JAL-2629 add ability to select HMMs

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 339a764..96612f9 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1318,6 +1318,7 @@ label.warning_hidden = Warning: {0} {1} is currently hidden
 label.auto_align_seqs = Automatically Align New Sequences
 label.hmmalign = Align Sequences to HMM
 label.hmmbuild = Build HMM from Alignment
+label.group_hmmbuild = Build HMM from Group
 label.hmmsearch = Search for Related Sequences
 label.change_hmmer_location = Set HMMER Installation Location
 warn.null_hmm = Please ensure the alignment contains a hidden Markov model.
@@ -1325,3 +1326,6 @@ label.ignore_below_background_frequency = Ignore Below Background Frequency
 label.information_description = Information content, measured in bits
 label.enter_location = Please enter the path of your HMMER binaries folder.
 label.invalid_hmmer_folder = The folder that you selected does not contain the necessary HMMER binaries.
+warn.no_selected_hmm = Please select a hidden Markov model sequence.
+label.select_hmm = Select HMM
+warn.no_sequence_data = No sequence data found.

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 0ebd271..e75798c 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -33,12 +33,14 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.ColourMenuHelper.ColourChangeListener;
+import jalview.hmmer.HMMBuildThread;
 import jalview.io.FileFormatI;
 import jalview.io.FileFormats;
 import jalview.io.FormatAdapter;
@@ -157,6 +159,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
   JMenuItem sequenceFeature = new JMenuItem();
 
+  JMenuItem hmmBuildGroup = new JMenuItem();
+
   JMenuItem textColour = new JMenuItem();
 
   JMenu jMenu1 = new JMenu();
@@ -179,7 +183,8 @@ 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);
   }
@@ -224,8 +229,8 @@ 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,
@@ -234,9 +239,9 @@ 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,
@@ -256,13 +261,13 @@ 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())
@@ -290,7 +295,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
               menuItem = new JMenuItem();
               menuItem.setText(MessageManager.formatMessage(
                       "label.2d_rna_structure_line",
-                      new Object[] { aa.label }));
+                      new Object[]
+              { aa.label }));
               menuItem.addActionListener(new ActionListener()
               {
                 @Override
@@ -318,7 +324,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
               menuItem = new JMenuItem();
               menuItem.setText(MessageManager.formatMessage(
                       "label.2d_rna_sequence_name",
-                      new Object[] { seq.getName() }));
+                      new Object[]
+              { seq.getName() }));
               menuItem.addActionListener(new ActionListener()
               {
                 @Override
@@ -350,12 +357,29 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       });
       add(menuItem);
 
+      if (sequence.isHMMConsensusSequence())
+      {
+        JMenuItem selectHMM = new JCheckBoxMenuItem();
+        selectHMM.setText(MessageManager.getString("label.select_hmm"));
+        selectHMM.addActionListener(new ActionListener()
+        {
+
+          @Override
+          public void actionPerformed(ActionEvent e)
+          {
+            selectHMM_actionPerformed(e);
+          }
+        });
+        add(selectHMM);
+      }
+
       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
@@ -416,8 +440,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     }
 
     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)
     {
@@ -451,7 +475,8 @@ 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<>(), reppdb = new Hashtable<>();
+      Hashtable<String, PDBEntry> pdbe = new Hashtable<>(),
+              reppdb = new Hashtable<>();
       SequenceI sqass = null;
       for (SequenceI sq : ap.av.getSequenceSelection())
       {
@@ -471,9 +496,9 @@ 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;
       }
     }
@@ -585,9 +610,11 @@ 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();
@@ -713,8 +740,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     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 +768,8 @@ 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 +841,8 @@ 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 +864,8 @@ 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 +886,9 @@ 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
@@ -897,10 +925,11 @@ 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(),
-                urlgenerator.getNumberInvolved(urlstub) }));
+    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 +976,8 @@ 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 +986,8 @@ 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 +996,8 @@ 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 +1006,8 @@ 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 +1027,8 @@ 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 +1076,8 @@ 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 +1133,18 @@ 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
@@ -1124,9 +1153,18 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         sequenceFeature_actionPerformed();
       }
     });
+    hmmBuildGroup.setText(MessageManager.getString("label.group_hmmbuild"));
+    hmmBuildGroup.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmBuildGroup_actionPerformed();
+      }
+    });
     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 +1179,12 @@ 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 +1193,8 @@ 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 +1205,8 @@ 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()
     {
 
