JAL-1120 patch for desktop

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index adbe906..4c8a251 100755 (executable)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -34,7 +34,7 @@ import jalview.jbgui.*;
  * @author $author$
  * @version $Revision$
  */
-public class PCAPanel extends GPCAPanel implements Runnable
+public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
 {
 
   PCA pca;
@@ -131,9 +131,18 @@ public class PCAPanel extends GPCAPanel implements Runnable
    */
   public void run()
   {
+    long progId=System.currentTimeMillis();
+    IProgressIndicator progress=this;
+    String message="Recalculating PCA";
+    if (getParent()==null) {
+      progress=ap.alignFrame;
+      message = "Calculating PCA";
+    }
+    progress.setProgressBar(message, progId);
     try
     {
       calcSettings.setEnabled(false);
+      
       pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide);
       pca.run();
 
@@ -181,6 +190,9 @@ public class PCAPanel extends GPCAPanel implements Runnable
       new OOMWarning("calculating PCA", er);
       return;
     }
+    finally {
+      progress.setProgressBar("", progId);
+    }
     calcSettings.setEnabled(true);
     repaint();
     if (getParent()==null)
@@ -192,16 +204,24 @@ public class PCAPanel extends GPCAPanel implements Runnable
   @Override
   protected void nuclSetting_actionPerfomed(ActionEvent arg0)
   {
+    if (!nucleotide)
+    {
     nucleotide=true;
     Thread worker = new Thread(this);
     worker.start();
+    }
+    
   }
   @Override
   protected void protSetting_actionPerfomed(ActionEvent arg0)
   {
+    
+    if (nucleotide)
+    {
     nucleotide=false;
     Thread worker = new Thread(this);
     worker.start();
+    }
   }
   /**
    * DOCUMENT ME!
@@ -609,7 +629,108 @@ public class PCAPanel extends GPCAPanel implements Runnable
     }
   }
 
+  // methods for implementing IProgressIndicator
+  // need to refactor to a reusable stub class
+  Hashtable progressBars, progressBarHandlers;
+
+  /*
+   * (non-Javadoc)
+   *
+   * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
+   */
   @Override
+  public void setProgressBar(String message, long id)
+  {
+    if (progressBars == null)
+    {
+      progressBars = new Hashtable();
+      progressBarHandlers = new Hashtable();
+    }
+
+    JPanel progressPanel;
+    Long lId = new Long(id);
+    GridLayout layout = (GridLayout) statusPanel.getLayout();
+    if (progressBars.get(lId) != null)
+    {
+      progressPanel = (JPanel) progressBars.get(new Long(id));
+      statusPanel.remove(progressPanel);
+      progressBars.remove(lId);
+      progressPanel = null;
+      if (message != null)
+      {
+        statusBar.setText(message);
+      }
+      if (progressBarHandlers.contains(lId))
+      {
+        progressBarHandlers.remove(lId);
+      }
+      layout.setRows(layout.getRows() - 1);
+    }
+    else
+    {
+      progressPanel = new JPanel(new BorderLayout(10, 5));
+
+      JProgressBar progressBar = new JProgressBar();
+      progressBar.setIndeterminate(true);
+
+      progressPanel.add(new JLabel(message), BorderLayout.WEST);
+      progressPanel.add(progressBar, BorderLayout.CENTER);
+
+      layout.setRows(layout.getRows() + 1);
+      statusPanel.add(progressPanel);
+
+      progressBars.put(lId, progressPanel);
+    }
+    // update GUI
+    // setMenusForViewport();
+    validate();
+  }
+
+  @Override
+  public void registerHandler(final long id,
+          final IProgressIndicatorHandler handler)
+  {
+    if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
+    {
+      throw new Error(
+              "call setProgressBar before registering the progress bar's handler.");
+    }
+    progressBarHandlers.put(new Long(id), handler);
+    final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
+    if (handler.canCancel())
+    {
+      JButton cancel = new JButton("Cancel");
+      final IProgressIndicator us = this;
+      cancel.addActionListener(new ActionListener()
+      {
+
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          handler.cancelActivity(id);
+          us.setProgressBar(
+                  "Cancelled "
+                          + ((JLabel) progressPanel.getComponent(0))
+                                  .getText(), id);
+        }
+      });
+      progressPanel.add(cancel, BorderLayout.EAST);
+    }
+  }
+
+  /**
+   *
+   * @return true if any progress bars are still active
+   */
+  @Override
+  public boolean operationInProgress()
+  {
+    if (progressBars != null && progressBars.size() > 0)
+    {
+      return true;
+    }
+    return false;
+  }
   @Override
   protected void resetButton_actionPerformed(ActionEvent e)
   {

diff --git a/src/jalview/jbgui/GPCAPanel.java b/src/jalview/jbgui/GPCAPanel.java
index e677f4d..c0905a8 100755 (executable)
--- a/src/jalview/jbgui/GPCAPanel.java
+++ b/src/jalview/jbgui/GPCAPanel.java
@@ -76,6 +76,10 @@ public class GPCAPanel extends JInternalFrame
   protected JMenu calcSettings=new JMenu();
   protected JCheckBoxMenuItem nuclSetting=new JCheckBoxMenuItem();
   protected JCheckBoxMenuItem protSetting=new JCheckBoxMenuItem();
+  
+  protected JLabel statusBar = new JLabel();
+  protected GridLayout statusPanelLayout = new GridLayout();
+  protected JPanel statusPanel=new JPanel();
   public GPCAPanel()
   {
     try
@@ -255,9 +259,15 @@ public class GPCAPanel extends JInternalFrame
       }
     });calcSettings.add(nuclSetting);
     calcSettings.add(protSetting);
-    
-    
-    this.getContentPane().add(jPanel2, BorderLayout.SOUTH);
+    statusPanel.setLayout(statusPanelLayout);
+    statusBar.setFont(new java.awt.Font("Verdana",0,12));
+    //statusPanel.setBackground(Color.lightGray);
+    //statusBar.setBackground(Color.lightGray);
+    //statusPanel.add(statusBar, null);
+    JPanel panelBar = new JPanel(new BorderLayout());
+    panelBar.add(jPanel2, BorderLayout.NORTH);
+    panelBar.add(statusPanel, BorderLayout.SOUTH);
+    this.getContentPane().add(panelBar, BorderLayout.SOUTH);
     jPanel2.add(jLabel1, null);
     jPanel2.add(xCombobox, null);
     jPanel2.add(jLabel2, null);