From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 16 Apr 2020 15:11:23 +0000 (+0100)
Subject: JAL-3567 report mapped location for virtual features in tooltip etc
X-Git-Tag: Develop-2_11_2_0-d20201215~33^2~5
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5a631296dd1dcc1df7b50487a647c27333696c74;p=jalview.git

JAL-3567 report mapped location for virtual features in tooltip etc
---

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 76f2705..6299c62 100644
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -20,6 +20,25 @@
  */
 package jalview.appletgui;
 
+import java.awt.CheckboxMenuItem;
+import java.awt.Frame;
+import java.awt.Menu;
+import java.awt.MenuItem;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.SortedMap;
+import java.util.TreeMap;
+import java.util.Vector;
+
 import jalview.analysis.AAFrequency;
 import jalview.analysis.AlignmentAnnotationUtils;
 import jalview.analysis.AlignmentUtils;
@@ -57,25 +76,6 @@ import jalview.schemes.ZappoColourScheme;
 import jalview.util.MessageManager;
 import jalview.util.UrlLink;
 
-import java.awt.CheckboxMenuItem;
-import java.awt.Frame;
-import java.awt.Menu;
-import java.awt.MenuItem;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.SortedMap;
-import java.util.TreeMap;
-import java.util.Vector;
-
 public class APopupMenu extends java.awt.PopupMenu
         implements ActionListener, ItemListener
 {
@@ -900,7 +900,7 @@ public class APopupMenu extends java.awt.PopupMenu
       contents.append(MessageManager
               .formatMessage("label.annotation_for_displayid", new Object[]
               { seq.getDisplayId(true) }));
-      new SequenceAnnotationReport(null).createSequenceAnnotationReport(
+      new SequenceAnnotationReport(false).createSequenceAnnotationReport(
               contents, seq, true, true, ap.seqPanel.seqCanvas.fr);
       contents.append("</p>");
     }
diff --git a/src/jalview/datamodel/MappedFeatures.java b/src/jalview/datamodel/MappedFeatures.java
index 0fa03cf..a42f34a 100644
--- a/src/jalview/datamodel/MappedFeatures.java
+++ b/src/jalview/datamodel/MappedFeatures.java
@@ -1,14 +1,15 @@
 package jalview.datamodel;
 
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
 import jalview.io.gff.Gff3Helper;
 import jalview.schemes.ResidueProperties;
+import jalview.util.MapList;
 import jalview.util.MappingUtils;
 import jalview.util.StringUtils;
 
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
 /**
  * A data bean to hold a list of mapped sequence features (e.g. CDS features
  * mapped from protein), and the mapping between the sequences. It also provides
@@ -18,22 +19,31 @@ import java.util.Set;
  */
 public class MappedFeatures
 {
+  /*
+   * VEP CSQ:HGVSp (if present) is a short-cut to the protein variant consequence
+   */
   private static final String HGV_SP = "HGVSp";
 
   private static final String CSQ = "CSQ";
 
   /*
-   * the mapping from one sequence to another
+   * the sequence the mapped features are on
    */
-  public final Mapping mapping;
+  private final SequenceI linkedSeq;
 
-  /**
-   * the sequence mapped from
+  /*
+   * the mapping between sequences;
+   * NB this could be in either sense
    */
-  public final SequenceI fromSeq;
+  private final Mapping mapping;
 
   /*
-   * features on the sequence mapped to that overlap the mapped positions
+   * if true, mapping is from the linked sequence, else to the linked sequence
+   */
+  private boolean mappingIsFromLinkedSequence;
+
+  /*
+   * features on linkedSeq that overlap the mapped positions
    */
   public final List<SequenceFeature> features;
 
