X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppVarna.java;h=37428642a15ab52a9283fef6fd9c2317032b88d0;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=da6c6e5325b9b48941cc31c903407a5a3e249f64;hpb=3e087813771dee914b78a955bf66ca4803e89797;p=jalview.git

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index da6c6e5..3742864 100644
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -1,157 +1,278 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
-import java.util.*;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-import java.awt.*;
-
-import javax.swing.*;
-import javax.swing.event.*;
-
-import java.awt.event.*;
-import java.io.*;
-
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.api.SequenceStructureBinding;
-import jalview.bin.Cache;
-import jalview.datamodel.*;
-import jalview.gui.ViewSelectionMenu.ViewSetProvider;
-import jalview.structure.*;
-import jalview.io.*;
-import jalview.schemes.*;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.RnaViewerModel;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.ext.varna.RnaModel;
+import jalview.structure.SecondaryStructureListener;
+import jalview.structure.SelectionListener;
+import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
 import jalview.util.ShiftList;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.util.Collection;
+import java.util.Hashtable;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JSplitPane;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
 import fr.orsay.lri.varna.VARNAPanel;
 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
-import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;
 import fr.orsay.lri.varna.interfaces.InterfaceVARNASelectionListener;
 import fr.orsay.lri.varna.models.BaseList;
-import fr.orsay.lri.varna.models.VARNAConfig;
+import fr.orsay.lri.varna.models.FullBackup;
 import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation;
 import fr.orsay.lri.varna.models.rna.ModeleBase;
-import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide;
 import fr.orsay.lri.varna.models.rna.RNA;
 
-public class AppVarna extends JInternalFrame implements
-        InterfaceVARNAListener, SelectionListener,
-        SecondaryStructureListener// implements
-                                  // Runnable,SequenceStructureBinding,
-                                  // ViewSetProvider
-        , InterfaceVARNASelectionListener, VamsasSource
-
+public class AppVarna extends JInternalFrame implements SelectionListener,
+        SecondaryStructureListener, InterfaceVARNASelectionListener,
+        VamsasSource
 {
-  AppVarnaBinding vab;
+  private static final byte[] PAIRS = new byte[] { '(', ')', '[', ']', '{',
+      '}', '<', '>' };
 
-  VARNAPanel varnaPanel;
+  private AppVarnaBinding vab;
 
-  public String name;
+  private AlignmentPanel ap;
 
-  public StructureSelectionManager ssm;
+  private String viewId;
+
+  private StructureSelectionManager ssm;
 
   /*
-   * public AppVarna(){ vab = new AppVarnaBinding(); initVarna(); }
+   * Lookup for sequence and annotation mapped to each RNA in the viewer. Using
+   * a linked hashmap means that order is preserved when saved to the project.
    */
+  private Map<RNA, RnaModel> models = new LinkedHashMap<RNA, RnaModel>();
+
+  private Map<RNA, ShiftList> offsets = new Hashtable<RNA, ShiftList>();
+
+  private Map<RNA, ShiftList> offsetsInv = new Hashtable<RNA, ShiftList>();
+
+  private JSplitPane split;
+
+  private VarnaHighlighter mouseOverHighlighter = new VarnaHighlighter();
 
-  AlignmentPanel ap;
+  private VarnaHighlighter selectionHighlighter = new VarnaHighlighter();
 
