X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=eb98d989e7151bac77c67431ceefc7f91b67d496;hb=c24ec44edbedba55005373c43bf712c047b56faa;hp=abc74372299b8bae567e50cccc93ec6bf0fe1d79;hpb=071a00a0f8ce9892254630595696c1c9d7c39ec7;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index abc7437..eb98d98 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -49,6 +49,7 @@ import java.beans.PropertyChangeEvent;
 import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
+import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
 import java.net.URL;
 import java.util.ArrayList;
@@ -111,6 +112,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SeqCigar;
@@ -139,6 +141,7 @@ import jalview.io.JnetAnnotationMaker;
 import jalview.io.NewickFile;
 import jalview.io.ScoreMatrixFile;
 import jalview.io.TCoffeeScoreFile;
+import jalview.io.exceptions.ImageOutputException;
 import jalview.io.vcf.VCFLoader;
 import jalview.jbgui.GAlignFrame;
 import jalview.project.Jalview2XML;
@@ -150,6 +153,7 @@ import jalview.util.HttpUtils;
 import jalview.util.ImageMaker.TYPE;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.util.imagemaker.BitmapImageSizing;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
 import jalview.ws.DBRefFetcher;
@@ -349,7 +353,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   void init()
   {
-    setFrameIcon(WindowIcons.alignmentIcon);
+    setFrameIcon(null);
 
     // setBackground(Color.white); // BH 2019
 
@@ -620,12 +624,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         // if (viewport.cursorMode)
         // {
         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
-        // //System.out.println("A");
+        // //jalview.bin.Console.outPrintln("A");
         // }
         // break;
         /*
          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
-         * System.out.println("closing bracket"); } break;
+         * jalview.bin.Console.outPrintln("closing bracket"); } break;
          */
         case KeyEvent.VK_DELETE:
         case KeyEvent.VK_BACK_SPACE:
@@ -826,7 +830,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               @Override
               public void propertyChange(PropertyChangeEvent evt)
               {
-                // // System.out.println("Discoverer property change.");
+                // // jalview.bin.Console.outPrintln("Discoverer property
+                // change.");
                 // if (evt.getPropertyName().equals("services"))
                 {
                   SwingUtilities.invokeLater(new Runnable()
@@ -835,7 +840,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     @Override
                     public void run()
                     {
-                      System.err.println(
+                      jalview.bin.Console.errPrintln(
                               "Rebuild WS Menu for service change");
                       BuildWebServiceMenu();
                     }
@@ -850,7 +855,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       public void internalFrameClosed(
               javax.swing.event.InternalFrameEvent evt)
       {
-        // System.out.println("deregistering discoverer listener");
+        // jalview.bin.Console.outPrintln("deregistering discoverer listener");
         Desktop.instance.removeJalviewPropertyChangeListener("services",
                 thisListener);
         closeMenuItem_actionPerformed(true);
@@ -979,14 +984,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void setProgressBar(String message, long id)
   {
-    progressBar.setProgressBar(message, id);
+    if (!Platform.isHeadless() && progressBar != null)
+      progressBar.setProgressBar(message, id);
   }
 
   @Override
   public void registerHandler(final long id,
           final IProgressIndicatorHandler handler)
   {
-    progressBar.registerHandler(id, handler);
+    if (progressBar != null)
+      progressBar.registerHandler(id, handler);
   }
 
   /**
@@ -996,7 +1003,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public boolean operationInProgress()
   {
-    return progressBar.operationInProgress();
+    return progressBar == null ? false : progressBar.operationInProgress();
   }
 
   /**
@@ -1245,8 +1252,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   public void saveAlignment(String file, FileFormatI format)
   {
+    saveAlignment(file, format, false);
+  }
+
+  public void saveAlignment(String file, FileFormatI format, boolean stdout)
+  {
     lastSaveSuccessful = true;
-    lastFilenameSaved = file;
+    if (!stdout)
+    {
+      lastFilenameSaved = file;
+    }
     lastFormatSaved = format;
 
     if (FileFormat.Jalview.equals(format))
@@ -1257,9 +1272,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         shortName = shortName
                 .substring(shortName.lastIndexOf(File.separatorChar) + 1);
       }
+      // TODO deal with stdout=true
       lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
               shortName);
 
