X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=7b310b18095a89f6f320f40a50ef1b554fd16468;hb=a7bc89415a6749ff89eb97f75fbc950a433a4935;hp=f9381b4af3a826894d3aa150afa852a7f5783498;hpb=01f8ff469a507604ed961418f7c80f9b245e60ca;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index f9381b4..7b310b1 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -59,6 +59,7 @@ import java.util.Hashtable;
 import java.util.List;
 import java.util.Locale;
 import java.util.Vector;
+import java.util.concurrent.Callable;
 
 import javax.swing.ButtonGroup;
 import javax.swing.JCheckBoxMenuItem;
@@ -349,6 +350,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   void init()
   {
+    setFrameIcon(null);
+
     // setBackground(Color.white); // BH 2019
 
     if (!Jalview.isHeadlessMode())
@@ -1259,6 +1262,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       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 }));
@@ -1267,97 +1276,89 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
-    Runnable cancelAction = new Runnable()
-    {
-      @Override
-      public void run()
+    Callable<Void> cancelAction = () -> {
+      lastSaveSuccessful = false;
+      return null;
+    };
+    Callable<Void> 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();
+        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 = 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);
+          Console.trace("ALIGNFRAME about to close file");
+          out.close();
+          Console.trace("ALIGNFRAME closed file");
+          AlignFrame.this.setTitle(file);
+          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));
+        }
 
-            out.print(output);
-            Console.trace("ALIGNFRAME about to close file");
-            out.close();
-            Console.trace("ALIGNFRAME closed file");
-            AlignFrame.this.setTitle(file);
-            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));
-          }
+        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);
         }
       }
+      return null;
     };
 
     /*
@@ -1373,7 +1374,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     else
     {
-      outputAction.run();
+      try
+      {
+        outputAction.call();
+      } catch (Exception e)
+      {
+        // TODO Auto-generated catch block
+        e.printStackTrace();
+      }
     }
   }
 
@@ -1390,34 +1398,29 @@ 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()
+    Callable<Void> 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();
       }
+      return null;
     };
 
     /*
@@ -1432,7 +1435,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     else
     {
-      outputAction.run();
+      try
+      {
+        outputAction.call();
+      } catch (Exception e)
+      {
+        e.printStackTrace();
+      }
     }
   }
 
@@ -1540,15 +1549,11 @@ 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);
+      return null;
     });
 
     chooser.showOpenDialog(this);
@@ -2470,36 +2475,31 @@ 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()]);
+    Callable 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)
-          {
-          }
         }
       }
+      return null;
     };
 
     /*
@@ -2523,7 +2523,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     else
     {
-      okAction.run();
+      try
+      {
+        okAction.call();
+      } catch (Exception e)
+      {
+        e.printStackTrace();
+      }
     }
   }
 
@@ -2909,6 +2915,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       viewport.setGatherViewsHere(true);
     }
     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
+
     return newap;
   }
 
@@ -3424,28 +3431,33 @@ 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(),
+    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()
             {
@@ -3454,7 +3466,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       javax.swing.event.InternalFrameEvent evt)
               {
                 overview.dispose();
-                alignPanel.setOverviewPanel(null);
+                thePanel.setOverviewPanel(null);
               }
             });
     if (getKeyListeners().length > 0)
@@ -3463,6 +3475,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     alignPanel.setOverviewPanel(overview);
+    alignPanel.setOverviewTitle(this);
+    
+    return overview;
   }
 
   @Override
@@ -4076,36 +4091,31 @@ 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);
       }
+      return null;
     });
     chooser.showOpenDialog(this);
   }
@@ -4959,7 +4969,19 @@ 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);
@@ -5884,16 +5906,12 @@ 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);
+      return null;
     });
     chooser.showOpenDialog(null);