X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=e36944f1f87916cec1aecbcb4ec8fac064c46d89;hb=6405be60655fe096cdbff89cccf0a5b12f8b7e80;hp=84be0ddcc7951c0ad9867ec1e3ccc4115996afa9;hpb=76776617eb3960193681eb733cb769f90639ce22;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 84be0dd..e36944f 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -25,6 +25,7 @@ import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
+import jalview.api.FeatureColourI;
 import jalview.api.FeatureRenderer;
 import jalview.api.FeatureSettingsControllerI;
 import jalview.api.SequenceStructureBinding;
@@ -75,6 +76,7 @@ import java.awt.BorderLayout;
 import java.awt.Canvas;
 import java.awt.CheckboxMenuItem;
 import java.awt.Color;
+import java.awt.FlowLayout;
 import java.awt.Font;
 import java.awt.FontMetrics;
 import java.awt.Frame;
@@ -83,6 +85,7 @@ import java.awt.Label;
 import java.awt.Menu;
 import java.awt.MenuBar;
 import java.awt.MenuItem;
+import java.awt.Panel;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.FocusEvent;
@@ -139,8 +142,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
    * @param title
    * @param embedded
    */
-  public AlignFrame(AlignmentI al, JalviewLite applet,
-          String title, boolean embedded)
+  public AlignFrame(AlignmentI al, JalviewLite applet, String title,
+          boolean embedded)
   {
     this(al, applet, title, embedded, true);
   }
@@ -155,8 +158,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
    * @param embedded
    * @param addToDisplay
    */
-  public AlignFrame(AlignmentI al, JalviewLite applet,
-          String title, boolean embedded, boolean addToDisplay)
+  public AlignFrame(AlignmentI al, JalviewLite applet, String title,
+          boolean embedded, boolean addToDisplay)
   {
     this(al, null, null, applet, title, embedded, addToDisplay);
   }
@@ -216,6 +219,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       viewport.setColumnSelection(columnSelection);
     }
+    viewport.setScaleAboveWrapped(scaleAbove.getState());
 
     alignPanel = new AlignmentPanel(this, viewport);
     avc = new jalview.controller.AlignViewController(this, viewport,
@@ -232,8 +236,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
-    showAlignmentAnnotations.setState(viewport.isShowAnnotation());
-    showSequenceAnnotations.setState(viewport.isShowAnnotation());
+    showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
+    showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
+    showAlignmentAnnotations.setState(true);
+    showSequenceAnnotations.setState(false);
 
     seqLimits.setState(viewport.getShowJVSuffix());
 
@@ -302,6 +308,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
     alignPanel.alabels.addKeyListener(this);
 