+      Console.debug("lastSaveSuccessful=" + lastSaveSuccessful);
+      if (lastSaveSuccessful)
+      {
+        this.getViewport().setSavedUpToDate(true);
+      }
+
       statusBar.setText(MessageManager.formatMessage(
               "label.successfully_saved_to_file_in_format", new Object[]
               { file, format }));
@@ -1268,95 +1290,102 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
-    Runnable cancelAction = new Runnable()
-    {
-      @Override
-      public void run()
+    Runnable cancelAction = () -> {
+      lastSaveSuccessful = false;
+    };
+    Runnable outputAction = () -> {
+      // todo defer this to inside formatSequences (or later)
+      AlignmentExportData exportData = viewport.getAlignExportData(options);
+      String output = new FormatAdapter(alignPanel, options)
+              .formatSequences(format, exportData.getAlignment(),
+                      exportData.getOmitHidden(),
+                      exportData.getStartEndPostions(),
+                      viewport.getAlignment().getHiddenColumns());
+      if (output == null)
       {
         lastSaveSuccessful = false;
       }
-    };
-    Runnable outputAction = new Runnable()
-    {
-      @Override
-      public void run()
+      else
       {
-        // todo defer this to inside formatSequences (or later)
-        AlignmentExportData exportData = viewport
-                .getAlignExportData(options);
-        String output = new FormatAdapter(alignPanel, options)
-                .formatSequences(format, exportData.getAlignment(),
-                        exportData.getOmitHidden(),
-                        exportData.getStartEndPostions(),
-                        viewport.getAlignment().getHiddenColumns());
-        if (output == null)
+        // create backupfiles object and get new temp filename destination
+        boolean doBackup = BackupFiles.getEnabled() && !stdout;
+        BackupFiles backupfiles = null;
+        if (doBackup)
         {
-          lastSaveSuccessful = false;
+          Console.trace("ALIGNFRAME making backupfiles object for " + file);
+          backupfiles = new BackupFiles(file);
         }
-        else
+        try
         {
-          // create backupfiles object and get new temp filename destination
-          boolean doBackup = BackupFiles.getEnabled();
-          BackupFiles backupfiles = null;
-          if (doBackup)
+          String tempFilePath = doBackup ? backupfiles.getTempFilePath()
+                  : file;
+          Console.trace("ALIGNFRAME setting PrintWriter");
+          PrintWriter out = stdout
+                  ? new PrintWriter(new OutputStreamWriter(System.out))
+                  : new PrintWriter(new FileWriter(tempFilePath));
+
+          if (backupfiles != null)
           {
-            Console.trace(
-                    "ALIGNFRAME making backupfiles object for " + file);
-            backupfiles = new BackupFiles(file);
+            Console.trace("ALIGNFRAME about to write to temp file "
+                    + backupfiles.getTempFilePath());
           }
-          try
-          {
-            String tempFilePath = doBackup ? backupfiles.getTempFilePath()
-                    : file;
-            Console.trace("ALIGNFRAME setting PrintWriter");
-            PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
-
-            if (backupfiles != null)
-            {
-              Console.trace("ALIGNFRAME about to write to temp file "
-                      + backupfiles.getTempFilePath());
-            }
 
-            out.print(output);
+          out.print(output);
+          out.flush();
+          if (!stdout)
+          {
             Console.trace("ALIGNFRAME about to close file");
             out.close();
             Console.trace("ALIGNFRAME closed file");
-            AlignFrame.this.setTitle(file);
+          }
+          AlignFrame.this.setTitle(stdout ? "STDOUT" : file);
+          if (stdout)
+          {
+            statusBar.setText(MessageManager.formatMessage(
+                    "label.successfully_printed_to_stdout_in_format",
+                    new Object[]
+                    { format.getName() }));
+          }
+          else
+          {
             statusBar.setText(MessageManager.formatMessage(
                     "label.successfully_saved_to_file_in_format",
                     new Object[]
                     { fileName, format.getName() }));
-            lastSaveSuccessful = true;
-          } catch (IOException e)
-          {
-            lastSaveSuccessful = false;
-            Console.error(
-                    "ALIGNFRAME Something happened writing the temp file");
-            Console.error(e.getMessage());
-            Console.debug(Cache.getStackTraceString(e));
-          } catch (Exception ex)
-          {
-            lastSaveSuccessful = false;
-            Console.error(
-                    "ALIGNFRAME Something unexpected happened writing the temp file");
-            Console.error(ex.getMessage());
-            Console.debug(Cache.getStackTraceString(ex));
           }
+          lastSaveSuccessful = true;
+        } catch (IOException e)
+        {
+          lastSaveSuccessful = false;
+          Console.error(
+                  "ALIGNFRAME Something happened writing the temp file");
+          Console.error(e.getMessage());
+          Console.debug(Cache.getStackTraceString(e));
+        } catch (Exception ex)
+        {
+          lastSaveSuccessful = false;
+          Console.error(
+                  "ALIGNFRAME Something unexpected happened writing the temp file");
+          Console.error(ex.getMessage());
+          Console.debug(Cache.getStackTraceString(ex));
+        }
 
