X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=25c6dd4edb0e0c3fd052a449e01093047b456bfe;hb=8956fdfd008d0d949814c4680a7b3a55969e39e1;hp=936e714291cd805296fa9adf1f68eb297ba50324;hpb=bb6c9d30f57964136b759376b121f121f61c11e6;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 936e714..25c6dd4 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -24,6 +24,7 @@ import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.CrossRef;
 import jalview.analysis.Dna;
+import jalview.analysis.GeneticCodeI;
 import jalview.analysis.ParseProperties;
 import jalview.analysis.SequenceIdMatcher;
 import jalview.api.AlignExportSettingI;
@@ -64,6 +65,7 @@ import jalview.gui.ColourMenuHelper.ColourChangeListener;
 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 import jalview.io.AlignmentProperties;
 import jalview.io.AnnotationFile;
+import jalview.io.BackupFiles;
 import jalview.io.BioJsHTMLOutput;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
@@ -963,6 +965,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return progressBar.operationInProgress();
   }
 
+  /**
+   * Sets the text of the status bar. Note that setting a null or empty value
+   * will cause the status bar to be hidden, with possibly undesirable flicker
+   * of the screen layout.
+   */
   @Override
   public void setStatus(String text)
   {
@@ -1187,9 +1194,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
       else
       {
+        // create backupfiles object and get new temp filename destination
+        BackupFiles backupfiles = new BackupFiles(file);
+
         try
         {
-          PrintWriter out = new PrintWriter(new FileWriter(file));
+          PrintWriter out = new PrintWriter(
+                  new FileWriter(backupfiles.getTempFilePath()));
 
           out.print(output);
           out.close();
@@ -1202,6 +1213,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           success = false;
           ex.printStackTrace();
         }
+
+        backupfiles.setWriteSuccess(success);
+        // do the backup file roll and rename the temp file to actual file
+        success = backupfiles.rollBackupsAndRenameTempFile();
+
       }
     }
 
@@ -2403,6 +2419,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
     viewport.setSelectionGroup(sg);
+    viewport.isSelectionGroupChanged(true);
     viewport.sendSelection();
     // JAL-2034 - should delegate to
     // alignPanel to decide if overview needs
@@ -3033,6 +3050,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.expandColSelection(sg, false);
     viewport.hideAllSelectedSeqs();
     viewport.hideSelectedColumns();
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }
@@ -3057,6 +3075,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void hideSelColumns_actionPerformed(ActionEvent e)
   {
     viewport.hideSelectedColumns();
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }
@@ -4258,14 +4277,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
    */
   @Override
-  public void showTranslation_actionPerformed(ActionEvent e)
+  public void showTranslation_actionPerformed(GeneticCodeI codeTable)
   {
     AlignmentI al = null;
     try
     {
       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
 
-      al = dna.translateCdna();
+      al = dna.translateCdna(codeTable);
     } catch (Exception ex)
     {
       jalview.bin.Cache.log.error(
@@ -4294,7 +4313,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       af.setFileFormat(this.currentFileFormat);
       final String newTitle = MessageManager
               .formatMessage("label.translation_of_params", new Object[]
-              { this.getTitle() });
+              { this.getTitle(), codeTable.getId() });
       af.setTitle(newTitle);
       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
       {