+    setAnnotationsVisibility();
+
     if (addToDisplay)
     {
       addToDisplay(embedded);
@@ -358,18 +366,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public boolean parseFeaturesFile(String file, String type,
           boolean autoenabledisplay)
   {
-    // TODO: test if importing a features file onto an alignment which already
-    // has features with links overwrites the original links.
-
-    Hashtable featureLinks = new Hashtable();
     boolean featuresFile = false;
     try
     {
-      featuresFile = new jalview.io.FeaturesFile(file, type)
-              .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
-                      .getFeatureRenderer().getFeatureColours(), featureLinks,
-                      true, viewport.applet.getDefaultParameter(
-                              "relaxedidmatch", false));
+      Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
+              .getFeatureRenderer().getFeatureColours();
+      boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
+              "relaxedidmatch", false);
+      featuresFile = new FeaturesFile(file, type).parse(
+              viewport.getAlignment(), colours, true, relaxedIdMatching);
     } catch (Exception ex)
     {
       ex.printStackTrace();
@@ -377,10 +382,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     if (featuresFile)
     {
-      if (featureLinks.size() > 0)
-      {
-        alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
-      }
       if (autoenabledisplay)
       {
         viewport.setShowSequenceFeatures(true);
@@ -552,8 +553,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     case KeyEvent.VK_F2:
       viewport.cursorMode = !viewport.cursorMode;
       statusBar.setText(MessageManager.formatMessage(
-              "label.keyboard_editing_mode", new String[]
-              { (viewport.cursorMode ? "on" : "off") }));
+              "label.keyboard_editing_mode",
+              new String[] { (viewport.cursorMode ? "on" : "off") }));
       if (viewport.cursorMode)
       {
         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
@@ -702,9 +703,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       // Hide everything by the current selection - this is a hack - we do the
       // invert and then hide
       // first check that there will be visible columns after the invert.
-      if ((viewport.getColumnSelection() != null
-              && viewport.getColumnSelection().getSelected() != null && viewport
-              .getColumnSelection().getSelected().size() > 0)
+      if (viewport.hasSelectedColumns()
               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
                       .getEndRes()))
       {
@@ -732,8 +731,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         hide = true;
         viewport.hideAllSelectedSeqs();
       }
-      else if (!(toggleCols && viewport.getColumnSelection().getSelected()
-              .size() > 0))
+      else if (!(toggleCols && viewport.hasSelectedColumns()))
       {
         viewport.showAllHiddenSeqs();
       }
@@ -741,7 +739,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     if (toggleCols)
     {
-      if (viewport.getColumnSelection().getSelected().size() > 0)
+      if (viewport.hasSelectedColumns())
       {
         viewport.hideSelectedColumns();
         if (!toggleSeqs)
@@ -753,6 +751,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       {
         viewport.showAllHiddenColumns();
       }
+      viewport.sendSelection();
     }
   }
 
@@ -812,8 +811,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     else if (source == annotationPanelMenuItem)
     {
-      viewport.setShowAnnotation(annotationPanelMenuItem.getState());
-      alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
+      boolean showAnnotations = annotationPanelMenuItem.getState();
+      showAlignmentAnnotations.setEnabled(showAnnotations);
+      showSequenceAnnotations.setEnabled(showAnnotations);
+      viewport.setShowAnnotation(showAnnotations);
+      alignPanel.setAnnotationVisible(showAnnotations);
     }
     else if (source == sequenceFeatures)
     {
@@ -913,7 +915,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   /**
    * Set the visibility state of sequence-related and/or alignment-related
-   * annotations depending on checkbox selections. Repaint after calling.
+   * annotations depending on checkbox selections, and repaint.
    * 
    * @param visible
    */
@@ -921,12 +923,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     boolean showForAlignment = showAlignmentAnnotations.getState();
     boolean showForSequences = showSequenceAnnotations.getState();
-    for (AlignmentAnnotation aa : alignPanel.getAlignment()
+    if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
+    {
+      for (AlignmentAnnotation aa : alignPanel.getAlignment()
             .getAlignmentAnnotation())
     {
       boolean visible = (aa.sequenceRef == null ? showForAlignment
               : showForSequences);
-        aa.visible = visible;
+      aa.visible = visible;
+      }
     }
     alignPanel.validateAnnotationDimensions(true);
     validate();
@@ -969,6 +974,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   @Override
   public void actionPerformed(ActionEvent evt)
   {
+    viewport.applet.currentAlignFrame = this;
+
     Object source = evt.getSource();
 