-          if (doBackup)
-          {
-            backupfiles.setWriteSuccess(lastSaveSuccessful);
-            Console.debug("ALIGNFRAME writing temp file was "
-                    + (lastSaveSuccessful ? "" : "NOT ") + "successful");
-            // do the backup file roll and rename the temp file to actual file
-            Console.trace(
-                    "ALIGNFRAME about to rollBackupsAndRenameTempFile");
-            lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
-            Console.debug(
-                    "ALIGNFRAME performed rollBackupsAndRenameTempFile "
-                            + (lastSaveSuccessful ? "" : "un")
-                            + "successfully");
-          }
+        if (doBackup)
+        {
+          backupfiles.setWriteSuccess(lastSaveSuccessful);
+          Console.debug("ALIGNFRAME writing temp file was "
+                  + (lastSaveSuccessful ? "" : "NOT ") + "successful");
+          // do the backup file roll and rename the temp file to actual file
+          Console.trace("ALIGNFRAME about to rollBackupsAndRenameTempFile");
+          lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
+          Console.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile "
+                  + (lastSaveSuccessful ? "" : "un") + "successfully");
+        }
+
+        Console.debug("lastSaveSuccessful=" + lastSaveSuccessful);
+        if (lastSaveSuccessful)
+        {
+          AlignFrame.this.getViewport().setSavedUpToDate(true);
         }
       }
     };
@@ -1374,7 +1403,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     else
     {
-      outputAction.run();
+      try
+      {
+        outputAction.run();
+      } catch (Exception e)
+      {
+        // TODO Auto-generated catch block
+        e.printStackTrace();
+      }
     }
   }
 
@@ -1391,33 +1427,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     FileFormatI fileFormat = FileFormats.getInstance()
             .forName(fileFormatName);
     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
-    Runnable outputAction = new Runnable()
-    {
-      @Override
-      public void run()
+    Runnable outputAction = () -> {
+      // todo defer this to inside formatSequences (or later)
+      AlignmentExportData exportData = viewport.getAlignExportData(options);
+      CutAndPasteTransfer cap = new CutAndPasteTransfer();
+      cap.setForInput(null);
+      try
       {
-        // todo defer this to inside formatSequences (or later)
-        AlignmentExportData exportData = viewport
-                .getAlignExportData(options);
-        CutAndPasteTransfer cap = new CutAndPasteTransfer();
-        cap.setForInput(null);
-        try
-        {
-          FileFormatI format = fileFormat;
-          cap.setText(new FormatAdapter(alignPanel, options)
-                  .formatSequences(format, exportData.getAlignment(),
-                          exportData.getOmitHidden(),
-                          exportData.getStartEndPostions(),
-                          viewport.getAlignment().getHiddenColumns()));
-          Desktop.addInternalFrame(cap, MessageManager.formatMessage(
-                  "label.alignment_output_command", new Object[]
-                  { fileFormat.getName() }), 600, 500);
-        } catch (OutOfMemoryError oom)
-        {
-          new OOMWarning("Outputting alignment as " + fileFormat.getName(),
-                  oom);
-          cap.dispose();
-        }
+        FileFormatI format = fileFormat;
+        cap.setText(new FormatAdapter(alignPanel, options).formatSequences(
+                format, exportData.getAlignment(),
+                exportData.getOmitHidden(),
+                exportData.getStartEndPostions(),
+                viewport.getAlignment().getHiddenColumns()));
+        Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+                "label.alignment_output_command", new Object[]
+                { fileFormat.getName() }), 600, 500);
+      } catch (OutOfMemoryError oom)
+      {
+        new OOMWarning("Outputting alignment as " + fileFormat.getName(),
+                oom);
+        cap.dispose();
       }
     };
 
