X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=850a09a0aa1c7a140c52ac87569a7a181ef648aa;hb=106a3890f956e2aa7780b2985f4326655912a558;hp=37cd8b312898798ad709d3537bda47304001d7fe;hpb=3538805166769a407d01240d196c723d9a458bed;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 37cd8b3..850a09a 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -31,8 +31,8 @@ import jalview.commands.EditCommand.Action;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
@@ -43,12 +43,10 @@ import jalview.io.FileFormatI;
 import jalview.io.FileFormats;
 import jalview.io.FormatAdapter;
 import jalview.io.SequenceAnnotationReport;
-import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.PIDColourScheme;
-import jalview.schemes.ResidueColourScheme;
 import jalview.util.GroupUrlLink;
 import jalview.util.GroupUrlLink.UrlStringTooLongException;
 import jalview.util.MessageManager;
@@ -57,7 +55,9 @@ import jalview.util.UrlLink;
 import java.awt.Color;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.BitSet;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.Hashtable;
@@ -180,7 +180,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
    * @param seq
    *          DOCUMENT ME!
    */
-  public PopupMenu(final AlignmentPanel ap, Sequence seq, List<String> links)
+  public PopupMenu(final AlignmentPanel ap, Sequence seq,
+          List<String> links)
   {
     this(ap, seq, links, null);
   }
@@ -225,8 +226,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
      * 'reference annotations' that may be added to the alignment. First for the
      * currently selected sequence (if there is one):
      */
-    final List<SequenceI> selectedSequence = (seq == null ? Collections
-            .<SequenceI> emptyList() : Arrays.asList(seq));
+    final List<SequenceI> selectedSequence = (seq == null
+            ? Collections.<SequenceI> emptyList()
+            : Arrays.asList(seq));
     buildAnnotationTypesMenus(seqShowAnnotationsMenu,
             seqHideAnnotationsMenu, selectedSequence);
     configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
@@ -235,9 +237,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     /*
      * And repeat for the current selection group (if there is one):
      */
-    final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null ? Collections
-            .<SequenceI> emptyList() : ap.av.getSelectionGroup()
-            .getSequences());
+    final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null
+            ? Collections.<SequenceI> emptyList()
+            : ap.av.getSelectionGroup().getSequences());
     buildAnnotationTypesMenus(groupShowAnnotationsMenu,
             groupHideAnnotationsMenu, selectedGroup);
     configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
@@ -257,13 +259,13 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       sequenceMenu.setText(sequence.getName());
       if (seq == ap.av.getAlignment().getSeqrep())
       {
-        makeReferenceSeq.setText(MessageManager
-                .getString("action.unmark_as_reference"));
+        makeReferenceSeq.setText(
+                MessageManager.getString("action.unmark_as_reference"));
       }
       else
       {
-        makeReferenceSeq.setText(MessageManager
-                .getString("action.set_as_reference"));
+        makeReferenceSeq.setText(
+                MessageManager.getString("action.set_as_reference"));
       }
 
       if (!ap.av.getAlignment().isNucleotide())
@@ -290,8 +292,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
                */
               menuItem = new JMenuItem();
               menuItem.setText(MessageManager.formatMessage(
-                      "label.2d_rna_structure_line",
-                      new Object[] { aa.label }));
+                      "label.2d_rna_structure_line", new Object[]
+                      { aa.label }));
               menuItem.addActionListener(new ActionListener()
               {
                 @Override
@@ -318,8 +320,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
               // TODO: make rnastrucF a bit more nice
               menuItem = new JMenuItem();
               menuItem.setText(MessageManager.formatMessage(
-                      "label.2d_rna_sequence_name",
-                      new Object[] { seq.getName() }));
+                      "label.2d_rna_sequence_name", new Object[]
+                      { seq.getName() }));
               menuItem.addActionListener(new ActionListener()
               {
                 @Override
@@ -354,9 +356,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       if (ap.av.getSelectionGroup() != null
               && ap.av.getSelectionGroup().getSize() > 1)
       {
-        menuItem = new JMenuItem(MessageManager.formatMessage(
-                "label.represent_group_with",
-                new Object[] { seq.getName() }));
+        menuItem = new JMenuItem(MessageManager
+                .formatMessage("label.represent_group_with", new Object[]
+                { seq.getName() }));
         menuItem.addActionListener(new ActionListener()
         {
           @Override
@@ -414,12 +416,12 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
         add(menuItem);
       }
-
     }
 