     if (source == inputText)
@@ -1066,11 +1073,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     else if (source == invertSequenceMenuItem)
     {
       invertSequenceMenuItem_actionPerformed();
+      // uncomment to slave sequence selections in split frame
+      // viewport.sendSelection();
     }
     else if (source == invertColSel)
     {
       viewport.invertColumnSelection();
       alignPanel.paintAlignment(true);
+      viewport.sendSelection();
     }
     else if (source == remove2LeftMenuItem)
     {
@@ -1104,27 +1114,34 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       viewport.showAllHiddenColumns();
       alignPanel.paintAlignment(true);
+      viewport.sendSelection();
     }
     else if (source == showSeqs)
     {
       viewport.showAllHiddenSeqs();
       alignPanel.paintAlignment(true);
+      // uncomment if we want to slave sequence selections in split frame
+      // viewport.sendSelection();
     }
     else if (source == hideColumns)
     {
       viewport.hideSelectedColumns();
       alignPanel.paintAlignment(true);
+      viewport.sendSelection();
     }
     else if (source == hideSequences
             && viewport.getSelectionGroup() != null)
     {
       viewport.hideAllSelectedSeqs();
       alignPanel.paintAlignment(true);
+      // uncomment if we want to slave sequence selections in split frame
+      // viewport.sendSelection();
     }
     else if (source == hideAllButSelection)
     {
       toggleHiddenRegions(false, false);
       alignPanel.paintAlignment(true);
+      viewport.sendSelection();
     }
     else if (source == hideAllSelection)
     {
@@ -1133,12 +1150,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       viewport.hideAllSelectedSeqs();
       viewport.hideSelectedColumns();
       alignPanel.paintAlignment(true);
+      viewport.sendSelection();
     }
     else if (source == showAllHidden)
     {
       viewport.showAllHiddenColumns();
       viewport.showAllHiddenSeqs();
       alignPanel.paintAlignment(true);
+      viewport.sendSelection();
     }
     else if (source == showGroupConsensus)
     {
@@ -1177,8 +1196,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       Frame frame = new Frame();
       frame.add(cap);
       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
-              "label.alignment_properties", new String[]
-              { getTitle() }), 400, 250);
+              "label.alignment_properties", new String[] { getTitle() }),
+              400, 250);
     }
     else if (source == overviewMenuItem)
     {
@@ -1339,8 +1358,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     Frame frame = new Frame();
     frame.add(cap);
     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
-            "label.alignment_output_command", new Object[]
-            { e.getActionCommand() }), 600, 500);
+            "label.alignment_output_command",
+            new Object[] { e.getActionCommand() }), 600, 500);
 
     FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
@@ -1379,13 +1398,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     return annotation;
   }
 
-  private Map<String,Object> getDisplayedFeatureCols()
+  private Map<String, FeatureColourI> getDisplayedFeatureCols()
   {
     if (alignPanel.getFeatureRenderer() != null
-            && viewport.getFeaturesDisplayed()!= null)
+            && viewport.getFeaturesDisplayed() != null)
     {
       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
-      
+
     }
     return null;
   }
@@ -1393,15 +1412,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public String outputFeatures(boolean displayTextbox, String format)
   {
     String features;
+    FeaturesFile formatter = new FeaturesFile();
     if (format.equalsIgnoreCase("Jalview"))
     {
-      features = new FeaturesFile().printJalviewFormat(viewport
+      features = formatter.printJalviewFormat(viewport
               .getAlignment().getSequencesArray(),
               getDisplayedFeatureCols());
     }
     else
     {
-      features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
+      features = formatter.printGffFormat(viewport.getAlignment()
               .getSequencesArray(), getDisplayedFeatureCols());
     }
 
@@ -1568,8 +1588,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       undoMenuItem.setEnabled(true);
       CommandI command = viewport.getHistoryList().peek();
       undoMenuItem.setLabel(MessageManager.formatMessage(
-              "label.undo_command", new Object[]
-              { command.getDescription() }));
+              "label.undo_command",
+              new Object[] { command.getDescription() }));
     }
     else
     {
@@ -1583,8 +1603,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
       CommandI command = viewport.getRedoList().peek();
       redoMenuItem.setLabel(MessageManager.formatMessage(
-              "label.redo_command", new Object[]
-              { command.getDescription() }));
+              "label.redo_command",
+              new Object[] { command.getDescription() }));
     }
     else
     {
@@ -1741,9 +1761,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
               viewport, complement);
       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
               up ? null : complement.getHiddenRepSequences(), up);
-      // TODO need to trigger a repaint of the complementary panel - how?
-      // would prefer to handle in SplitFrame but it is not overriding key
-      // listener chiz
+      getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
     }
   }
 