@@ -1433,7 +1463,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     else
     {
-      outputAction.run();
+      try
+      {
+        outputAction.run();
+      } catch (Exception e)
+      {
+        e.printStackTrace();
+      }
     }
   }
 
@@ -1447,19 +1483,75 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
-    htmlSVG.exportHTML(null);
+    try
+    {
+      htmlSVG.exportHTML(null);
+    } catch (ImageOutputException x)
+    {
+      // report problem to console and raise dialog
+    }
   }
 
   @Override
   public void bioJSMenuItem_actionPerformed(ActionEvent e)
   {
     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
-    bjs.exportHTML(null);
+    try
+    {
+      bjs.exportHTML(null);
+    } catch (ImageOutputException x)
+    {
+      // report problem to console and raise dialog
+    }
   }
 
   public void createImageMap(File file, String image)
   {
-    alignPanel.makePNGImageMap(file, image);
+    try
+    {
+      alignPanel.makePNGImageMap(file, image);
+    } catch (ImageOutputException x)
+    {
+      // report problem to console and raise dialog
+    }
+  }
+
+  @Override
+  public void createPNG_actionPerformed(ActionEvent e)
+  {
+    try
+    {
+      createPNG(null);
+    } catch (ImageOutputException ioex)
+    {
+      // raise dialog, and report via console
+    }
+  }
+
+  @Override
+  public void createEPS_actionPerformed(ActionEvent e)
+  {
+    try
+    {
+      createEPS(null);
+    } catch (ImageOutputException ioex)
+    {
+      // raise dialog, and report via console
+    }
+
+  }
+
+  @Override
+  public void createSVG_actionPerformed(ActionEvent e)
+  {
+    try
+    {
+      createSVG(null);
+    } catch (ImageOutputException ioex)
+    {
+      // raise dialog, and report via console
+    }
+
   }
 
   /**
@@ -1468,10 +1560,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param f
    */
-  @Override
-  public void createPNG(File f)
+  public void createPNG(File f) throws ImageOutputException
+  {
+    createPNG(f, null, BitmapImageSizing.nullBitmapImageSizing());
+  }
+
+  public void createPNG(File f, String renderer, BitmapImageSizing userBis)
+          throws ImageOutputException
   {
-    alignPanel.makeAlignmentImage(TYPE.PNG, f);
+    alignPanel.makeAlignmentImage(TYPE.PNG, f, renderer, userBis);
   }
 
   /**
@@ -1480,10 +1577,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param f
    */
-  @Override
-  public void createEPS(File f)
+  public void createEPS(File f) throws ImageOutputException
+  {
+    createEPS(f, null);
+  }
+
+  public void createEPS(File f, String renderer) throws ImageOutputException
   {
-    alignPanel.makeAlignmentImage(TYPE.EPS, f);
+    alignPanel.makeAlignmentImage(TYPE.EPS, f, renderer);
   }
 
   /**
@@ -1492,10 +1593,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param f
    */
-  @Override
-  public void createSVG(File f)
+  public void createSVG(File f) throws ImageOutputException
   {
-    alignPanel.makeAlignmentImage(TYPE.SVG, f);
+    createSVG(f, null);
+  }
+
+  public void createSVG(File f, String renderer) throws ImageOutputException
+  {
+    alignPanel.makeAlignmentImage(TYPE.SVG, f, renderer);
   }
 