-  public AppVarna(String sname, SequenceI seq, String strucseq, String struc,
-          String name, AlignmentPanel ap)
+  private class VarnaHighlighter
   {
-    this.ap = ap;
-    ArrayList<RNA> rnaList = new ArrayList<RNA>();
-    RNA rna1 = new RNA(name);
-    try
+    private HighlightRegionAnnotation _lastHighlight;
+
+    private RNA _lastRNAhighlighted = null;
+
+    public VarnaHighlighter()
     {
-      rna1.setRNA(strucseq, replaceOddGaps(struc));
-    } catch (ExceptionUnmatchedClosingParentheses e2)
+
+    }
+
+    /**
+     * Constructor when restoring from Varna session, including any highlight
+     * state
+     * 
+     * @param rna
+     */
+    public VarnaHighlighter(RNA rna)
     {
-      e2.printStackTrace();
-    } catch (ExceptionFileFormatOrSyntax e3)
+      // TODO nice try but doesn't work; do we need a highlighter per model?
+      _lastRNAhighlighted = rna;
+      List<HighlightRegionAnnotation> highlights = rna.getHighlightRegion();
+      if (highlights != null && !highlights.isEmpty())
+      {
+        _lastHighlight = highlights.get(0);
+      }
+    }
+
+    public void highlightRegion(RNA rna, int start, int end)
     {
-      e3.printStackTrace();
+      clearLastSelection();
+      HighlightRegionAnnotation highlight = new HighlightRegionAnnotation(
+              rna.getBasesBetween(start, end));
+      rna.addHighlightRegion(highlight);
+      _lastHighlight = highlight;
+      _lastRNAhighlighted = rna;
+    }
+
+    public HighlightRegionAnnotation getLastHighlight()
+    {
+      return _lastHighlight;
+    }
+
+    /**
+     * Clears all structure selection and refreshes the display
+     */
+    public void clearSelection()
+    {
+      if (_lastRNAhighlighted != null)
+      {
+        _lastRNAhighlighted.getHighlightRegion().clear();
+        vab.updateSelectedRNA(_lastRNAhighlighted);
+        _lastRNAhighlighted = null;
+        _lastHighlight = null;
+      }
     }
-    RNA trim = trimRNA(rna1, "trimmed "+sname);
-    rnaList.add(trim);
-    rnaList.add(rna1);
-    rnas.put(seq, rna1);
-    rnas.put(seq, trim);
-    rna1.setName(sname+" (with gaps)");
-
-    {
-      seqs.put(trim, seq);
-      seqs.put(rna1, seq);
-
-      /**
-       * if (false || seq.getStart()!=1) { for (RNA rshift:rnaList) { ShiftList
-       * shift=offsets.get(rshift); if (shift==null) { offsets.put(rshift,
-       * shift=new ShiftList());} shift.addShift(1, seq.getStart()-1);
-       * offsetsInv.put(rshift, shift.getInverse()); } }
-       **/
+
+    /**
+     * Clear the last structure selection
+     */
+    public void clearLastSelection()
+    {
+      if (_lastRNAhighlighted != null)
+      {
+        _lastRNAhighlighted.removeHighlightRegion(_lastHighlight);
+        _lastRNAhighlighted = null;
+        _lastHighlight = null;
+      }
     }
-    vab = new AppVarnaBinding(rnaList);
-    // vab = new AppVarnaBinding(seq,struc);
-    // System.out.println("Hallo: "+name);
-    this.name = sname+" trimmed to "+name;
+  }
+
+  /**
+   * Constructor
+   * 
+   * @param seq
+   *          the RNA sequence
+   * @param aa
+   *          the annotation with the secondary structure string
+   * @param ap
+   *          the AlignmentPanel creating this object
+   */
+  public AppVarna(SequenceI seq, AlignmentAnnotation aa, AlignmentPanel ap)
+  {
+    this(ap);
+
+    String sname = aa.sequenceRef == null ? "secondary structure (alignment)"
+            : seq.getName() + " structure";
+    String theTitle = sname
+            + (aa.sequenceRef == null ? " trimmed to " + seq.getName() : "");
+    theTitle = MessageManager.formatMessage("label.varna_params",
+            new String[] { theTitle });
+    setTitle(theTitle);
+
+    String gappedTitle = sname + " (with gaps)";
+    RnaModel gappedModel = new RnaModel(gappedTitle, aa, seq, null, true);
+    addModel(gappedModel, gappedTitle);
+
+    String trimmedTitle = "trimmed " + sname;
+    RnaModel trimmedModel = new RnaModel(trimmedTitle, aa, seq, null, false);
+    addModel(trimmedModel, trimmedTitle);
+    vab.setSelectedIndex(0);
+  }
+
+  /**
+   * Constructor that links the viewer to a parent panel (but has no structures
+   * yet - use addModel to add them)
+   * 
+   * @param ap
+   */
+  protected AppVarna(AlignmentPanel ap)
+  {
+    this.ap = ap;
+    this.viewId = System.currentTimeMillis() + "." + this.hashCode();
+    vab = new AppVarnaBinding();
     initVarna();
-    ssm = ap.getStructureSelectionManager();
+
+    this.ssm = ap.getStructureSelectionManager();
     ssm.addStructureViewerListener(this);
     ssm.addSelectionListener(this);
+    addInternalFrameListener(new InternalFrameAdapter()
+    {
+      @Override
+      public void internalFrameClosed(InternalFrameEvent evt)
+      {
+        close();
+      }
+    });
   }
 