     SequenceGroup sg = ap.av.getSelectionGroup();
-    boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment()
-            .getGroups().contains(sg) : false;
+    boolean isDefinedGroup = (sg != null)
+            ? ap.av.getAlignment().getGroups().contains(sg)
+            : false;
 
     if (sg != null && sg.getSize() > 0)
     {
@@ -428,6 +430,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
       ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
 
+      conservationMenuItem.setEnabled(!sg.isNucleotide());
+
       if (sg.cs != null)
       {
         if (sg.cs.conservationApplied())
@@ -451,7 +455,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         buildGroupURLMenu(sg, groupLinks);
       }
       // Add a 'show all structures' for the current selection
-      Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(), reppdb = new Hashtable<String, PDBEntry>();
+      Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
+
       SequenceI sqass = null;
       for (SequenceI sq : ap.av.getSequenceSelection())
       {
@@ -471,9 +476,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       }
       if (pdbe.size() > 0)
       {
-        final PDBEntry[] pe = pdbe.values().toArray(
-                new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
-                new PDBEntry[reppdb.size()]);
+        final PDBEntry[] pe = pdbe.values()
+                .toArray(new PDBEntry[pdbe.size()]),
+                pr = reppdb.values().toArray(new PDBEntry[reppdb.size()]);
         final JMenuItem gpdbview, rpdbview;
       }
     }
@@ -518,7 +523,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
   void addFeatureLinks(final SequenceI seq, List<String> links)
   {
     JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
-    Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
+    Map<String, List<String>> linkset = new LinkedHashMap<>();
 
     for (String link : links)
     {
@@ -585,9 +590,11 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     showMenu.removeAll();
     hideMenu.removeAll();
 
-    final List<String> all = Arrays.asList(new String[] { MessageManager
-            .getString("label.all") });
-    addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
+    final List<String> all = Arrays
+            .asList(new String[]
+            { MessageManager.getString("label.all") });
+    addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true,
+            true);
     addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
             false);
     showMenu.addSeparator();
@@ -602,8 +609,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
      * the insertion order, which is the order of the annotations on the
      * alignment.
      */
-    Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
-    Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
+    Map<String, List<List<String>>> shownTypes = new LinkedHashMap<>();
+    Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<>();
     AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
             AlignmentAnnotationUtils.asList(annotations), forSequences);
 
@@ -709,12 +716,12 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
     SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
     String[][] idandseqs = GroupUrlLink.formStrings(seqs);
-    Hashtable<String, Object[]> commonDbrefs = new Hashtable<String, Object[]>();
+    Hashtable<String, Object[]> commonDbrefs = new Hashtable<>();
     for (int sq = 0; sq < seqs.length; sq++)
     {
 
-      int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
-              .findPosition(sg.getEndRes());
+      int start = seqs[sq].findPosition(sg.getStartRes()),
+              end = seqs[sq].findPosition(sg.getEndRes());
       // just collect ids from dataset sequence
       // TODO: check if IDs collected from selecton group intersects with the
       // current selection, too
@@ -741,8 +748,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
           if (((String[]) sarray[1])[sq] == null)
           {
-            if (!dbr[d].hasMap()
-                    || (dbr[d].getMap().locateMappedRange(start, end) != null))
+            if (!dbr[d].hasMap() || (dbr[d].getMap()
+                    .locateMappedRange(start, end) != null))
             {
               ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
               ((int[]) sarray[0])[0]++;
@@ -814,9 +821,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         int type = urlLink.getGroupURLType() & 3;
         // first two bits ofurlLink type bitfield are sequenceids and sequences
         // TODO: FUTURE: ensure the groupURL menu structure can be generalised
-        addshowLink(linkMenus[type], label
-                + (((type & 1) == 1) ? ("("
-                        + (usingNames ? "Names" : ltarget) + ")") : ""),
+        addshowLink(linkMenus[type],
+                label + (((type & 1) == 1)
+                        ? ("(" + (usingNames ? "Names" : ltarget) + ")")
+                        : ""),
                 urlLink, urlset);
         addMenu = true;
       }
@@ -838,7 +846,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     }
   }
 