   @Override
@@ -1541,15 +1646,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             .getString("label.load_jalview_annotations");
     chooser.setDialogTitle(tooltip);
     chooser.setToolTipText(tooltip);
-    chooser.setResponseHandler(0, new Runnable()
-    {
-      @Override
-      public void run()
-      {
-        String choice = chooser.getSelectedFile().getPath();
-        Cache.setProperty("LAST_DIRECTORY", choice);
-        loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
-      }
+    chooser.setResponseHandler(0, () -> {
+      String choice = chooser.getSelectedFile().getPath();
+      Cache.setProperty("LAST_DIRECTORY", choice);
+      loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
     });
 
     chooser.showOpenDialog(this);
@@ -2281,10 +2381,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         .intValue();
               }
             }
-            alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
-            // was
-            // duplicated
-            // earlier
+            // annotation was duplicated earlier
+            alignment.addAnnotation(sequences[i].getAnnotation()[a]);
+            // take care of contact matrix too
+            ContactMatrixI cm = sequences[i]
+                    .getContactMatrixFor(sequences[i].getAnnotation()[a]);
+            if (cm != null)
+            {
+              alignment.addContactListFor(sequences[i].getAnnotation()[a],
+                      cm);
+            }
+
             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
                     a);
           }
@@ -2392,7 +2499,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     } catch (Exception ex)
     {
       ex.printStackTrace();
-      System.out.println("Exception whilst pasting: " + ex);
+      jalview.bin.Console.outPrintln("Exception whilst pasting: " + ex);
       // could be anything being pasted in here
     }
 
@@ -2440,7 +2547,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     } catch (Exception ex)
     {
       ex.printStackTrace();
-      System.out.println("Exception whilst pasting: " + ex);
+      jalview.bin.Console.outPrintln("Exception whilst pasting: " + ex);
       // could be anything being pasted in here
     } catch (OutOfMemoryError oom)
     {
@@ -2471,34 +2578,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return;
     }
 
-    Runnable okAction = new Runnable()
-    {
-      @Override
-      public void run()
-      {
-        SequenceI[] cut = sg.getSequences()
-                .toArray(new SequenceI[sg.getSize()]);
+    Runnable okAction = () -> {
+      SequenceI[] cut = sg.getSequences()
+              .toArray(new SequenceI[sg.getSize()]);
 
-        addHistoryItem(new EditCommand(
-                MessageManager.getString("label.cut_sequences"), Action.CUT,
-                cut, sg.getStartRes(),
-                sg.getEndRes() - sg.getStartRes() + 1,
-                viewport.getAlignment()));
+      addHistoryItem(new EditCommand(
+              MessageManager.getString("label.cut_sequences"), Action.CUT,
+              cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+              viewport.getAlignment()));
 
-        viewport.setSelectionGroup(null);
-        viewport.sendSelection();
-        viewport.getAlignment().deleteGroup(sg);
+      viewport.setSelectionGroup(null);
+      viewport.sendSelection();
+      viewport.getAlignment().deleteGroup(sg);
 
-        viewport.firePropertyChange("alignment", null,
-                viewport.getAlignment().getSequences());
-        if (viewport.getAlignment().getHeight() < 1)
+      viewport.firePropertyChange("alignment", null,
+              viewport.getAlignment().getSequences());
+      if (viewport.getAlignment().getHeight() < 1)
+      {
+        try
+        {
+          AlignFrame.this.setClosed(true);
+        } catch (Exception ex)
         {
-          try
-          {
-            AlignFrame.this.setClosed(true);
-          } catch (Exception ex)
-          {
-          }
         }
       }
     };
@@ -2524,7 +2625,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     else
     {
-      okAction.run();
+      try
+      {
+        okAction.run();
+      } catch (Exception e)
+      {
+        e.printStackTrace();
+      }
     }
   }
 
@@ -2630,6 +2737,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.invertColumnSelection();
     alignPanel.paintAlignment(true, false);
+    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
     viewport.sendSelection();
   }
 
@@ -2910,6 +3018,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       viewport.setGatherViewsHere(true);
     }
     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
+
     return newap;
   }
 