@@ -74,7 +84,8 @@ public class MappedFeatures
           char res, List<SequenceFeature> theFeatures)
   {
     mapping = theMapping;
-    fromSeq = from;
+    linkedSeq = from;
+    mappingIsFromLinkedSequence = mapping.to != linkedSeq;
     toPosition = pos;
     toResidue = res;
     features = theFeatures;
@@ -90,13 +101,13 @@ public class MappedFeatures
     {
       codonPos = codonPositions;
       baseCodon = new char[3];
-      int cdsStart = fromSeq.getStart();
+      int cdsStart = linkedSeq.getStart();
       baseCodon[0] = Character
-              .toUpperCase(fromSeq.getCharAt(codonPos[0] - cdsStart));
+              .toUpperCase(linkedSeq.getCharAt(codonPos[0] - cdsStart));
       baseCodon[1] = Character
-              .toUpperCase(fromSeq.getCharAt(codonPos[1] - cdsStart));
+              .toUpperCase(linkedSeq.getCharAt(codonPos[1] - cdsStart));
       baseCodon[2] = Character
-              .toUpperCase(fromSeq.getCharAt(codonPos[2] - cdsStart));
+              .toUpperCase(linkedSeq.getCharAt(codonPos[2] - cdsStart));
     }
     else
     {
@@ -233,4 +244,47 @@ public class MappedFeatures
 
     return vars.toString();
   }
+
+  /**
+   * Answers the name of the linked sequence holding any mapped features
+   * 
+   * @return
+   */
+  public String getLinkedSequenceName()
+  {
+    return linkedSeq == null ? null : linkedSeq.getName();
+  }
+
+  /**
+   * Answers the mapped ranges (as one or more [start, end] positions) which
+   * correspond to the given [begin, end] range of the linked sequence.
+   * 
+   * <pre>
+   * Example: MappedFeatures with CDS features mapped to peptide 
+   * CDS/200-220 gtc aac TGa acGt att AAC tta
+   * mapped to PEP/6-7 WN by mapping [206, 207, 210, 210, 215, 217] to [6, 7]
+   * getMappedPositions(206, 206) should return [6, 6]
+   * getMappedPositions(200, 214) should return [6, 6]
+   * getMappedPositions(210, 215) should return [6, 7]
+   * </pre>
+   * 
+   * @param begin
+   * @param end
+   * @return
+   */
+  public int[] getMappedPositions(int begin, int end)
+  {
+    MapList map = mapping.getMap();
+    return mappingIsFromLinkedSequence ? map.locateInTo(begin, end)
+            : map.locateInFrom(begin, end);
+  }
+
+  public boolean isFromCds()
+  {
+    if (mapping.getMap().getFromRatio() == 3)
+    {
+      return mappingIsFromLinkedSequence;
+    }
+    return !mappingIsFromLinkedSequence;
+  }
 }
diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 2dd9cf0..df268f8 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -20,13 +20,6 @@
  */
 package jalview.datamodel;
 
-import jalview.datamodel.features.FeatureAttributeType;
-import jalview.datamodel.features.FeatureAttributes;
-import jalview.datamodel.features.FeatureLocationI;
-import jalview.datamodel.features.FeatureSourceI;
-import jalview.datamodel.features.FeatureSources;
-import jalview.util.StringUtils;
-
 import java.util.Comparator;
 import java.util.LinkedHashMap;
 import java.util.Map;
@@ -35,6 +28,13 @@ import java.util.SortedMap;
 import java.util.TreeMap;
 import java.util.Vector;
 
+import jalview.datamodel.features.FeatureAttributeType;
+import jalview.datamodel.features.FeatureAttributes;
+import jalview.datamodel.features.FeatureLocationI;
+import jalview.datamodel.features.FeatureSourceI;
+import jalview.datamodel.features.FeatureSources;
+import jalview.util.StringUtils;
+
 /**
  * A class that models a single contiguous feature on a sequence. If flag
  * 'contactFeature' is true, the start and end positions are interpreted instead
@@ -586,13 +586,17 @@ public class SequenceFeature implements FeatureLocationI
   }
 