@@ -1232,7 +1270,20 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     jMenu1.add(outline);
     jMenu1.add(displayNonconserved);
   }
-  
+
+  protected void hmmBuildGroup_actionPerformed()
+  {
+    new Thread(new HMMBuildThread(ap.alignFrame)).start();
+    ap.repaint();
+
+  }
+
+  protected void selectHMM_actionPerformed(ActionEvent e)
+  {
+    HiddenMarkovModel hmm = ap.av.getSequenceSelection()[0].getHMM();
+    ap.av.setSelectedHMM(hmm);
+  }
+
   /**
    * Constructs the entries for the colour menu
    */
@@ -1249,8 +1300,8 @@ 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
@@ -1260,8 +1311,8 @@ 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
@@ -1271,15 +1322,15 @@ 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());
       }
     });
 
@@ -1340,8 +1391,7 @@ 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();
     }
   }
@@ -1371,8 +1421,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     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);
@@ -1482,19 +1532,15 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     for (SequenceI seq : sequences)
     {
       contents.append("<p><h2>"
-              + MessageManager
-                      .formatMessage(
-                              "label.create_sequence_details_report_annotation_for",
-                              new Object[] { seq.getDisplayId(true) })
+              + 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()
+              .createSequenceAnnotationReport(contents, seq, true, true,
+                      (ap.getSeqPanel().seqCanvas.fr != null)
+                              ? ap.getSeqPanel().seqCanvas.fr.getMinMax()
                               : null);
       contents.append("</p>");
     }
@@ -1502,9 +1548,11 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
     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);
+            (sequences.length == 1
+                    ? new Object[]
+                    { sequences[0].getDisplayId(true) }
+                    : new Object[]
+            { MessageManager.getString("label.selection") })), 500, 400);
 
   }
 
@@ -1552,8 +1600,7 @@ 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());
 
@@ -1599,9 +1646,9 @@ 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());
@@ -1633,8 +1680,8 @@ 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);
@@ -1692,14 +1739,12 @@ 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(' ', '_'));
@@ -1708,8 +1753,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
     sequence.setDescription(dialog.getDescription());
 
-    ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
-            .getSequences());
+    ap.av.firePropertyChange("alignment", null,
+            ap.av.getAlignment().getSequences());
 
   }
 
@@ -1857,8 +1902,8 @@ 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());
 
     }
   }
@@ -1867,9 +1912,10 @@ 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;
 
@@ -1877,8 +1923,10 @@ 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()
@@ -1904,7 +1952,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       if (start <= end)
       {
         seqs.add(sg.getSequenceAt(i).getDatasetSequence());
-        features.add(new SequenceFeature(null, null, null, start, end, null));
+        features.add(
+                new SequenceFeature(null, null, null, start, end, null));
       }
     }
 
@@ -1957,8 +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);
 
@@ -1966,15 +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());
       }
     }
   }

diff --git a/src/jalview/hmmer/HMMAlignThread.java b/src/jalview/hmmer/HMMAlignThread.java
index 2674c8c..49fc49d 100644 (file)
--- a/src/jalview/hmmer/HMMAlignThread.java
+++ b/src/jalview/hmmer/HMMAlignThread.java
@@ -24,6 +24,7 @@ import java.util.List;
 import java.util.Map;
 
 import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
 
 public class HMMAlignThread implements Runnable
 {
@@ -71,7 +72,6 @@ public class HMMAlignThread implements Runnable
     {
       dataset = alignment.getDataset();
     }
-    hmm = alignment.getSequenceAt(0).getHMM();
     newFrame = createNewFrame;
     featureSettings = af.getFeatureRenderer().getSettings();
   }
@@ -79,6 +79,16 @@ public class HMMAlignThread implements Runnable
   @Override
   public void run()
   {
+    if (af.getViewport().getSelectedHMM() == null)
+    {
+      JOptionPane.showMessageDialog(af,
+              MessageManager.getString("warn.no_selected_hmm"));
+      return;
+    }
+    else
+    {
+      hmm = af.getViewport().getSelectedHMM();
+    }
     barID = System.currentTimeMillis();
     af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
             barID);
@@ -212,16 +222,6 @@ public class HMMAlignThread implements Runnable
     inputTemp.delete();
   }
 
