Merge branch 'feature/JAL-3127_seqidChainshading' into merge/JAL-3127

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 03daeb4..a587ac3 100644 (file)
--- 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;
@@ -135,6 +136,7 @@ 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;
@@ -964,6 +966,11 @@ 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)
   {
@@ -2735,6 +2742,12 @@ 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
@@ -3044,6 +3057,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.expandColSelection(sg, false);
     viewport.hideAllSelectedSeqs();
     viewport.hideSelectedColumns();
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }
@@ -3068,6 +3082,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void hideSelColumns_actionPerformed(ActionEvent e)
   {
     viewport.hideSelectedColumns();
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }
@@ -3337,6 +3352,7 @@ 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());
     changeColour(cs);
   }
@@ -4269,14 +4285,14 @@ 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(
@@ -4305,7 +4321,7 @@ 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))
       {
@@ -5293,7 +5309,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
       alignPanel.updateAnnotation();
-      alignPanel.paintAlignment(true, true);
+      alignPanel.paintAlignment(true,
+              viewport.needToUpdateStructureViews());
     }
   }
 
@@ -5579,15 +5596,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     colourMenu.add(textColour);
     colourMenu.addSeparator();
 
-    ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
-            false);
+    ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
+            viewport.getAlignment(), false);
 
+    colourMenu.add(annotationColour);
+    bg.add(annotationColour);
     colourMenu.addSeparator();
     colourMenu.add(conservationMenuItem);
     colourMenu.add(modifyConservation);
     colourMenu.add(abovePIDThreshold);
     colourMenu.add(modifyPID);
-    colourMenu.add(annotationColour);
 
     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);