   /**
-   * Answers an html-formatted report of feature details
+   * Answers an html-formatted report of feature details. If parameter
+   * {@code mf} is not null, the feature is a virtual linked feature, and
+   * details included both the original location and the mapped location
+   * (CDS/peptide).
    * 
    * @param seqName
+   * @param mf
    * 
    * @return
    */
-  public String getDetailsReport(String seqName)
+  public String getDetailsReport(String seqName, MappedFeatures mf)
   {
     FeatureSourceI metadata = FeatureSources.getInstance()
             .getSource(source);
@@ -600,9 +604,25 @@ public class SequenceFeature implements FeatureLocationI
     StringBuilder sb = new StringBuilder(128);
     sb.append("<br>");
     sb.append("<table>");
-    sb.append(String.format(ROW_DATA, "Location", seqName,
+    String name = mf == null ? seqName : mf.getLinkedSequenceName();
+    sb.append(String.format(ROW_DATA, "Location", name,
             begin == end ? begin
                     : begin + (isContactFeature() ? ":" : "-") + end));
+    if (mf != null)
+    {
+      int[] beginRange = mf.getMappedPositions(begin, begin);
+      int[] endRange = mf.getMappedPositions(end, end);
+      int from = beginRange[0];
+      int to = endRange[endRange.length - 1];
+      String s = mf.isFromCds() ? "Peptide Location" : "Coding location";
+      sb.append(String.format(ROW_DATA, s, seqName, from == to ? from
+              : from + (isContactFeature() ? ":" : "-") + to));
+      if (mf.isFromCds())
+      {
+        sb.append(String.format(ROW_DATA, "Consequence",
+                mf.findProteinVariants(this), ""));
+      }
+    }
     sb.append(String.format(ROW_DATA, "Type", type, ""));
     String desc = StringUtils.stripHtmlTags(description);
     sb.append(String.format(ROW_DATA, "Description", desc, ""));
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 2b1507a..3ce9d4d 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -20,17 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.gui.SeqPanel.MousePos;
-import jalview.io.SequenceAnnotationReport;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.viewmodel.AlignmentViewport;
-import jalview.viewmodel.ViewportRanges;
-
 import java.awt.BorderLayout;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
@@ -44,6 +33,17 @@ import javax.swing.JPopupMenu;
 import javax.swing.SwingUtilities;
 import javax.swing.ToolTipManager;
 
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.SeqPanel.MousePos;
+import jalview.io.SequenceAnnotationReport;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
+
 /**
  * This panel hosts alignment sequence ids and responds to mouse clicks on them,
  * as well as highlighting ids matched by a search from the Find menu.
@@ -62,8 +62,6 @@ public class IdPanel extends JPanel
 
   ScrollThread scrollThread = null;
 
-  String linkImageURL;
-
   int offy;
 
   // int width;
@@ -84,8 +82,7 @@ public class IdPanel extends JPanel
     this.av = av;
     alignPanel = parent;
     setIdCanvas(new IdCanvas(av));
-    linkImageURL = getClass().getResource("/images/link.gif").toString();
-    seqAnnotReport = new SequenceAnnotationReport(linkImageURL);
+    seqAnnotReport = new SequenceAnnotationReport(true);
     setLayout(new BorderLayout());
     add(getIdCanvas(), BorderLayout.CENTER);
     addMouseListener(this);
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 187090b..568f7f1 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -20,6 +20,31 @@
  */
 package jalview.gui;
 
+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;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+import java.util.SortedMap;
+import java.util.TreeMap;
+import java.util.Vector;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JColorChooser;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JPopupMenu;
+import javax.swing.JRadioButtonMenuItem;
+
 import jalview.analysis.AAFrequency;
 import jalview.analysis.AlignmentAnnotationUtils;
 import jalview.analysis.AlignmentUtils;
@@ -56,31 +81,6 @@ import jalview.util.StringUtils;
 import jalview.util.UrlLink;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
-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;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Objects;
-import java.util.SortedMap;
-import java.util.TreeMap;
-import java.util.Vector;
-
-import javax.swing.ButtonGroup;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JColorChooser;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JPopupMenu;
-import javax.swing.JRadioButtonMenuItem;
-
 /**
  * The popup menu that is displayed on right-click on a sequence id, or in the
  * sequence alignment.
@@ -755,14 +755,16 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
   }
 
