Merge branch 'bug/JAL-3099alignmentVisibleWidth' into merge/JAL-3099

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index a2336a0..b080a25 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)
   {
@@ -1154,7 +1160,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
       }
 
-      success = new Jalview2XML().saveAlignment(this, file, shortName);
+      success = new jalview.project.Jalview2XML().saveAlignment(this, file,
+              shortName);
 
       statusBar.setText(MessageManager.formatMessage(
               "label.successfully_saved_to_file_in_format", new Object[]
@@ -1186,9 +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();
@@ -1201,6 +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();
+
       }
     }
 
@@ -2397,15 +2413,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-    SequenceGroup sg = new SequenceGroup();
-
-    for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
-    {
-      sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
-    }
+    SequenceGroup sg = new SequenceGroup(
+            viewport.getAlignment().getSequences());
 
     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
@@ -2701,7 +2714,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     /*
      * Create a new AlignmentPanel (with its own, new Viewport)
      */
-    AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
+    AlignmentPanel newap = new jalview.project.Jalview2XML()
+            .copyAlignPanel(alignPanel);
     if (!copyAnnotation)
     {
       /*
@@ -2888,7 +2902,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.setFollowHighlight(state);
     if (state)
     {
-      alignPanel.scrollToPosition(viewport.getSearchResults(), false);
+      alignPanel.scrollToPosition(viewport.getSearchResults());
     }
   }
 
@@ -3035,6 +3049,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.expandColSelection(sg, false);
     viewport.hideAllSelectedSeqs();
     viewport.hideSelectedColumns();
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }
@@ -3059,6 +3074,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void hideSelColumns_actionPerformed(ActionEvent e)
   {
     viewport.hideSelectedColumns();
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }
@@ -5399,7 +5415,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   public List<? extends AlignmentViewPanel> getAlignPanels()
   {
-    return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+    // alignPanels is never null
+    // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+    return alignPanels;
   }
 
   /**