new SequenceFetcher gui and visual delay indication for initialisation and fetching

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 15cbf01..e64b8e4 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -45,7 +45,7 @@ import jalview.ws.*;
  * @version $Revision$
  */
 public class AlignFrame
-    extends GAlignFrame implements DropTargetListener
+    extends GAlignFrame implements DropTargetListener, IProgressIndicator
 {
   /** DOCUMENT ME!! */
   public static final int DEFAULT_WIDTH = 700;
@@ -555,6 +555,9 @@ public class AlignFrame
 
 
   Hashtable progressBars;
+  /* (non-Javadoc)
+   * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
+   */
   public void setProgressBar(String message, long id)
   {
     if(progressBars == null)
@@ -3468,7 +3471,7 @@ public class AlignFrame
       Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
       // TODO: move GUI generation code onto service implementation - so a client instance attaches itself to the GUI with method call like jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance, alignframe)
       Vector wsmenu = new Vector();
-      final AlignFrame af = this;
+      final IProgressIndicator af = this;
       if (msaws != null)
       {
         // Add any Multiple Sequence Alignment Services

diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java
index 09c8a3e..e695d3d 100755 (executable)
--- a/src/jalview/gui/DasSourceBrowser.java
+++ b/src/jalview/gui/DasSourceBrowser.java
@@ -269,11 +269,10 @@ public class DasSourceBrowser
     refresh.setVisible(false);\r
     progressBar.setVisible(true);\r
     progressBar.setIndeterminate(true);\r
-\r
-    dasSources = jalview.ws.DasSequenceFeatureFetcher.getDASSources();\r
-\r
-    appendLocalSources();\r
-\r
+    // Refresh the source list.\r
+    dasSources=null;\r
+    getDASSource();\r
+    \r
     init();\r
 \r
     loadingDasSources = false;\r
@@ -298,7 +297,10 @@ public class DasSourceBrowser
 \r
     return selected;\r
   }\r
-\r
+  /**\r
+   * retrieve das sources from registry and add local source list\r
+   * @return\r
+   */\r
   public DasSource[] getDASSource()\r
   {\r
     if (dasSources == null)\r

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index ed968f8..262a9be 100755 (executable)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -19,6 +19,7 @@
 package jalview.gui;
 
 import jalview.io.*;
+
 import java.awt.*;
 import java.awt.datatransfer.*;
 import java.awt.dnd.*;
@@ -38,7 +39,7 @@ import javax.swing.event.MenuListener;
  */
 public class Desktop
     extends jalview.jbgui.GDesktop implements DropTargetListener,
-    ClipboardOwner
+    ClipboardOwner, IProgressIndicator
 {
   /** DOCUMENT ME!! */
   public static Desktop instance;
@@ -829,7 +830,7 @@ public class Desktop
 
   public void inputSequence_actionPerformed(ActionEvent e)
   {
-    new SequenceFetcher(null);
+    new SequenceFetcher(this);
   }
 
   JPanel progressPanel;
@@ -1390,4 +1391,27 @@ public class Desktop
               JOptionPane.ERROR_MESSAGE);
     }
   }
+
+  /**
+   *  Progress bars managed by the IProgressIndicator method.
+   */
+  private Hashtable progressBars;
+  /* (non-Javadoc)
+   * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
+   */
+  public void setProgressBar(String message, long id)
+  {
+    if(progressBars == null)
+    {
+      progressBars = new Hashtable();
+    }
+
+    if(progressBars.get( new Long(id) )!=null)
+    {
+      JProgressBar progressPanel = (JProgressBar)progressBars.remove( new Long(id) );
+       removeProgressPanel(progressPanel);
+    } else {
+      progressBars.put(new Long(id), addProgressPanel(message));
+    }
+  }
 }

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 1675304..53f75a4 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -23,6 +23,7 @@ import java.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
+
 import javax.swing.*;
 
 import MCview.*;
@@ -33,6 +34,7 @@ import jalview.io.*;
 import jalview.ws.DBRefFetcher;
 import jalview.ws.ebi.EBIFetchClient;
 import jalview.ws.seqfetcher.ASequenceFetcher;
+import jalview.ws.seqfetcher.DbSourceProxy;
 
 import java.awt.Rectangle;
 import java.awt.BorderLayout;
@@ -41,16 +43,56 @@ import java.awt.Dimension;
 public class SequenceFetcher
 extends JPanel implements Runnable
 {
-  ASequenceFetcher sfetch; 
+  // ASequenceFetcher sfetch; 
   JInternalFrame frame;
+  IProgressIndicator guiWindow;
   AlignFrame alignFrame;
   StringBuffer result;
   final String noDbSelected = "-- Select Database --";
   Hashtable sources = new Hashtable();
-  public SequenceFetcher(AlignFrame af)
+  private static ASequenceFetcher sfetch=null;
+  public SequenceFetcher(IProgressIndicator guiIndic)
   {
-    alignFrame = af;
-    sfetch = new jalview.ws.SequenceFetcher();
+      final IProgressIndicator guiWindow = guiIndic;
+      final SequenceFetcher us = this;
+      // launch initialiser thread
+      Thread sf = new Thread(new Runnable() {
+
+        public void run()
+        {
+          if (sfetch==null)
+          {
+            /**
+           * give a visual indication that sequence fetcher construction is occuring
+           */
+          if ( guiWindow!=null )
+            {
+              guiWindow.setProgressBar("Initialising Sequence Database Fetchers", this.hashCode());
+            }
+            ASequenceFetcher sf = new jalview.ws.SequenceFetcher();
+            if ( guiWindow!=null )
+            {
+              guiWindow.setProgressBar("Initialising Sequence Database Fetchers", this.hashCode());
+            }
+            sfetch = sf;
+            
+          }
+          us.initGui(guiWindow);
+        }
+      });
+      sf.start();
+  }
+  /**
+   * called by thread spawned by constructor
+   * @param guiWindow
+   */
+  private void initGui(IProgressIndicator guiWindow) {
+    this.guiWindow = guiWindow;
+    if (guiWindow instanceof AlignFrame)
+    {
+      alignFrame = (AlignFrame) guiWindow;
+    }
+      
     database.addItem(noDbSelected);
     /*
      * Dynamically generated database list
@@ -108,6 +150,7 @@ extends JPanel implements Runnable
     this.setLayout(borderLayout2);
 