+  /**
+   * Constructor given viewer data read from a saved project file
+   * 
+   * @param model
+   * @param ap
+   *          the (or a) parent alignment panel
+   */
+  public AppVarna(RnaViewerModel model, AlignmentPanel ap)
+  {
+    this(ap);
+    setTitle(model.title);
+    this.viewId = model.viewId;
+    setBounds(model.x, model.y, model.width, model.height);
+    this.split.setDividerLocation(model.dividerLocation);
+  }
+
+  /**
+   * Constructs a split pane with an empty selection list and display panel, and
+   * adds it to the desktop
+   */
   public void initVarna()
   {
-    // vab.setFinishedInit(false);
-    varnaPanel = vab.get_varnaPanel();
+    VARNAPanel varnaPanel = vab.get_varnaPanel();
     setBackground(Color.white);
-    JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, true,
+    split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, true,
             vab.getListPanel(), varnaPanel);
     getContentPane().setLayout(new BorderLayout());
     getContentPane().add(split, BorderLayout.CENTER);
-    // getContentPane().add(vab.getTools(), BorderLayout.NORTH);
-    varnaPanel.addVARNAListener(this);
+
     varnaPanel.addSelectionListener(this);
-    jalview.gui.Desktop.addInternalFrame(this, "VARNA -" + name,
-            getBounds().width, getBounds().height);
+    jalview.gui.Desktop.addInternalFrame(this, "", getBounds().width,
+            getBounds().height);
     this.pack();
     showPanel(true);
   }
 
-  public String replaceOddGaps(String oldStr)
-  {
-    String patternStr = "[^([{<>}])]";
-    String replacementStr = ".";
-    Pattern pattern = Pattern.compile(patternStr);
-    Matcher matcher = pattern.matcher(oldStr);
-    String newStr = matcher.replaceAll(replacementStr);
-    return newStr;
-  }
-
+  /**
+   * Constructs a new RNA model from the given one, without gaps. Also
+   * calculates and saves a 'shift list'
+   * 
+   * @param rna
+   * @param name
+   * @return
+   */
   public RNA trimRNA(RNA rna, String name)
   {
     ShiftList offset = new ShiftList();
+
     RNA rnaTrim = new RNA(name);
     try
     {
-      rnaTrim.setRNA(rna.getSeq(), replaceOddGaps(rna.getStructDBN()));
+      String structDBN = rna.getStructDBN(true);
+      rnaTrim.setRNA(rna.getSeq(), replaceOddGaps(structDBN));
     } catch (ExceptionUnmatchedClosingParentheses e2)
     {
       e2.printStackTrace();
@@ -160,19 +281,23 @@ public class AppVarna extends JInternalFrame implements
       e3.printStackTrace();
     }
 