   /**
-   * Add a link to show feature details for each sequence feature
+   * Add a menu item to show feature details for each sequence feature. Any
+   * linked 'virtual' features (CDS/protein) are also optionally found and
+   * included.
    * 
    * @param features
-   * @param column
    * @param seq
+   * @param column
    */
   protected void addFeatureDetails(List<SequenceFeature> features,
-          SequenceI seq, int column)
+          final SequenceI seq, final int column)
   {
     /*
      * add features in CDS/protein complement at the corresponding
@@ -797,39 +799,49 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     String name = seq.getName();
     for (final SequenceFeature sf : features)
     {
-      addFeatureDetailsMenuItem(details, name, sf);
+      addFeatureDetailsMenuItem(details, name, sf, null);
     }
 
     if (mf != null)
     {
-      name = mf.fromSeq == seq ? mf.mapping.getTo().getName()
-              : mf.fromSeq.getName();
       for (final SequenceFeature sf : mf.features)
       {
-        addFeatureDetailsMenuItem(details, name, sf);
+        addFeatureDetailsMenuItem(details, name, sf, mf);
       }
     }
   }
 
   /**
-   * A helper method to add one menu item whose action is to show details for one
-   * feature. The menu text includes feature description, but this may be
+   * A helper method to add one menu item whose action is to show details for
+   * one feature. The menu text includes feature description, but this may be
    * truncated.
    * 
    * @param details
    * @param seqName
    * @param sf
+   * @param mf
    */
   void addFeatureDetailsMenuItem(JMenu details, final String seqName,
-          final SequenceFeature sf)
+          final SequenceFeature sf, MappedFeatures mf)
   {
     int start = sf.getBegin();
     int end = sf.getEnd();
+    if (mf != null)
+    {
+      /*
+       * show local rather than linked feature coordinates
+       */
+      int[] beginRange = mf.getMappedPositions(start, start);
+      start = beginRange[0];
+      int[] endRange = mf.getMappedPositions(end, end);
+      end = endRange[endRange.length - 1];
+    }
     StringBuilder desc = new StringBuilder();
     desc.append(sf.getType()).append(" ").append(String.valueOf(start));
     if (start != end)
     {
-      desc.append("-").append(String.valueOf(end));
+      desc.append(sf.isContactFeature() ? ":" : "-");
+      desc.append(String.valueOf(end));
     }
     String description = sf.getDescription();
     if (description != null)
@@ -860,26 +872,27 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        showFeatureDetails(seqName, sf);
+        showFeatureDetails(sf, seqName, mf);
       }
     });
     details.add(item);
   }
 
   /**
-   * Opens a panel showing a text report of feature dteails
-   * 
-   * @param seqName
+   * Opens a panel showing a text report of feature details
    * 
    * @param sf
+   * @param seqName
+   * @param mf
    */
-  protected void showFeatureDetails(String seqName, SequenceFeature sf)
+  protected void showFeatureDetails(SequenceFeature sf, String seqName,
+          MappedFeatures mf)
   {
     CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
     // it appears Java's CSS does not support border-collapse :-(
     cap.addStylesheetRule("table { border-collapse: collapse;}");
     cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
-    cap.setText(sf.getDetailsReport(seqName));
+    cap.setText(sf.getDetailsReport(seqName, mf));
 
     Desktop.addInternalFrame(cap,
             MessageManager.getString("label.feature_details"), 500, 500);
@@ -1763,7 +1776,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
               "label.create_sequence_details_report_annotation_for",
               new Object[]
               { seq.getDisplayId(true) }) + "</h2></p><p>");
-      new SequenceAnnotationReport(null).createSequenceAnnotationReport(
+      new SequenceAnnotationReport(false).createSequenceAnnotationReport(
               contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
       contents.append("</p>");
     }
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 27ceb27..f28217d 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -207,8 +207,6 @@ public class SeqPanel extends JPanel
 