-  private void addSeqs(AlignFrame alignFrame, Map<Integer, SequenceI> map)
-  {
-    for (Map.Entry<Integer, SequenceI> entry : map.entrySet())
-    {
-      SequenceI seq = entry.getValue();
-      Integer pos = entry.getKey();
-      cmds.addHMMConsensusSequence(alignFrame, seq, pos);
-    }
-  }
-
   private void prepareAlignment()
   {
     // hmmSeqs = alignment.getHMMConsensusSequences(true);

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index ee129db..aa3a22d 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -36,6 +36,7 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.ProfileI;
 import jalview.datamodel.Profiles;
@@ -99,6 +100,8 @@ public abstract class AlignmentViewport
 
   protected Deque<CommandI> redoList = new ArrayDeque<>();
 
+  HiddenMarkovModel selectedHMM;
+
   /**
    * alignment displayed in the viewport. Please use get/setter
    */
@@ -928,6 +931,7 @@ public abstract class AlignmentViewport
   /**
    * trigger update of information annotation
    */
+  @Override
   public void updateInformation(final AlignmentViewPanel ap)
   {
     if (calculator
@@ -1970,12 +1974,11 @@ public abstract class AlignmentViewport
     }
     updateInformation(ap);
 
-    Map<Integer, SequenceI> hmmSequences;
+    List<SequenceI> hmmSequences;
     hmmSequences = alignment.getHMMConsensusSequences(false);
 
-    for (Map.Entry<Integer, SequenceI> entry : hmmSequences.entrySet())
+    for (SequenceI seq : hmmSequences)
     {
-      SequenceI seq = entry.getValue();
       seq.updateHMMMapping();
     }
 
@@ -2111,24 +2114,31 @@ public abstract class AlignmentViewport
     }
   }
 
+  @Override
   public void initInformation()
   {
-    for (SequenceI seq : alignment.getHMMConsensusSequences())
-    {
-      AlignmentAnnotation information;
-      information = new AlignmentAnnotation(seq.getName(),
-              MessageManager.getString("label.information_description"),
-              new Annotation[1], 0f, 6.52f, AlignmentAnnotation.BAR_GRAPH);
-      information.hasText = true;
-      information.autoCalculated = true;
-      information.hasText = true;
-      information.autoCalculated = false;
-      information.sequenceRef = seq;
-      information.setCalcId("HMM annotation");
-      this.information.add(information);
-      hinformation.add(new Profiles(new ProfileI[1]));
-      alignment.addAnnotation(information);
-      seq.updateHMMMapping();
+    for (SequenceI seq : alignment.getHMMConsensusSequences(false))
+    {
+      if (!seq.hasHMMAnnotation())
+      {
+        AlignmentAnnotation information;
+        information = new AlignmentAnnotation(seq.getName(),
+                MessageManager.getString("label.information_description"),
+                new Annotation[1], 0f, 6.52f,
+                AlignmentAnnotation.BAR_GRAPH);
+        information.hasText = true;
+        information.autoCalculated = true;
+        information.hasText = true;
+        information.autoCalculated = false;
+        information.sequenceRef = seq;
+        information.setCalcId("HMM annotation");
+        this.information.add(information);
+        hinformation.add(new Profiles(new ProfileI[1]));
+        alignment.addAnnotation(information);
+        seq.updateHMMMapping();
+        seq.setHasInfo(true);
+        seq.addAlignmentAnnotation(information);
+      }
     }
 
   }
@@ -3042,4 +3052,24 @@ public abstract class AlignmentViewport
     return searchResults;
   }
 
+  /**
+   * Gets the selected hidden Markov model
+   * 
+   * @return
+   */
+  public HiddenMarkovModel getSelectedHMM()
+  {
+    return selectedHMM;
+  }
+
+  /**
+   * Sets the selected hidden Markov model
+   * 
+   * @param selectedHMM
+   */
+  public void setSelectedHMM(HiddenMarkovModel selectedHMM)
+  {
+    this.selectedHMM = selectedHMM;
+  }
+
 }