JAL-1742 don't offer to align another chain to the same structure

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 61073e3..553ddd2 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -99,7 +99,6 @@ import jalview.ws.seqfetcher.DbSourceProxy;
 
 import java.awt.BorderLayout;
 import java.awt.Component;
-import java.awt.GridLayout;
 import java.awt.Rectangle;
 import java.awt.Toolkit;
 import java.awt.datatransfer.Clipboard;
@@ -133,17 +132,13 @@ import java.util.List;
 import java.util.Set;
 import java.util.Vector;
 
-import javax.swing.JButton;
 import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JEditorPane;
 import javax.swing.JInternalFrame;
-import javax.swing.JLabel;
 import javax.swing.JLayeredPane;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
 import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JProgressBar;
 import javax.swing.JRadioButtonMenuItem;
 import javax.swing.JScrollPane;
 import javax.swing.SwingUtilities;
@@ -315,6 +310,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   void init()
   {
+    progressBar = new ProgressBar(this.statusPanel, this.statusBar);
+
     avc = new jalview.controller.AlignViewController(this, viewport,
             alignPanel);
     if (viewport.getAlignmentConservationAnnotation() == null)
@@ -873,9 +870,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     updateEditMenuBar();
   }
 
-  // methods for implementing IProgressIndicator
-  // need to refactor to a reusable stub class
-  Hashtable progressBars, progressBarHandlers;
+  private IProgressIndicator progressBar;
 
   /*
    * (non-Javadoc)
@@ -885,78 +880,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @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();
+    progressBar.setProgressBar(message, id);
   }
 
   @Override
   public void registerHandler(final long id,
           final IProgressIndicatorHandler handler)
   {
-    if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
-    {
-      throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
-    }
-    progressBarHandlers.put(new Long(id), handler);
-    final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
-    if (handler.canCancel())
-    {
-      JButton cancel = new JButton(
-              MessageManager.getString("action.cancel"));
-      final IProgressIndicator us = this;
-      cancel.addActionListener(new ActionListener()
-      {
-
-        @Override
-        public void actionPerformed(ActionEvent e)
-        {
-          handler.cancelActivity(id);
-          us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new Object[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
-        }
-      });
-      progressPanel.add(cancel, BorderLayout.EAST);
-    }
+    progressBar.registerHandler(id, handler);
   }
 
   /**
@@ -966,18 +897,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public boolean operationInProgress()
   {
-    if (progressBars != null && progressBars.size() > 0)
-    {
-      return true;
-    }
-    return false;
+    return progressBar.operationInProgress();
   }
 
   @Override
   public void setStatus(String text)
   {
     statusBar.setText(text);
-  };
+  }
 
   /*
    * Added so Castor Mapping file can obtain Jalview Version
@@ -1342,8 +1269,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void bioJSMenuItem_actionPerformed(ActionEvent e)
   {
-    new BioJsHTMLOutput(alignPanel,
+    BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel,
             alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+    bjs.exportJalviewAlignmentAsBioJsHtmlFile();
   }
   public void createImageMap(File file, String image)
   {
@@ -5964,6 +5892,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     for (AlignmentAnnotation aa : alignPanel.getAlignment()
             .getAlignmentAnnotation())
     {
+      /*
+       * don't display non-positional annotations on an alignment
+       */
+      if (aa.annotations == null)
+      {
+        continue;
+      }
       boolean apply = (aa.sequenceRef == null && forAlignment)
               || (aa.sequenceRef != null && forSequences);
       if (apply)