-  private void addshowLinks(JMenu linkMenu, Collection<List<String>> linkset)
+  private void addshowLinks(JMenu linkMenu,
+          Collection<List<String>> linkset)
   {
     for (List<String> linkstrset : linkset)
     {
@@ -859,8 +868,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
   private void addshowLink(JMenu linkMenu, String label, final String url)
   {
     JMenuItem item = new JMenuItem(label);
-    item.setToolTipText(MessageManager.formatMessage(
-            "label.open_url_param", new Object[] { url }));
+    item.setToolTipText(MessageManager.formatMessage("label.open_url_param",
+            new Object[]
+            { url }));
     item.addActionListener(new ActionListener()
     {
       @Override
@@ -897,9 +907,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
           final GroupUrlLink urlgenerator, final Object[] urlstub)
   {
     JMenuItem item = new JMenuItem(label);
-    item.setToolTipText(MessageManager.formatMessage(
-            "label.open_url_seqs_param",
-            new Object[] { urlgenerator.getUrl_prefix(),
+    item.setToolTipText(MessageManager
+            .formatMessage("label.open_url_seqs_param", new Object[]
+            { urlgenerator.getUrl_prefix(),
                 urlgenerator.getNumberInvolved(urlstub) }));
     // TODO: put in info about what is being sent.
     item.addActionListener(new ActionListener()
@@ -947,8 +957,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       }
     });
     sequenceMenu.setText(MessageManager.getString("label.sequence"));
-    sequenceName.setText(MessageManager
-            .getString("label.edit_name_description"));
+    sequenceName.setText(
+            MessageManager.getString("label.edit_name_description"));
     sequenceName.addActionListener(new ActionListener()
     {
       @Override
@@ -957,8 +967,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         sequenceName_actionPerformed();
       }
     });
-    chooseAnnotations.setText(MessageManager
-            .getString("action.choose_annotations"));
+    chooseAnnotations
+            .setText(MessageManager.getString("action.choose_annotations"));
     chooseAnnotations.addActionListener(new ActionListener()
     {
       @Override
@@ -967,8 +977,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         chooseAnnotations_actionPerformed(e);
       }
     });
-    sequenceDetails.setText(MessageManager
-            .getString("label.sequence_details"));
+    sequenceDetails
+            .setText(MessageManager.getString("label.sequence_details"));
     sequenceDetails.addActionListener(new ActionListener()
     {
       @Override
@@ -977,8 +987,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         sequenceDetails_actionPerformed();
       }
     });
-    sequenceSelDetails.setText(MessageManager
-            .getString("label.sequence_details"));
+    sequenceSelDetails
+            .setText(MessageManager.getString("label.sequence_details"));
     sequenceSelDetails.addActionListener(new ActionListener()
     {
       @Override
@@ -998,8 +1008,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         unGroupMenuItem_actionPerformed();
       }
     });
-    createGroupMenuItem.setText(MessageManager
-            .getString("action.create_group"));
+    createGroupMenuItem
+            .setText(MessageManager.getString("action.create_group"));
     createGroupMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -1047,8 +1057,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         showColourText_actionPerformed();
       }
     });
-    displayNonconserved.setText(MessageManager
-            .getString("label.show_non_conserved"));
+    displayNonconserved
+            .setText(MessageManager.getString("label.show_non_conserved"));
     displayNonconserved.setState(true);
     displayNonconserved.addActionListener(new ActionListener()
     {
@@ -1104,18 +1114,18 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         changeCase(e);
       }
     });
-    outputMenu.setText(MessageManager.getString("label.out_to_textbox")
-            + "...");
-    seqShowAnnotationsMenu.setText(MessageManager
-            .getString("label.show_annotations"));
-    seqHideAnnotationsMenu.setText(MessageManager
-            .getString("label.hide_annotations"));
-    groupShowAnnotationsMenu.setText(MessageManager
-            .getString("label.show_annotations"));
-    groupHideAnnotationsMenu.setText(MessageManager
-            .getString("label.hide_annotations"));
-    sequenceFeature.setText(MessageManager
-            .getString("label.create_sequence_feature"));
+    outputMenu.setText(
+            MessageManager.getString("label.out_to_textbox") + "...");
+    seqShowAnnotationsMenu
+            .setText(MessageManager.getString("label.show_annotations"));
+    seqHideAnnotationsMenu
+            .setText(MessageManager.getString("label.hide_annotations"));
+    groupShowAnnotationsMenu
+            .setText(MessageManager.getString("label.show_annotations"));
+    groupHideAnnotationsMenu
+            .setText(MessageManager.getString("label.hide_annotations"));
+    sequenceFeature.setText(
+            MessageManager.getString("label.create_sequence_feature"));
     sequenceFeature.addActionListener(new ActionListener()
     {
       @Override
@@ -1125,8 +1135,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       }
     });
     jMenu1.setText(MessageManager.getString("label.group"));
-    pdbStructureDialog.setText(MessageManager
-            .getString("label.show_pdbstruct_dialog"));
+    pdbStructureDialog.setText(
+            MessageManager.getString("label.show_pdbstruct_dialog"));
     pdbStructureDialog.addActionListener(new ActionListener()
     {
       @Override
@@ -1141,12 +1151,12 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       }
     });
 