-    StringBuffer seq = new StringBuffer(rnaTrim.getSeq());
-    StringBuffer struc = new StringBuffer(rnaTrim.getStructDBN());
-    int ofstart = -1, sleng = rnaTrim.getSeq().length();
+    String seq = rnaTrim.getSeq();
+    StringBuilder struc = new StringBuilder(256);
+    struc.append(rnaTrim.getStructDBN(true));
+    int ofstart = -1;
+    int sleng = seq.length();
+
     for (int i = 0; i < sleng; i++)
     {
-      // TODO: Jalview utility for gap detection java.utils.isGap()
-      // TODO: Switch to jalview rna datamodel
-      if (jalview.util.Comparison.isGap(seq.charAt(i)))
+      if (Comparison.isGap(seq.charAt(i)))
       {
         if (ofstart == -1)
         {
           ofstart = i;
         }
+        /*
+         * mark base or base & pair in the structure with *
+         */
         if (!rnaTrim.findPair(i).isEmpty())
         {
           int m = rnaTrim.findPair(i).get(1);
@@ -201,35 +326,37 @@ public class AppVarna extends JInternalFrame implements
       offset.addShift(offset.shift(ofstart), ofstart - sleng);
       ofstart = -1;
     }
-    String newSeq = rnaTrim.getSeq().replace("-", "");
-    rnaTrim.getSeq().replace(".", "");
+
+    /*
+     * remove the marked gaps from the structure
+     */
     String newStruc = struc.toString().replace("*", "");
 
+    /*
+     * remove gaps from the sequence
+     */
+    String newSeq = AlignSeq.extractGaps(Comparison.GapChars, seq);
+
     try
     {
       rnaTrim.setRNA(newSeq, newStruc);
       registerOffset(rnaTrim, offset);
     } catch (ExceptionUnmatchedClosingParentheses e)
     {
-      // TODO Auto-generated catch block
       e.printStackTrace();
     } catch (ExceptionFileFormatOrSyntax e)
     {
-      // TODO Auto-generated catch block
       e.printStackTrace();
     }
     return rnaTrim;
   }
 
-  // needs to be many-many
-  Map<RNA, SequenceI> seqs = new Hashtable<RNA, SequenceI>();
-
-  Map<SequenceI, RNA> rnas = new Hashtable<SequenceI, RNA>();
-
-  Map<RNA, ShiftList> offsets = new Hashtable<RNA, ShiftList>();
-
-  Map<RNA, ShiftList> offsetsInv = new Hashtable<RNA, ShiftList>();
-
+  /**
+   * Save the sequence to structure mapping, and also its inverse.
+   * 
+   * @param rnaTrim
+   * @param offset
+   */
   private void registerOffset(RNA rnaTrim, ShiftList offset)
   {
     offsets.put(rnaTrim, offset);
@@ -241,115 +368,37 @@ public class AppVarna extends JInternalFrame implements
     this.setVisible(show);
   }
 