@@ -1879,8 +1897,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
       {
-        copiedHiddenColumns.addElement(new int[]
-        { region[0] - hiddenOffset, region[1] - hiddenOffset });
+        copiedHiddenColumns.addElement(new int[] {
+            region[0] - hiddenOffset, region[1] - hiddenOffset });
       }
     }
     else
@@ -1977,14 +1995,17 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
       if (newAlignment)
       {
-        String newtitle = MessageManager.getString("label.copied_sequences");
-        if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
+        String newtitle = MessageManager
+                .getString("label.copied_sequences");
+        if (getTitle().startsWith(
+                MessageManager.getString("label.copied_sequences")))
         {
           newtitle = getTitle();
         }
         else
         {
-          newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
+          newtitle = newtitle.concat(MessageManager.formatMessage(
+                  "label.from_msname", new String[] { getTitle() }));
         }
         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
                 viewport.applet, newtitle, false);
@@ -2054,9 +2075,32 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       seqs.addElement(seq);
     }
 
-    // If the cut affects all sequences, remove highlighted columns
+    /*
+     * If the cut affects all sequences, warn, remove highlighted columns
+     */
     if (sg.getSize() == viewport.getAlignment().getHeight())
     {
+      boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
+              .getAlignment().getWidth()) ? true : false;
+      if (isEntireAlignWidth)
+      {
+        String title = MessageManager.getString("label.delete_all");
+        Panel infoPanel = new Panel();
+        infoPanel.setLayout(new FlowLayout());
+        infoPanel
+                .add(new Label(MessageManager.getString("warn.delete_all")));
+
+        final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
+        dialog.setMainPanel(infoPanel);
+        dialog.ok.setLabel(MessageManager.getString("action.ok"));
+        dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
+        dialog.setVisible(true);
+
+        if (!dialog.accept)
+        {
+          return;
+        }
+      }
       viewport.getColumnSelection().removeElements(sg.getStartRes(),
               sg.getEndRes() + 1);
     }
@@ -2187,7 +2231,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
     viewport.setSelectionGroup(sg);
-    alignPanel.paintAlignment(true);
+    // JAL-2034 - should delegate to
+    // alignPanel to decide if overview needs
+    // updating.
+    alignPanel.paintAlignment(false);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
     viewport.sendSelection();
   }
@@ -2204,7 +2251,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     viewport.setSelectionGroup(null);
     alignPanel.idPanel.idCanvas.searchResults = null;
     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
-    alignPanel.paintAlignment(true);
+    // JAL-2034 - should delegate to
+    // alignPanel to decide if overview needs
+    // updating.
+    alignPanel.paintAlignment(false);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
     viewport.sendSelection();
   }
@@ -2234,7 +2284,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     ColumnSelection colSel = viewport.getColumnSelection();
     int column;
 
-    if (colSel.size() > 0)
+    if (!colSel.isEmpty())
     {
       if (trimLeft)
       {
@@ -2259,23 +2309,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       TrimRegionCommand trimRegion;
       if (trimLeft)
       {
-        trimRegion = new TrimRegionCommand("Remove Left",
-                TrimRegionCommand.TRIM_LEFT, seqs, column,
-                viewport.getAlignment(), viewport.getColumnSelection(),
-                viewport.getSelectionGroup());
+        trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
+                column, viewport.getAlignment());
         viewport.setStartRes(0);
       }
       else
       {
-        trimRegion = new TrimRegionCommand("Remove Right",
-                TrimRegionCommand.TRIM_RIGHT, seqs, column,
-                viewport.getAlignment(), viewport.getColumnSelection(),
-                viewport.getSelectionGroup());
+        trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
+                column, viewport.getAlignment());
       }
 
       statusBar.setText(MessageManager.formatMessage(
-              "label.removed_columns", new String[]
-              { Integer.valueOf(trimRegion.getSize()).toString() }));
+              "label.removed_columns",
+              new String[] { Integer.valueOf(trimRegion.getSize())
+                      .toString() }));
       addHistoryItem(trimRegion);
 