-    rnaStructureMenu.setText(MessageManager
-            .getString("label.view_rna_structure"));
+    rnaStructureMenu
+            .setText(MessageManager.getString("label.view_rna_structure"));
 
     // colStructureMenu.setText("Colour By Structure");
-    editSequence.setText(MessageManager.getString("label.edit_sequence")
-            + "...");
+    editSequence.setText(
+            MessageManager.getString("label.edit_sequence") + "...");
     editSequence.addActionListener(new ActionListener()
     {
       @Override
@@ -1155,8 +1165,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         editSequence_actionPerformed(actionEvent);
       }
     });
-    makeReferenceSeq.setText(MessageManager
-            .getString("label.mark_as_representative"));
+    makeReferenceSeq.setText(
+            MessageManager.getString("label.mark_as_representative"));
     makeReferenceSeq.addActionListener(new ActionListener()
     {
 
@@ -1167,8 +1177,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
       }
     });
-    hideInsertions.setText(MessageManager
-            .getString("label.hide_insertions"));
+    hideInsertions
+            .setText(MessageManager.getString("label.hide_insertions"));
     hideInsertions.addActionListener(new ActionListener()
     {
 
@@ -1178,12 +1188,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         hideInsertions_actionPerformed(e);
       }
     });
-    /*
-     * annotationMenuItem.setText("By Annotation");
-     * annotationMenuItem.addActionListener(new ActionListener() { public void
-     * actionPerformed(ActionEvent actionEvent) {
-     * annotationMenuItem_actionPerformed(actionEvent); } });
-     */
+
     groupMenu.add(sequenceSelDetails);
     add(groupMenu);
     add(sequenceMenu);
@@ -1237,7 +1242,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     jMenu1.add(outline);
     jMenu1.add(displayNonconserved);
   }
-  
+
   /**
    * Constructs the entries for the colour menu
    */
@@ -1254,8 +1259,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       }
     });
 
