Merge remote-tracking branch 'origin/tasks/JAL-3035_remove_dasobert_dependency' into...

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 936e714..606e2e7 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -64,6 +64,7 @@ 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 +964,11 @@ 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 +1193,13 @@ 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 +1212,11 @@ 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 +2418,7 @@ 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