@@ -3425,29 +3534,34 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Opens an Overview panel for the alignment, unless one is open already
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void overviewMenuItem_actionPerformed(ActionEvent e)
   {
+    boolean showHiddenRegions = Cache
+            .getDefault(Preferences.SHOW_OV_HIDDEN_AT_START, false);
+    openOverviewPanel(showHiddenRegions);
+  }
+
+  public OverviewPanel openOverviewPanel(boolean showHidden)
+  {
     if (alignPanel.overviewPanel != null)
     {
-      return;
+      return alignPanel.overviewPanel;
     }
-
     JInternalFrame frame = new JInternalFrame();
-    final OverviewPanel overview = new OverviewPanel(alignPanel);
+    final OverviewPanel overview = new OverviewPanel(alignPanel, frame,
+            showHidden);
     frame.setContentPane(overview);
-    Desktop.addInternalFrame(frame, MessageManager
-            .formatMessage("label.overview_params", new Object[]
-            { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
-            true, true);
-    frame.setFrameIcon(WindowIcons.overviewIcon);
+    Desktop.addInternalFrame(frame, "", true, frame.getWidth(),
+            frame.getHeight(), true, true);
+    frame.setFrameIcon(null);
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    final AlignmentPanel thePanel = this.alignPanel;
     frame.addInternalFrameListener(
             new javax.swing.event.InternalFrameAdapter()
             {
@@ -3456,7 +3570,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       javax.swing.event.InternalFrameEvent evt)
               {
                 overview.dispose();
-                alignPanel.setOverviewPanel(null);
+                thePanel.setOverviewPanel(null);
               }
             });
     if (getKeyListeners().length > 0)
@@ -3465,6 +3579,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     alignPanel.setOverviewPanel(overview);
+    alignPanel.setOverviewTitle(this);
+
+    return overview;
   }
 
   @Override
@@ -4078,35 +4195,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     chooser.setToolTipText(
             MessageManager.getString("label.load_tree_file"));
 
-    chooser.setResponseHandler(0, new Runnable()
-    {
-      @Override
-      public void run()
+    chooser.setResponseHandler(0, () -> {
+      String filePath = chooser.getSelectedFile().getPath();
+      Cache.setProperty("LAST_DIRECTORY", filePath);
+      NewickFile fin = null;
+      try
       {
-        String filePath = chooser.getSelectedFile().getPath();
-        Cache.setProperty("LAST_DIRECTORY", filePath);
-        NewickFile fin = null;
-        try
-        {
-          fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
-                  DataSourceType.FILE));
-          viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
-        } catch (Exception ex)
-        {
-          JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
-                  MessageManager
-                          .getString("label.problem_reading_tree_file"),
-                  JvOptionPane.WARNING_MESSAGE);
-          ex.printStackTrace();
-        }
-        if (fin != null && fin.hasWarningMessage())
-        {
-          JvOptionPane.showMessageDialog(Desktop.desktop,
-                  fin.getWarningMessage(),
-                  MessageManager.getString(
-                          "label.possible_problem_with_tree_file"),
-                  JvOptionPane.WARNING_MESSAGE);
-        }
+        fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
+                DataSourceType.FILE));
+        viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
+      } catch (Exception ex)
+      {
+        JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
+                MessageManager.getString("label.problem_reading_tree_file"),
+                JvOptionPane.WARNING_MESSAGE);
+        ex.printStackTrace();
+      }
+      if (fin != null && fin.hasWarningMessage())
+      {
+        JvOptionPane.showMessageDialog(Desktop.desktop,
+                fin.getWarningMessage(),
+                MessageManager
+                        .getString("label.possible_problem_with_tree_file"),
+                JvOptionPane.WARNING_MESSAGE);
       }
     });
     chooser.showOpenDialog(this);
@@ -4173,6 +4284,57 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return tp;
   }
 
+  public void showContactMapTree(AlignmentAnnotation aa, ContactMatrixI cm)
+  {
+    int x = 4, y = 5;
+    int w = 400, h = 500;
+
+    try
+    {
+      NewickFile fin = new NewickFile(
+              new FileParse(cm.getNewick(), DataSourceType.PASTE));
+      String title = aa.label + " " + cm.getTreeMethod() + " tree"
+              + (aa.sequenceRef != null
+                      ? (" for " + aa.sequenceRef.getDisplayId(false))
+                      : "");
+
+      showColumnWiseTree(fin, aa, title, w, h, x, y);
+    } catch (Throwable xx)
+    {
+      Console.error("Unexpected exception showing tree for contact matrix",
+              xx);
+    }
+  }
+
+  public TreePanel showColumnWiseTree(NewickFile nf, AlignmentAnnotation aa,
+          String treeTitle, int w, int h, int x, int y)
+  {
+    try
+    {
+      nf.parse();
+      if (nf.getTree() == null)
+      {
+        return null;
+      }
+      TreePanel tp = new TreePanel(alignPanel, nf, aa, treeTitle);
+
+      tp.setSize(w, h);
+
+      if (x > 0 && y > 0)
+      {
+        tp.setLocation(x, y);
+      }
+
+      Desktop.addInternalFrame(tp, treeTitle, w, h);
+      return tp;
+    } catch (Throwable xx)
+    {
+      Console.error("Unexpected exception showing tree for contact matrix",
+              xx);
+    }
+    return null;
+  }
+
   private boolean buildingMenu = false;
 