-    abovePIDColour.setText(MessageManager
-            .getString("label.above_identity_threshold"));
+    abovePIDColour.setText(
+            MessageManager.getString("label.above_identity_threshold"));
     abovePIDColour.addActionListener(new ActionListener()
     {
       @Override
@@ -1265,8 +1270,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       }
     });
 
-    modifyPID.setText(MessageManager
-            .getString("label.modify_identity_threshold"));
+    modifyPID.setText(
+            MessageManager.getString("label.modify_identity_threshold"));
     modifyPID.addActionListener(new ActionListener()
     {
       @Override
@@ -1276,15 +1281,15 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       }
     });
 
-    conservationMenuItem.setText(MessageManager
-            .getString("action.by_conservation"));
+    conservationMenuItem
+            .setText(MessageManager.getString("action.by_conservation"));
     conservationMenuItem.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        conservationMenuItem_actionPerformed(conservationMenuItem
-                .isSelected());
+        conservationMenuItem_actionPerformed(
+                conservationMenuItem.isSelected());
       }
     });
 
@@ -1345,8 +1350,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
       // .getName());
       // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
-      SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
-              .getName());
+      SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
       SliderPanel.showPIDSlider();
     }
   }
@@ -1373,11 +1377,11 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
      * Temporary store to hold distinct calcId / type pairs for the tooltip.
      * Using TreeMap means calcIds are shown in alphabetical order.
      */
-    SortedMap<String, String> tipEntries = new TreeMap<String, String>();
-    final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
+    SortedMap<String, String> tipEntries = new TreeMap<>();
+    final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
     AlignmentI al = this.ap.av.getAlignment();
-    AlignmentUtils.findAddableReferenceAnnotations(forSequences,
-            tipEntries, candidates, al);
+    AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
+            candidates, al);
     if (!candidates.isEmpty())
     {
       StringBuilder tooltip = new StringBuilder(64);
@@ -1449,16 +1453,59 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
   protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
   {
-    if (sequence != null)
+
+    HiddenColumns hidden = new HiddenColumns();
+    BitSet inserts = new BitSet(), mask = new BitSet();
+
+    // set mask to preserve existing hidden columns outside selected group
+    if (ap.av.hasHiddenColumns())
+    {
+      ap.av.getAlignment().getHiddenColumns().markHiddenRegions(mask);
+    }
+
+    boolean markedPopup = false;
+    // mark inserts in current selection
+    if (ap.av.getSelectionGroup() != null)
     {
-      ColumnSelection cs = ap.av.getColumnSelection();
-      if (cs == null)
+      // mark just the columns in the selection group to be hidden
+      inserts.set(ap.av.getSelectionGroup().getStartRes(),
+              ap.av.getSelectionGroup().getEndRes() + 1);
+
+      // and clear that part of the mask
+      mask.andNot(inserts);
+
+      // now clear columns without gaps
+      for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
       {
-        cs = new ColumnSelection();
+        if (sq == sequence)
+        {
+          markedPopup = true;
+        }
+        inserts.and(sq.getInsertionsAsBits());
       }
-      cs.hideInsertionsFor(sequence);
-      ap.av.setColumnSelection(cs);
     }
+    else
+    {
+      // initially, mark all columns to be hidden
+      inserts.set(0, ap.av.getAlignment().getWidth());
+
+      // and clear out old hidden regions completely
+      mask.clear();
+    }
+
+    // now mark for sequence under popup if we haven't already done it
+    if (!markedPopup && sequence != null)
+    {
+      inserts.and(sequence.getInsertionsAsBits());
+    }
+
+    // finally, preserve hidden regions outside selection
+    inserts.or(mask);
+
+    // and set hidden columns accordingly
+    hidden.hideMarkedBits(inserts);
+
+    ap.av.getAlignment().setHiddenColumns(hidden);
     refresh();
   }
 