   StringBuffer keyboardNo2;
 
-  java.net.URL linkImageURL;
-
   private final SequenceAnnotationReport seqARep;
 
   StringBuilder tooltipText = new StringBuilder();
@@ -229,8 +227,7 @@ public class SeqPanel extends JPanel
    */
   public SeqPanel(AlignViewport viewport, AlignmentPanel alignPanel)
   {
-    linkImageURL = getClass().getResource("/images/link.gif");
-    seqARep = new SequenceAnnotationReport(linkImageURL.toString());
+    seqARep = new SequenceAnnotationReport(true);
     ToolTipManager.sharedInstance().registerComponent(this);
     ToolTipManager.sharedInstance().setInitialDelay(0);
     ToolTipManager.sharedInstance().setDismissDelay(10000);
@@ -1047,9 +1044,9 @@ public class SeqPanel extends JPanel
     {
       List<SequenceFeature> features = ap.getFeatureRenderer()
               .findFeaturesAtColumn(sequence, column + 1);
-      unshownFeatures = seqARep.appendFeaturesLengthLimit(tooltipText, pos,
-              features,
-              this.ap.getSeqPanel().seqCanvas.fr, MAX_TOOLTIP_LENGTH);
+      unshownFeatures = seqARep.appendFeatures(tooltipText, pos,
+              features, this.ap.getSeqPanel().seqCanvas.fr,
+              MAX_TOOLTIP_LENGTH);
 
       /*
        * add features in CDS/protein complement at the corresponding
@@ -1067,9 +1064,8 @@ public class SeqPanel extends JPanel
                   pos);
           if (mf != null)
           {
-            unshownFeatures = seqARep.appendFeaturesLengthLimit(
-                    tooltipText, pos, mf, fr2,
-                    MAX_TOOLTIP_LENGTH);
+            unshownFeatures = seqARep.appendFeatures(tooltipText,
+                    pos, mf, fr2, MAX_TOOLTIP_LENGTH);
           }
         }
       }
diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index a8a3746..92473ec 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -20,6 +20,18 @@
  */
 package jalview.io;
 
+import java.awt.Color;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.TreeMap;
+
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.SequenceIdMatcher;
 import jalview.api.AlignViewportI;
@@ -44,18 +56,6 @@ import jalview.util.MapList;
 import jalview.util.ParseHtmlBodyAndLinks;
 import jalview.util.StringUtils;
 
-import java.awt.Color;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.TreeMap;
-
 /**
  * Parses and writes features files, which may be in Jalview, GFF2 or GFF3
  * format. These are tab-delimited formats but with differences in the use of
@@ -736,7 +736,6 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
 
       if (mf != null)
       {
-        MapList mapping = mf.mapping.getMap();
         for (SequenceFeature sf : mf.features)
         {
           /*
@@ -752,9 +751,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
             found.add(sf);
             int begin = sf.getBegin();
             int end = sf.getEnd();
-            int[] range = mf.mapping.getTo() == seq.getDatasetSequence()
-                    ? mapping.locateInTo(begin, end)
-                    : mapping.locateInFrom(begin, end);
+            int[] range = mf.getMappedPositions(begin, end);
             SequenceFeature sf2 = new SequenceFeature(sf, range[0],
                     range[1], group, sf.getScore());
             complementary.add(sf2);
diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 0125277..8328e7a 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -20,6 +20,13 @@
  */
 package jalview.io;
 
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Comparator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
 import jalview.api.FeatureColourI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
@@ -32,13 +39,6 @@ import jalview.util.StringUtils;
 import jalview.util.UrlLink;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Comparator;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-
 /**
  * generate HTML reports for a sequence
  * 
@@ -56,12 +56,12 @@ public class SequenceAnnotationReport
 
   private static final int MAX_SOURCES = 40;
 