   /**
@@ -4185,7 +4347,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       try
       {
-        System.err.println("Waiting for building menu to finish.");
+        jalview.bin.Console
+                .errPrintln("Waiting for building menu to finish.");
         Thread.sleep(10);
       } catch (Exception e)
       {
@@ -4201,7 +4364,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         final List<JMenuItem> legacyItems = new ArrayList<>();
         try
         {
-          // System.err.println("Building ws menu again "
+          // jalview.bin.Console.errPrintln("Building ws menu again "
           // + Thread.currentThread());
           // TODO: add support for context dependent disabling of services based
           // on
@@ -4739,7 +4902,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                                     Desktop.instance);
                     if (pe != null)
                     {
-                      System.err.println("Associated file : "
+                      jalview.bin.Console.errPrintln("Associated file : "
                               + (fm[0].toString()) + " with "
                               + toassoc.getDisplayId(true));
                       assocfiles++;
@@ -4961,7 +5124,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     if (index > -1)
     {
+      /*
+       * update current Overview window title (if there is one)
+       * to add view name "Original" if necessary
+       */
+      alignPanel.setOverviewTitle(this);
+
+      /*
+       * switch panels and set Overview title (if there is one
+       * because it was opened automatically)
+       */
       alignPanel = alignPanels.get(index);
+      alignPanel.setOverviewTitle(this);
+
       viewport = alignPanel.av;
       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
       setMenusFromViewport(viewport);
@@ -5625,7 +5800,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    *          update non-sequence-related annotations
    */
   @Override
-  protected void setAnnotationsVisibility(boolean visible,
+  public void setAnnotationsVisibility(boolean visible,
           boolean forSequences, boolean forAlignment)
   {
     AlignmentAnnotation[] anns = alignPanel.getAlignment()
@@ -5760,7 +5935,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               viewport.getAlignment()));
     } catch (Exception ex)
     {
-      System.err.println(ex.getMessage());
+      jalview.bin.Console.errPrintln(ex.getMessage());
       return;
     }
   }
@@ -5782,7 +5957,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         console.runScript();
       } catch (Exception ex)
       {
-        System.err.println((ex.toString()));
+        jalview.bin.Console.errPrintln((ex.toString()));
         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                 MessageManager.getString("label.couldnt_run_groovy_script"),
                 MessageManager.getString("label.groovy_support_failed"),
@@ -5791,7 +5966,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     else
     {
-      System.err.println("Can't run Groovy script as console not found");
+      jalview.bin.Console
+              .errPrintln("Can't run Groovy script as console not found");
     }
   }
 
@@ -5831,6 +6007,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     | ActionEvent.CTRL_MASK)) != 0);
   }
 
+  @Override
+  protected void copyHighlightedColumns_actionPerformed(
+          ActionEvent actionEvent)
+  {
+    avc.copyHighlightedRegionsToClipboard();
+  }
+
   /**
    * Rebuilds the Colour menu, including any user-defined colours which have
    * been loaded either on startup or during the session
@@ -5879,16 +6062,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
     final AlignFrame us = this;
-    chooser.setResponseHandler(0, new Runnable()
-    {
-      @Override
-      public void run()
-      {
-        String choice = chooser.getSelectedFile().getPath();
-        Cache.setProperty("LAST_DIRECTORY", choice);
-        SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
-        new VCFLoader(choice).loadVCF(seqs, us);
-      }
+    chooser.setResponseHandler(0, () -> {
+      String choice = chooser.getSelectedFile().getPath();
+      Cache.setProperty("LAST_DIRECTORY", choice);
+      SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
+      new VCFLoader(choice).loadVCF(seqs, us);
     });
     chooser.showOpenDialog(null);
 
@@ -5907,6 +6085,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     return lastFeatureSettingsBounds;
   }
+
 }
 
 class PrintThread extends Thread