@@ -1478,30 +1525,27 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     StringBuilder contents = new StringBuilder(128);
     for (SequenceI seq : sequences)
     {
-      contents.append("<p><h2>"
-              + MessageManager
-                      .formatMessage(
-                              "label.create_sequence_details_report_annotation_for",
-                              new Object[] { seq.getDisplayId(true) })
-              + "</h2></p><p>");
-      new SequenceAnnotationReport(null)
-              .createSequenceAnnotationReport(
-                      contents,
-                      seq,
-                      true,
-                      true,
-                      (ap.getSeqPanel().seqCanvas.fr != null) ? ap
-                              .getSeqPanel().seqCanvas.fr.getMinMax()
-                              : null);
+      contents.append("<p><h2>" + MessageManager.formatMessage(
+              "label.create_sequence_details_report_annotation_for",
+              new Object[]
+              { seq.getDisplayId(true) }) + "</h2></p><p>");
+      new SequenceAnnotationReport(null).createSequenceAnnotationReport(
+              contents, seq, true, true,
+              (ap.getSeqPanel().seqCanvas.fr != null)
+                      ? ap.getSeqPanel().seqCanvas.fr.getMinMax()
+                      : null);
       contents.append("</p>");
     }
     cap.setText("<html>" + contents.toString() + "</html>");
 
-    Desktop.addInternalFrame(cap, MessageManager.formatMessage(
-            "label.sequence_details_for",
-            (sequences.length == 1 ? new Object[] { sequences[0]
-                    .getDisplayId(true) } : new Object[] { MessageManager
-                    .getString("label.selection") })), 500, 400);
+    Desktop.addInternalFrame(cap,
+            MessageManager.formatMessage("label.sequence_details_for",
+                    (sequences.length == 1 ? new Object[]
+                    { sequences[0].getDisplayId(true) }
+                            : new Object[]
+                            { MessageManager
+                                    .getString("label.selection") })),
+            500, 400);
 
   }
 
@@ -1517,7 +1561,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
   void refresh()
   {
     ap.updateAnnotation();
-    ap.paintAlignment(true);
+    // removed paintAlignment(true) here:
+    // updateAnnotation calls paintAlignment already, so don't need to call
+    // again
 
     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
   }
@@ -1534,7 +1580,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
    * @param e
    *          DOCUMENT ME!
    */
-  protected void abovePIDColour_actionPerformed(boolean selected)
+  public void abovePIDColour_actionPerformed(boolean selected)
   {
     SequenceGroup sg = getGroup();
     if (sg.cs == null)
@@ -1549,8 +1595,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
               sg.getStartRes(), sg.getEndRes() + 1));
 
       int threshold = SliderPanel.setPIDSliderSource(ap,
-              sg.getGroupColourScheme(), getGroup()
-              .getName());
+              sg.getGroupColourScheme(), getGroup().getName());
 
       sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
 
@@ -1585,7 +1630,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
    * @param e
    *          DOCUMENT ME!
    */
-  protected void conservationMenuItem_actionPerformed(boolean selected)
+  public void conservationMenuItem_actionPerformed(boolean selected)
   {
     SequenceGroup sg = getGroup();
     if (sg.cs == null)
@@ -1596,9 +1641,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     if (selected)
     {
       // JBPNote: Conservation name shouldn't be i18n translated
-      Conservation c = new Conservation("Group", sg.getSequences(ap.av
-              .getHiddenRepSequences()), sg.getStartRes(),
-              sg.getEndRes() + 1);
+      Conservation c = new Conservation("Group",
+              sg.getSequences(ap.av.getHiddenRepSequences()),
+              sg.getStartRes(), sg.getEndRes() + 1);
 
       c.calculate();
       c.verdict(false, ap.av.getConsPercGaps());
@@ -1619,24 +1664,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     refresh();
   }
 