-  private boolean _started = false;
-
-  public void run()
-  {
-    _started = true;
-
-    try
-    {
-      initVarna();
-    } catch (OutOfMemoryError oomerror)
-    {
-      new OOMWarning("When trying to open the Varna viewer!", oomerror);
-    } catch (Exception ex)
-    {
-      Cache.log.error("Couldn't open Varna viewer!", ex);
-    }
-  }
-
-  @Override
-  public void onUINewStructure(VARNAConfig v, RNA r)
-  {
-
-  }
-
-  @Override
-  public void onWarningEmitted(String s)
-  {
-    // TODO Auto-generated method stub
-
-  }
-
-  private class VarnaHighlighter
-  {
-    private HighlightRegionAnnotation _lastHighlight;
-
-    private RNA _lastRNAhighlighted = null;
-
-    public void highlightRegion(RNA rna, int start, int end)
-    {
-      clearSelection(null);
-      HighlightRegionAnnotation highlight = new HighlightRegionAnnotation(
-              rna.getBasesBetween(start, end));
-      rna.addHighlightRegion(highlight);
-      _lastHighlight = highlight;
-      _lastRNAhighlighted = rna;
-
-    }
-
-    public HighlightRegionAnnotation getLastHighlight()
-    {
-      return _lastHighlight;
-    }
-
-    public RNA getLastRNA()
-    {
-      return _lastRNAhighlighted;
-    }
-
-    public void clearSelection(AppVarnaBinding vab)
-    {
-      if (_lastRNAhighlighted != null)
-      {
-        _lastRNAhighlighted.removeHighlightRegion(_lastHighlight);
-        if (vab != null)
-        {
-          vab.updateSelectedRNA(_lastRNAhighlighted);
-        }
-        _lastRNAhighlighted = null;
-        _lastHighlight = null;
-
-      }
-    }
-  }
-
-  VarnaHighlighter mouseOverHighlighter = new VarnaHighlighter(),
-          selectionHighlighter = new VarnaHighlighter();
-
   /**
    * If a mouseOver event from the AlignmentPanel is noticed the currently
    * selected RNA in the VARNA window is highlighted at the specific position.
    * To be able to remove it before the next highlight it is saved in
    * _lastHighlight
+   * 
+   * @param sequence
+   * @param index
+   *          the aligned sequence position (base 0)
+   * @param position
+   *          the dataset sequence position (base 1)
    */
   @Override
-  public void mouseOverSequence(SequenceI sequence, int index)
+  public void mouseOverSequence(SequenceI sequence, final int index,
+          final int position)
   {
     RNA rna = vab.getSelectedRNA();
-    if (seqs.get(rna) == sequence)
+    if (rna == null)
     {
-      ShiftList shift = offsets.get(rna);
-      if (shift != null)
-      {
-   //      System.err.print("Orig pos:"+index);
-         index = shift.shift(index);
-   //      System.err.println("\nFinal pos:"+index);
-      }
-      mouseOverHighlighter.highlightRegion(rna, index, index);
+      return;
+    }
+    RnaModel rnaModel = models.get(rna);
+    if (rnaModel.seq == sequence)
+    {
+      int highlightPos = rnaModel.gapped ? index : position - 1;
+      mouseOverHighlighter.highlightRegion(rna, highlightPos, highlightPos);
       vab.updateSelectedRNA(rna);
     }
   }
 
   @Override
-  public void onStructureRedrawn()
-  {
-    // TODO Auto-generated method stub
-
-  }
-
-  @Override
   public void selection(SequenceGroup seqsel, ColumnSelection colsel,
           SelectionSource source)
   {
@@ -359,10 +408,14 @@ public class AppVarna extends JInternalFrame implements
       // TODO - reuse many-one panel-view system in jmol viewer
       return;
     }
+    RNA rna = vab.getSelectedRNA();
+    if (rna == null)
+    {
+      return;
+    }
     if (seqsel != null && seqsel.getSize() > 0)
     {
       int start = seqsel.getStartRes(), end = seqsel.getEndRes();
-      RNA rna = vab.getSelectedRNA();
       ShiftList shift = offsets.get(rna);
       if (shift != null)
       {
@@ -377,27 +430,30 @@ public class AppVarna extends JInternalFrame implements
     }
     else
     {
-      selectionHighlighter.clearSelection(vab);
+      selectionHighlighter.clearSelection();
     }
   }
 