     database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
     jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
     jLabel1.setText(
@@ -120,6 +163,23 @@ extends JPanel implements Runnable
         ok_actionPerformed();
       }
     });
+    clear.setText("Clear");
+    clear.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        clear_actionPerformed();
+      }
+    });
+
+    example.setText("Example");
+    example.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        example_actionPerformed();
+      }
+    });
     close.setText("Close");
     close.addActionListener(new ActionListener()
     {
@@ -141,28 +201,74 @@ extends JPanel implements Runnable
     jPanel3.setLayout(borderLayout1);
     borderLayout1.setVgap(5);
     jPanel1.add(ok);
+    jPanel1.add(example);
+    jPanel1.add(clear);
     jPanel1.add(close);
-    jPanel3.add(jPanel2, java.awt.BorderLayout.WEST);
-    jPanel2.add(database);
+    jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
+    jPanel2.setLayout(borderLayout3);
+    
+    database.addActionListener(new ActionListener() {
+
+      public void actionPerformed(ActionEvent e)
+      {
+        DbSourceProxy db=null;
+        try {
+          db = sfetch.getSourceProxy((String)sources.get(database.getSelectedItem()));
+          dbeg.setText("Example query: "+db.getTestQuery());
+        } catch (Exception ex)
+        {
+          dbeg.setText("");
+        }
+        jPanel2.repaint();
+      }
+    });
+    dbeg.setText("");
+    jPanel2.add(database, java.awt.BorderLayout.NORTH);
+    jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
+    jPanel2.add(jLabel1, java.awt.BorderLayout.SOUTH);
+    // jPanel2.setPreferredSize(new Dimension())
     jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
-    jPanel3.add(jLabel1, java.awt.BorderLayout.NORTH);
     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
     this.add(jPanel3, java.awt.BorderLayout.CENTER);
+    this.add(jPanel2,java.awt.BorderLayout.NORTH);
     jScrollPane1.getViewport().add(textArea);
+    
 
   }
+  protected void example_actionPerformed()
+  {
+    DbSourceProxy db=null;
+    try {
+      db = sfetch.getSourceProxy((String)sources.get(database.getSelectedItem()));
+      textArea.setText(db.getTestQuery());
+    } catch (Exception ex)
+    {
+    }
+    jPanel3.repaint();
+  }
 
+  protected void clear_actionPerformed()
+  {
+    textArea.setText("");
+    jPanel3.repaint();
+  }
+  JLabel dbeg = new JLabel();
   JComboBox database = new JComboBox();
   JLabel jLabel1 = new JLabel();
   JButton ok = new JButton();
+  JButton clear = new JButton();
+  JButton example = new JButton();
   JButton close = new JButton();
   JPanel jPanel1 = new JPanel();
   JTextArea textArea = new JTextArea();
   JScrollPane jScrollPane1 = new JScrollPane();
   JPanel jPanel2 = new JPanel();
   JPanel jPanel3 = new JPanel();
+  JPanel jPanel4 = new JPanel();
+  
   BorderLayout borderLayout1 = new BorderLayout();
   BorderLayout borderLayout2 = new BorderLayout();
+  BorderLayout borderLayout3 = new BorderLayout();
   public void close_actionPerformed(ActionEvent e)
   {
     try
@@ -213,8 +319,10 @@ extends JPanel implements Runnable
     }
     AlignmentI aresult=null;
     try {
+      guiWindow.setProgressBar("Fetching Sequences from "+database.getSelectedItem(), Thread.currentThread().hashCode());
       aresult = sfetch.getSourceProxy((String)sources.get(database.getSelectedItem()))
       .getSequenceRecords(textArea.getText());
+      
     }
     catch (Exception e)
     {
@@ -224,6 +332,19 @@ extends JPanel implements Runnable
       System.err.println("Retrieval failed for source ='"+database.getSelectedItem()+"' and query\n'"+textArea.getText()+"'\n");
       e.printStackTrace();
     }
+    catch (OutOfMemoryError e)
+    {
+      showErrorMessage("Out of Memory when retrieving " + textArea.getText()
+              + " from " + database.getSelectedItem()+"\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
+      e.printStackTrace();
+    }
+    catch (Error e)
+    {
+      showErrorMessage("Serious Error retrieving " + textArea.getText()
+              + " from " + database.getSelectedItem());
+      e.printStackTrace();
+    }
+    guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
     if (aresult!=null)
     {
       parseResult(aresult, null, null);