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JAL-3676 Removed BACKUPFILESPRESETENTRY logging for opening the file browser. Changed...
[jalview.git] / src / jalview / gui / AlignFrame.java
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d03b2c7..b2e05c5 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -20,6 +20,54 @@
  */
 package jalview.gui;
 
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DropTargetDragEvent;
+import java.awt.dnd.DropTargetDropEvent;
+import java.awt.dnd.DropTargetEvent;
+import java.awt.dnd.DropTargetListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseEvent;
+import java.awt.print.PageFormat;
+import java.awt.print.PrinterJob;
+import java.beans.PropertyChangeEvent;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Deque;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JEditorPane;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.CrossRef;
@@ -91,6 +139,7 @@ import jalview.schemes.ColourSchemes;
 import jalview.schemes.ResidueColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
 import jalview.ws.DBRefFetcher;
@@ -100,53 +149,6 @@ import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
-import java.awt.BorderLayout;
-import java.awt.Component;
-import java.awt.Rectangle;
-import java.awt.Toolkit;
-import java.awt.datatransfer.Clipboard;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.StringSelection;
-import java.awt.datatransfer.Transferable;
-import java.awt.dnd.DnDConstants;
-import java.awt.dnd.DropTargetDragEvent;
-import java.awt.dnd.DropTargetDropEvent;
-import java.awt.dnd.DropTargetEvent;
-import java.awt.dnd.DropTargetListener;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.FocusAdapter;
-import java.awt.event.FocusEvent;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.awt.event.KeyAdapter;
-import java.awt.event.KeyEvent;
-import java.awt.event.MouseEvent;
-import java.awt.print.PageFormat;
-import java.awt.print.PrinterJob;
-import java.beans.PropertyChangeEvent;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.PrintWriter;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Deque;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
-import javax.swing.ButtonGroup;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JEditorPane;
-import javax.swing.JInternalFrame;
-import javax.swing.JLayeredPane;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JScrollPane;
-import javax.swing.SwingUtilities;
-
 /**
  * DOCUMENT ME!
  * 
@@ -1169,7 +1171,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       statusBar.setText(MessageManager.formatMessage(
               "label.successfully_saved_to_file_in_format", new Object[]
-              { fileName, format }));
+              { file, format }));
 
     }
     else
@@ -1198,39 +1200,66 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       else
       {
         // create backupfiles object and get new temp filename destination
+        Cache.log.trace("ALIGNFRAME making backupfiles object for " + file);
         BackupFiles backupfiles = new BackupFiles(file);
 
         try
         {
-          PrintWriter out = new PrintWriter(
-                  new FileWriter(backupfiles.getTempFilePath()));
+          String tempFilePath = backupfiles.getTempFilePath();
+          Cache.log.trace(
+                  "ALIGNFRAME setting PrintWriter to " + tempFilePath);
+          PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
+
+          Cache.log.trace(
+                  "ALIGNFRAME about to write to temp file " + tempFilePath);
 
           out.print(output);
+          Cache.log.trace("ALIGNFRAME about to close file");
           out.close();
+          Cache.log.trace("ALIGNFRAME closed file");
           this.setTitle(file);
           statusBar.setText(MessageManager.formatMessage(
                   "label.successfully_saved_to_file_in_format", new Object[]
-                  { fileName, format.getName() }));
+                  { file, format.getName() }));
+        } catch (IOException e)
+        {
+          success = false;
+          Cache.log.error(
+                  "ALIGNFRAME Something happened writing the temp file");
+          Cache.log.error(e.getMessage());
+          Cache.log.debug(Cache.getStackTraceString(e));
+
         } catch (Exception ex)
         {
           success = false;
-          ex.printStackTrace();
+          Cache.log.error(
+                  "ALIGNFRAME Something unexpected happened writing the temp file");
+          Cache.log.error(ex.getMessage());
+          Cache.log.debug(Cache.getStackTraceString(ex));
         }
 
         backupfiles.setWriteSuccess(success);
+        Cache.log.debug("ALIGNFRAME writing temp file was "
+                + (success ? "" : "NOT ") + "successful");
         // do the backup file roll and rename the temp file to actual file
+        Cache.log.trace("ALIGNFRAME about to rollBackupsAndRenameTempFile");
         success = backupfiles.rollBackupsAndRenameTempFile();
+        Cache.log.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile "
+                + (success ? "" : "un") + "successfully");
 
       }
     }
 
     if (!success)
     {
-      JvOptionPane.showInternalMessageDialog(this, MessageManager
-              .formatMessage("label.couldnt_save_file", new Object[]
-              { fileName }),
-              MessageManager.getString("label.error_saving_file"),
-              JvOptionPane.WARNING_MESSAGE);
+      if (!Platform.isHeadless())
+      {
+        JvOptionPane.showInternalMessageDialog(this, MessageManager
+                .formatMessage("label.couldnt_save_file", new Object[]
+                { file }),
+                MessageManager.getString("label.error_saving_file"),
+                JvOptionPane.WARNING_MESSAGE);
+      }
     }
 
     return success;
@@ -2737,8 +2766,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (viewport.getViewName() == null)
     {
-      viewport.setViewName(MessageManager
-              .getString("label.view_name_original"));
+      viewport.setViewName(
+              MessageManager.getString("label.view_name_original"));
     }
 
     /*
@@ -3367,8 +3396,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
      * otherwise set the chosen colour scheme (or null for 'None')
      */
     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
-            viewport,
-            viewport.getAlignment(), viewport.getHiddenRepSequences());
+            viewport, viewport.getAlignment(),
+            viewport.getHiddenRepSequences());
     changeColour(cs);
   }
 
@@ -5695,6 +5724,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   private Rectangle lastFeatureSettingsBounds = null;
+
   @Override
   public void setFeatureSettingsGeometry(Rectangle bounds)
   {