+  private static String linkImageURL;
+
   private static final String[][] PRIMARY_SOURCES = new String[][] {
       DBRefSource.CODINGDBS, DBRefSource.DNACODINGDBS,
       DBRefSource.PROTEINDBS };
 
-  final String linkImageURL;
-
   /*
    * Comparator to order DBRefEntry by Source + accession id (case-insensitive),
    * with 'Primary' sources placed before others, and 'chromosome' first of all
@@ -120,14 +120,30 @@ public class SequenceAnnotationReport
     }
   };
 
-  public SequenceAnnotationReport(String linkURL)
+  private boolean forTooltip;
+
+  /**
+   * Constructor given a flag which affects behaviour
+   * <ul>
+   * <li>if true, generates feature details suitable to show in a tooltip</li>
+   * <li>if false, generates feature details in a form suitable for the sequence
+   * details report</li>
+   * </ul>
+   * 
+   * @param isForTooltip
+   */
+  public SequenceAnnotationReport(boolean isForTooltip)
   {
-    this.linkImageURL = linkURL;
+    this.forTooltip = isForTooltip;
+    if (linkImageURL == null)
+    {
+      linkImageURL = getClass().getResource("/images/link.gif").toString();
+    }
   }
 
   /**
-   * Append text for the list of features to the tooltip Returns number of
-   * features left if maxlength limit is (or would have been) reached
+   * Append text for the list of features to the tooltip. Returns the number of
+   * features not added if maxlength limit is (or would have been) reached.
    * 
    * @param sb
    * @param residuePos
@@ -135,7 +151,7 @@ public class SequenceAnnotationReport
    * @param minmax
    * @param maxlength
    */
-  public int appendFeaturesLengthLimit(final StringBuilder sb,
+  public int appendFeatures(final StringBuilder sb,
           int residuePos, List<SequenceFeature> features,
           FeatureRendererModel fr, int maxlength)
   {
@@ -150,16 +166,10 @@ public class SequenceAnnotationReport
     return 0;
   }
 
-  public void appendFeatures(final StringBuilder sb, int residuePos,
-          List<SequenceFeature> features, FeatureRendererModel fr)
-  {
-    appendFeaturesLengthLimit(sb, residuePos, features, fr, 0);
-  }
-
   /**
-   * Appends text for mapped features (e.g. CDS feature for peptide or vice versa)
-   * Returns number of features left if maxlength limit is (or would have been)
-   * reached
+   * Appends text for mapped features (e.g. CDS feature for peptide or vice
+   * versa) Returns number of features left if maxlength limit is (or would have
+   * been) reached.
    * 
    * @param sb
    * @param residuePos
@@ -167,7 +177,7 @@ public class SequenceAnnotationReport
    * @param fr
    * @param maxlength
    */
-  public int appendFeaturesLengthLimit(StringBuilder sb, int residuePos,
+  public int appendFeatures(StringBuilder sb, int residuePos,
           MappedFeatures mf, FeatureRendererModel fr, int maxlength)
   {
     for (int i = 0; i < mf.features.size(); i++)
@@ -181,12 +191,6 @@ public class SequenceAnnotationReport
     return 0;
   }
 