-  public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
-  {
-    SequenceGroup sg = getGroup();
-    if (sg == null)
-    {
-      return;
-    }
-
-    AnnotationColourGradient acg = new AnnotationColourGradient(
-            sequence.getAnnotation()[0], null,
-            AnnotationColourGradient.NO_THRESHOLD);
-
-    acg.setPredefinedColours(true);
-    sg.setColourScheme(acg);
-
-    refresh();
-  }
-
   /**
    * DOCUMENT ME!
    * 
@@ -1648,8 +1675,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
     SequenceGroup sg = getGroup();
     EditNameDialog dialog = new EditNameDialog(sg.getName(),
-            sg.getDescription(), "       "
-                    + MessageManager.getString("label.group_name") + " ",
+            sg.getDescription(),
+            "       " + MessageManager.getString("label.group_name") + " ",
             MessageManager.getString("label.group_description") + " ",
             MessageManager.getString("label.edit_group_name_description"),
             ap.alignFrame);
@@ -1694,8 +1721,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
             "       " + MessageManager.getString("label.sequence_name")
                     + " ",
             MessageManager.getString("label.sequence_description") + " ",
-            MessageManager
-                    .getString("label.edit_sequence_name_description"),
+            MessageManager.getString(
+                    "label.edit_sequence_name_description"),
             ap.alignFrame);
 
     if (!dialog.accept)
@@ -1707,24 +1734,22 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     {
       if (dialog.getName().indexOf(" ") > -1)
       {
-        JvOptionPane
-                .showMessageDialog(
-                        ap,
-                        MessageManager
-                                .getString("label.spaces_converted_to_backslashes"),
-                        MessageManager
-                                .getString("label.no_spaces_allowed_sequence_name"),
-                        JvOptionPane.WARNING_MESSAGE);
+        JvOptionPane.showMessageDialog(ap,
+                MessageManager
+                        .getString("label.spaces_converted_to_backslashes"),
+                MessageManager
+                        .getString("label.no_spaces_allowed_sequence_name"),
+                JvOptionPane.WARNING_MESSAGE);
       }
 
       sequence.setName(dialog.getName().replace(' ', '_'));
-      ap.paintAlignment(false);
+      ap.paintAlignment(false, false);
     }
 
     sequence.setDescription(dialog.getDescription());
 
-    ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
-            .getSequences());
+    ap.av.firePropertyChange("alignment", null,
+            ap.av.getAlignment().getSequences());
 
   }
 
@@ -1872,8 +1897,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
       ap.alignFrame.addHistoryItem(caseCommand);
 
-      ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
-              .getSequences());
+      ap.av.firePropertyChange("alignment", null,
+              ap.av.getAlignment().getSequences());
 
     }
   }
@@ -1882,9 +1907,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     cap.setForInput(null);
-    Desktop.addInternalFrame(cap, MessageManager.formatMessage(
-            "label.alignment_output_command",
-            new Object[] { e.getActionCommand() }), 600, 500);
+    Desktop.addInternalFrame(cap, MessageManager
+            .formatMessage("label.alignment_output_command", new Object[]
+            { e.getActionCommand() }), 600, 500);
 
     String[] omitHidden = null;
 
@@ -1892,8 +1917,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     // or we simply trust the user wants
     // wysiwig behaviour
 
-    FileFormatI fileFormat = FileFormats.getInstance().forName(e.getActionCommand());
-    cap.setText(new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
+    FileFormatI fileFormat = FileFormats.getInstance()
+            .forName(e.getActionCommand());
+    cap.setText(
+            new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
   }
 
   public void sequenceFeature_actionPerformed()
@@ -1904,33 +1931,37 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       return;
     }
 
-    int rsize = 0, gSize = sg.getSize();
-    SequenceI[] rseqs, seqs = new SequenceI[gSize];
-    SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
+    List<SequenceI> seqs = new ArrayList<>();
+    List<SequenceFeature> features = new ArrayList<>();
 
