X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=e17b3316c4ddb6b3541cffb7682b611b10137c5e;hb=a134511be07a998f7b80168dd26b632d53ed66b4;hp=bf9569b85119899dab22c86dda60e0cd52c9df74;hpb=ea976fa3d06c5fa75d9b89dafe5560dbae7fdb1d;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index bf9569b..e17b331 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;
@@ -964,6 +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)
   {
@@ -2408,15 +2414,12 @@ 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
@@ -2738,6 +2741,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     newap.av.setRedoList(viewport.getRedoList());
 
     /*
+     * copy any visualisation settings that are not saved in the project
+     */
+    newap.av.setColourAppliesToAllGroups(
+            viewport.getColourAppliesToAllGroups());
+
+    /*
      * Views share the same mappings; need to deregister any new mappings
      * created by copyAlignPanel, and register the new reference to the shared
      * mappings
@@ -2900,7 +2909,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.setFollowHighlight(state);
     if (state)
     {
-      alignPanel.scrollToPosition(viewport.getSearchResults(), false);
+      alignPanel.scrollToPosition(viewport.getSearchResults());
     }
   }
 
@@ -3047,6 +3056,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.expandColSelection(sg, false);
     viewport.hideAllSelectedSeqs();
     viewport.hideSelectedColumns();
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }
@@ -3071,6 +3081,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void hideSelColumns_actionPerformed(ActionEvent e)
   {
     viewport.hideSelectedColumns();
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }
@@ -4272,14 +4283,14 @@ 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(
@@ -4308,7 +4319,7 @@ 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))
       {