       for (SequenceGroup sg : viewport.getAlignment().getGroups())
@@ -2316,8 +2363,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     addHistoryItem(removeGapCols);
 
     statusBar.setText(MessageManager.formatMessage(
-            "label.removed_empty_columns", new String[]
-            { Integer.valueOf(removeGapCols.getSize()).toString() }));
+            "label.removed_empty_columns",
+            new String[] { Integer.valueOf(removeGapCols.getSize())
+                    .toString() }));
 
     // This is to maintain viewport position on first residue
     // of first sequence
@@ -2499,7 +2547,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     if (alignPanel != null
             && (fr = alignPanel.getFeatureRenderer()) != null)
     {
-      
+
       fr.setGroupVisibility(Arrays.asList(groups), state);
       alignPanel.seqPanel.seqCanvas.repaint();
       if (alignPanel.overviewPanel != null)
@@ -2550,8 +2598,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     frame.add(overview);
     // +50 must allow for applet frame window
     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
-            "label.overview_params", new String[]
-            { this.getTitle() }), overview.getPreferredSize().width,
+            "label.overview_params", new String[] { this.getTitle() }),
+            overview.getPreferredSize().width,
             overview.getPreferredSize().height + 50);
 
     frame.pack();
@@ -2572,9 +2620,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   }
 
+  @Override
   public void changeColour(ColourSchemeI cs)
   {
-    int threshold = 0;
 
     if (cs != null)
     {
@@ -2597,15 +2645,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     viewport.setGlobalColourScheme(cs);
 
-    if (alignPanel.getOverviewPanel() != null)
-    {
-      alignPanel.getOverviewPanel().updateOverviewImage();
-    }
-
-    jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager(viewport.applet)
-            .sequenceColoursChanged(alignPanel);
-
     alignPanel.paintAlignment(true);
   }
 
@@ -2837,8 +2876,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
     // HistoryItem.SORT));
     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
-            "label.order_by_params", new String[]
-            { title }), oldOrder, viewport.getAlignment()));
+            "label.order_by_params", new String[] { title }), oldOrder,
+            viewport.getAlignment()));
     alignPanel.paintAlignment(true);
   }
 
@@ -2935,12 +2974,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         // lite and application
         g.setFont(new Font("Helvetica", Font.BOLD, 14));
         g.drawString(MessageManager.formatMessage(
-                "label.jalviewLite_release", new String[]
-                { version }), x, y += fh);
+                "label.jalviewLite_release", new String[] { version }), x,
+                y += fh);
         g.setFont(new Font("Helvetica", Font.BOLD, 12));
         g.drawString(MessageManager.formatMessage(
-                "label.jaview_build_date", new String[]
-                { builddate }), x, y += fh);
+                "label.jaview_build_date", new String[] { builddate }), x,
+                y += fh);
         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
         g.drawString(MessageManager.getString("label.jalview_authors_1"),
                 x, y += fh * 1.5);
@@ -3001,10 +3040,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
           MessageManager.getString("label.load_features_annotations"));
 
   MenuItem outputFeatures = new MenuItem(
-          MessageManager.getString("label.export_features").concat("..."));
+          MessageManager.getString("label.export_features"));
 
   MenuItem outputAnnotations = new MenuItem(
-          MessageManager.getString("label.export_annotations").concat("..."));
+          MessageManager.getString("label.export_annotations"));
 
   MenuItem closeMenuItem = new MenuItem(
           MessageManager.getString("action.close"));
@@ -3253,8 +3292,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     removeAllGapsMenuItem.setLabel(MessageManager
             .getString("action.remove_all_gaps"));
     removeAllGapsMenuItem.addActionListener(this);
-    removeRedundancyMenuItem.setLabel(MessageManager.getString(
-            "action.remove_redundancy").concat("..."));
+    removeRedundancyMenuItem.setLabel(MessageManager
+            .getString("action.remove_redundancy"));
     removeRedundancyMenuItem.addActionListener(this);
 