+    /*
+     * assemble dataset sequences, and template new sequence features,
+     * for the amend features dialog
+     */
+    int gSize = sg.getSize();
     for (int i = 0; i < gSize; i++)
     {
       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
       int end = sg.findEndRes(sg.getSequenceAt(i));
       if (start <= end)
       {
-        seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
-        features[rsize] = new SequenceFeature(null, null, null, start, end,
-                "Jalview");
-        rsize++;
+        seqs.add(sg.getSequenceAt(i).getDatasetSequence());
+        features.add(new SequenceFeature(null, null, start, end, null));
       }
     }
-    rseqs = new SequenceI[rsize];
-    tfeatures = new SequenceFeature[rsize];
-    System.arraycopy(seqs, 0, rseqs, 0, rsize);
-    System.arraycopy(features, 0, tfeatures, 0, rsize);
-    features = tfeatures;
-    seqs = rseqs;
-    if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
-            features, true, ap))
-    {
-      ap.alignFrame.setShowSeqFeatures(true);
-      ap.highlightSearchResults(null);
+
+    /*
+     * an entirely gapped region will generate empty lists of sequence / features
+     */
+    if (!seqs.isEmpty())
+    {
+      if (ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+              .amendFeatures(seqs, features, true, ap))
+      {
+        ap.alignFrame.setShowSeqFeatures(true);
+        ap.av.setSearchResults(null); // clear highlighting
+        ap.repaint(); // draw new/amended features
+      }
     }
   }
 
@@ -1975,8 +2006,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
       EditNameDialog dialog = new EditNameDialog(
               sequence.getSequenceAsString(sg.getStartRes(),
-                      sg.getEndRes() + 1), null,
-              MessageManager.getString("label.edit_sequence"), null,
+                      sg.getEndRes() + 1),
+              null, MessageManager.getString("label.edit_sequence"), null,
               MessageManager.getString("label.edit_sequence"),
               ap.alignFrame);
 
@@ -1984,15 +2015,15 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       {
         EditCommand editCommand = new EditCommand(
                 MessageManager.getString("label.edit_sequences"),
-                Action.REPLACE, dialog.getName().replace(' ',
-                        ap.av.getGapCharacter()),
+                Action.REPLACE,
+                dialog.getName().replace(' ', ap.av.getGapCharacter()),
                 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
                 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
 
         ap.alignFrame.addHistoryItem(editCommand);
 
-        ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
-                .getSequences());
+        ap.av.firePropertyChange("alignment", null,
+                ap.av.getAlignment().getSequences());
       }
     }
   }
@@ -2007,28 +2038,19 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
   public void changeColour_actionPerformed(String colourSchemeName)
   {
     SequenceGroup sg = getGroup();
-    if (ResidueColourScheme.USER_DEFINED.equals(colourSchemeName))
-    {
-      /*
-       * open a panel to load or configure a user-defined colour scheme
-       */
-      new UserDefinedColours(ap, sg);
-    }
-    else
+    /*
+     * switch to the chosen colour scheme (or null for None)
+     */
+    ColourSchemeI colourScheme = ColourSchemes.getInstance()
+            .getColourScheme(colourSchemeName, sg,
+                    ap.av.getHiddenRepSequences());
+    sg.setColourScheme(colourScheme);
+    if (colourScheme instanceof Blosum62ColourScheme
+            || colourScheme instanceof PIDColourScheme)
     {
-      /*
-       * switch to the chosen colour scheme (or null for None)
-       */
-      ColourSchemeI colourScheme = ColourSchemes.getInstance().getColourScheme(
-              colourSchemeName, sg, ap.av.getHiddenRepSequences());
-      sg.setColourScheme(colourScheme);
-      if (colourScheme instanceof Blosum62ColourScheme
-              || colourScheme instanceof PIDColourScheme)
-      {
-        sg.cs.setConsensus(AAFrequency.calculate(
-                sg.getSequences(ap.av.getHiddenRepSequences()),
-                sg.getStartRes(), sg.getEndRes() + 1));
-      }
+      sg.cs.setConsensus(AAFrequency.calculate(
+              sg.getSequences(ap.av.getHiddenRepSequences()),
+              sg.getStartRes(), sg.getEndRes() + 1));
     }
 
     refresh();