
+  public void setProgressIndicator(IProgressIndicator progressIndicator)
+  {
+    this.progressIndicator = progressIndicator;
+  }
 }