     /*
@@ -3278,7 +3317,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     grpsFromSelection.addActionListener(this);
     createGroup.setLabel(MessageManager.getString("action.create_group"));
     unGroup.setLabel(MessageManager.getString("action.remove_group"));
-    annotationColumnSelection.setLabel("Select by Annotation");
+    annotationColumnSelection.setLabel(MessageManager
+            .getString("action.select_by_annotation"));
     annotationColumnSelection.addActionListener(this);
 
     /*
@@ -3308,7 +3348,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     hideAllSelection.addActionListener(this);
     showAllHidden.addActionListener(this);
     featureSettings.setLabel(MessageManager
-            .getString("label.feature_settings"));
+            .getString("action.feature_settings"));
     featureSettings.addActionListener(this);
     sequenceFeatures.setLabel(MessageManager
             .getString("label.show_sequence_features"));
@@ -3359,8 +3399,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             MessageManager.getString("label.sort_annotations_by_label"));
     showAutoFirst = new CheckboxMenuItem(
             MessageManager.getString("label.show_first"));
+    showAutoFirst.setState(false); // pending applet parameter
+    setShowAutoCalculatedAbove(showAutoFirst.getState());
     showAutoLast = new CheckboxMenuItem(
             MessageManager.getString("label.show_last"));
+    showAutoLast.setState(!showAutoFirst.getState());
     showAlignmentAnnotations.addItemListener(this);
     showSequenceAnnotations.addItemListener(this);
     sortAnnBySequence.addItemListener(this);
@@ -3471,10 +3514,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
     nucleotideColour.addActionListener(this);
     modifyPID.setLabel(MessageManager
-            .getString("label.modify_identity_thereshold"));
+            .getString("label.modify_identity_threshold"));
     modifyPID.addActionListener(this);
     modifyConservation.setLabel(MessageManager
-            .getString("label.modify_conservation_thereshold"));
+            .getString("label.modify_conservation_threshold"));
     modifyConservation.addActionListener(this);
     annotationColour.setLabel(MessageManager
             .getString("action.by_annotation"));
@@ -3728,6 +3771,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     this.add(statusBar, BorderLayout.SOUTH);
   }
 
+  @Override
   public void setStatus(String string)
   {
     statusBar.setText(string);
@@ -3805,8 +3849,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       add(statusBar, BorderLayout.SOUTH);
       add(alignPanel, BorderLayout.CENTER);
       // and register with the applet so it can pass external API calls to us
-      jalview.bin.JalviewLite.addFrame(this, this.getTitle(),
-              frameWidth,
+      jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
               frameHeight);
     }
   }
@@ -3922,8 +3965,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // TODO: search for a jmv that involves viewer
     if (jmv == null)
     { // create a new viewer/jalview binding.
-      jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
-      { seqs });
+      jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
     }
     return jmv;
 
@@ -4006,8 +4048,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       {
         if (seqs[i] != null)
         {
-          sequences.addElement(new Object[]
-          { seqs[i], (chains != null) ? chains[i] : null });
+          sequences.addElement(new Object[] { seqs[i],
+              (chains != null) ? chains[i] : null });
         }
       }
       seqs = new SequenceI[sequences.size()];
@@ -4020,8 +4062,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         chains[i] = (String) oj[1];
       }
     }
-    return new Object[]
-    { seqs, chains };
+    return new Object[] { seqs, chains };
 
   }
 
@@ -4209,7 +4250,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     this.splitFrame = sf;
   }
 
-    // may not need this
+  // may not need this
   @Override
   public void setShowSeqFeatures(boolean b)
   {
@@ -4224,6 +4265,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // setMenusFromViewport(viewport);
 
   }
+
   @Override
   public void refreshFeatureUI(boolean enableIfNecessary)
   {