+  /**
+   * Respond to a change of the base hovered over in the Varna viewer
+   */
   @Override
-  public void onHoverChanged(ModeleBase arg0, ModeleBase arg1)
+  public void onHoverChanged(ModeleBase previousBase, ModeleBase newBase)
   {
     RNA rna = vab.getSelectedRNA();
     ShiftList shift = offsetsInv.get(rna);
-    SequenceI seq = seqs.get(rna);
-    if (arg1 != null && seq != null)
+    SequenceI seq = models.get(rna).seq;
+    if (newBase != null && seq != null)
     {
       if (shift != null)
       {
-        int i = shift.shift(arg1.getIndex());
- //       System.err.println("shifted "+(arg1.getIndex())+" to "+i);
+        int i = shift.shift(newBase.getIndex());
+        // System.err.println("shifted "+(arg1.getIndex())+" to "+i);
         ssm.mouseOverVamsasSequence(seq, i, this);
       }
       else
       {
-        ssm.mouseOverVamsasSequence(seq, arg1.getIndex(), this);
+        ssm.mouseOverVamsasSequence(seq, newBase.getIndex(), this);
       }
     }
   }
@@ -410,4 +466,287 @@ public class AppVarna extends JInternalFrame implements
 
   }
 
+  /**
+   * Returns the path to a temporary file containing a representation of the
+   * state of one Varna display
+   * 
+   * @param rna
+   * 
+   * @return
+   */
+  public String getStateInfo(RNA rna)
+  {
+    return vab.getStateInfo(rna);
+  }
+
+  public AlignmentPanel getAlignmentPanel()
+  {
+    return ap;
+  }
+
+  public String getViewId()
+  {
+    return viewId;
+  }
+
+  /**
+   * Returns true if any of the viewer's models (not necessarily the one
+   * currently displayed) is for the given sequence
+   * 
+   * @param seq
+   * @return
+   */
+  public boolean isListeningFor(SequenceI seq)
+  {
+    for (RnaModel model : models.values())
+    {
+      if (model.seq == seq)
+      {
+        return true;
+      }
+    }
+    return false;
+  }
+
+  /**
+   * Returns a value representing the horizontal split divider location
+   * 
+   * @return
+   */
+  public int getDividerLocation()
+  {
+    return split == null ? 0 : split.getDividerLocation();
+  }
+
+  /**
+   * Tidy up as necessary when the viewer panel is closed
+   */
+  protected void close()
+  {
+    /*
+     * Deregister as a listener, to release references to this object
+     */
+    if (ssm != null)
+    {
+      ssm.removeStructureViewerListener(AppVarna.this, null);
+      ssm.removeSelectionListener(AppVarna.this);
+    }
+  }
+
+  /**
+   * Returns the secondary structure annotation that this viewer displays for
+   * the given sequence
+   * 
+   * @return
+   */
+  public AlignmentAnnotation getAnnotation(SequenceI seq)
+  {
+    for (RnaModel model : models.values())
+    {
+      if (model.seq == seq)
+      {
+        return model.ann;
+      }
+    }
+    return null;
+  }
+
+  public int getSelectedIndex()
+  {
+    return this.vab.getSelectedIndex();
+  }
+
+  /**
+   * Returns the set of models shown by the viewer
+   * 
+   * @return
+   */
+  public Collection<RnaModel> getModels()
+  {
+    return models.values();
+  }
+
+  /**
+   * Add a model (e.g. loaded from project file)
+   * 
+   * @param rna
+   * @param modelName
+   */
+  public RNA addModel(RnaModel model, String modelName)
+  {
+    if (!model.ann.isValidStruc())
+    {
+      throw new IllegalArgumentException("Invalid RNA structure annotation");
+    }
+
+    /*
+     * opened on request in Jalview session
+     */
+    RNA rna = new RNA(modelName);
+    String struc = model.ann.getRNAStruc();
+    struc = replaceOddGaps(struc);
+
+    String strucseq = model.seq.getSequenceAsString();
+    try
+    {
+      rna.setRNA(strucseq, struc);
+    } catch (ExceptionUnmatchedClosingParentheses e2)
+    {
+      e2.printStackTrace();
+    } catch (ExceptionFileFormatOrSyntax e3)
+    {
+      e3.printStackTrace();
+    }
+
+    if (!model.gapped)
+    {
+      rna = trimRNA(rna, modelName);
+    }
+    models.put(rna, new RnaModel(modelName, model.ann, model.seq, rna,
+            model.gapped));
+    vab.addStructure(rna);
+    return rna;
+  }
+
+  /**
+   * Constructs a shift list that describes the gaps in the sequence
+   * 
+   * @param seq
+   * @return
+   */
+  protected ShiftList buildOffset(SequenceI seq)
+  {
+    // TODO refactor to avoid duplication with trimRNA()
+    // TODO JAL-1789 bugs in use of ShiftList here
+    ShiftList offset = new ShiftList();
+    int ofstart = -1;
+    int sleng = seq.getLength();
+    char[] seqChars = seq.getSequence();
+
+    for (int i = 0; i < sleng; i++)
+    {
+      if (Comparison.isGap(seqChars[i]))
+      {
+        if (ofstart == -1)
+        {
+          ofstart = i;
+        }
+      }
+      else
+      {
+        if (ofstart > -1)
+        {
+          offset.addShift(offset.shift(ofstart), ofstart - i);
+          ofstart = -1;
+        }
+      }
+    }
+    // final gap
+    if (ofstart > -1)
+    {
+      offset.addShift(offset.shift(ofstart), ofstart - sleng);
+      ofstart = -1;
+    }
+    return offset;
+  }
+
+  /**
+   * Set the selected index in the model selection list
+   * 
+   * @param selectedIndex
+   */
+  public void setInitialSelection(final int selectedIndex)
+  {
+    /*
+     * empirically it needs a second for Varna/AWT to finish loading/drawing
+     * models for this to work; SwingUtilities.invokeLater _not_ a solution;
+     * explanation and/or better solution welcome!
+     */
+    synchronized (this)
+    {
+      try
+      {
+        wait(1000);
+      } catch (InterruptedException e)
+      {
+        // meh
+      }
+    }
+    vab.setSelectedIndex(selectedIndex);
+  }
+
+  /**
+   * Add a model with associated Varna session file
+   * 
+   * @param rna
+   * @param modelName
+   */
+  public RNA addModelSession(RnaModel model, String modelName,
+          String sessionFile)
+  {
+    if (!model.ann.isValidStruc())
+    {
+      throw new IllegalArgumentException("Invalid RNA structure annotation");
+    }
+
+    try
+    {
+      FullBackup fromSession = vab.vp.loadSession(sessionFile);
+      vab.addStructure(fromSession.rna, fromSession.config);
+      RNA rna = fromSession.rna;
+      // copy the model, but now including the RNA object
+      RnaModel newModel = new RnaModel(model.title, model.ann, model.seq,
+              rna, model.gapped);
+      if (!model.gapped)
+      {
+        registerOffset(rna, buildOffset(model.seq));
+      }
+      models.put(rna, newModel);
+      // capture rna selection state when saved
+      selectionHighlighter = new VarnaHighlighter(rna);
+      return fromSession.rna;
+    } catch (ExceptionLoadingFailed e)
+    {
+      System.err
+              .println("Error restoring Varna session: " + e.getMessage());
+      return null;
+    }
+  }
+
+  /**
+   * Replace everything except RNA secondary structure characters with a period
+   * 
+   * @param s
+   * @return
+   */
+  public static String replaceOddGaps(String s)
+  {
+    if (s == null)
+    {
+      return null;
+    }
+
+    // this is measured to be 10 times faster than a regex replace
+    boolean changed = false;
+    byte[] bytes = s.getBytes();
+    for (int i = 0; i < bytes.length; i++)
+    {
+      boolean ok = false;
+      // todo check for ((b >= 'a' && b <= 'z') || (b >= 'A' && b <= 'Z')) if
+      // wanted also
+      for (int j = 0; !ok && (j < PAIRS.length); j++)
+      {
+        if (bytes[i] == PAIRS[j])
+        {
+          ok = true;
+        }
+      }
+      if (!ok)
+      {
+        bytes[i] = '.';
+        changed = true;
+      }
+    }
+    return changed ? new String(bytes) : s;
+  }
 }