-  public void appendFeatures(StringBuilder sb, int residuePos,
-          MappedFeatures mf, FeatureRendererModel fr)
-  {
-    appendFeaturesLengthLimit(sb, residuePos, mf, fr, 0);
-  }
-
   /**
    * Appends the feature at rpos to the given buffer
    * 
@@ -199,19 +203,44 @@ public class SequenceAnnotationReport
           FeatureRendererModel fr, SequenceFeature feature,
           MappedFeatures mf, int maxlength)
   {
+    int begin = feature.getBegin();
+    int end = feature.getEnd();
+
+    /*
+     * if this is a virtual features, convert begin/end to the
+     * coordinates of the sequence it is mapped to
+     */
+    int[] beginRange = null;
+    int[] endRange = null;
+    if (mf != null)
+    {
+      beginRange = mf.getMappedPositions(begin, begin);
+      endRange = mf.getMappedPositions(end, end);
+      begin = beginRange[0];
+      end = endRange[endRange.length - 1];
+    }
+
     StringBuilder sb = new StringBuilder();
     if (feature.isContactFeature())
     {
-      if (feature.getBegin() == rpos || feature.getEnd() == rpos)
+      /*
+       * include if rpos is at start or end position of [mapped] feature
+       */
+      boolean showContact = (mf == null) && (rpos == begin || rpos == end);
+      boolean showMappedContact = (mf != null) && ((rpos >= beginRange[0]
+              && rpos <= beginRange[beginRange.length - 1])
+              || (rpos >= endRange[0]
+                      && rpos <= endRange[endRange.length - 1]));
+      if (showContact || showMappedContact)
       {
         if (sb0.length() > 6)
         {
           sb.append("<br/>");
         }
-        sb.append(feature.getType()).append(" ").append(feature.getBegin())
-                .append(":").append(feature.getEnd());
+        sb.append(feature.getType()).append(" ").append(begin).append(":")
+                .append(end);
       }
-      return appendTextMaxLengthReached(sb0, sb, maxlength);
+      return appendText(sb0, sb, maxlength);
     }
 
     if (sb0.length() > 6)
@@ -226,11 +255,11 @@ public class SequenceAnnotationReport
       if (rpos != 0)
       {
         // we are marking a positional feature
-        sb.append(feature.begin);
-      }
-      if (feature.begin != feature.end)
-      {
-        sb.append(" ").append(feature.end);
+        sb.append(begin);
+        if (begin != end)
+        {
+          sb.append(" ").append(end);
+        }
       }
 
       String description = feature.getDescription();
@@ -291,27 +320,28 @@ public class SequenceAnnotationReport
         }
       }
     }
-    return appendTextMaxLengthReached(sb0, sb, maxlength);
+    return appendText(sb0, sb, maxlength);
   }
 
-  void appendFeature(final StringBuilder sb, int rpos,
-          FeatureRendererModel fr, SequenceFeature feature,
-          MappedFeatures mf)
-  {
-    appendFeature(sb, rpos, fr, feature, mf, 0);
-  }
-
-  private static boolean appendTextMaxLengthReached(StringBuilder sb0,
-          StringBuilder sb, int maxlength)
+  /**
+   * Appends sb to sb0, and returns false, unless maxlength is not zero and
+   * appending would make the result longer than or equal to maxlength, in which
+   * case the append is not done and returns true
+   * 
+   * @param sb0
+   * @param sb
+   * @param maxlength
+   * @return
+   */
+  private static boolean appendText(StringBuilder sb0, StringBuilder sb,
+          int maxlength)
   {
-    boolean ret = false;
     if (maxlength == 0 || sb0.length() + sb.length() < maxlength)
     {
       sb0.append(sb);
       return false;
-    } else {
-      return true;
     }
+    return true;
   }
 
   /**
@@ -466,7 +496,7 @@ public class SequenceAnnotationReport
               .getNonPositionalFeatures())
       {
         int sz = -sb.length();
-        appendFeature(sb, 0, fr, sf, null);
+        appendFeature(sb, 0, fr, sf, null, 0);
         sz += sb.length();
         maxWidth = Math.max(maxWidth, sz);
       }
diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 9a8a086..0a667aa 100644
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -20,6 +20,20 @@
  */
 package jalview.viewmodel.seqfeatures;
 
+import java.awt.Color;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.concurrent.ConcurrentHashMap;
+
 import jalview.api.AlignViewportI;
 import jalview.api.FeatureColourI;
 import jalview.api.FeaturesDisplayedI;
@@ -38,20 +52,6 @@ import jalview.renderer.seqfeatures.FeatureRenderer;
 import jalview.schemes.FeatureColour;
 import jalview.util.ColorUtils;
 
-import java.awt.Color;
-import java.beans.PropertyChangeListener;
-import java.beans.PropertyChangeSupport;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.concurrent.ConcurrentHashMap;
-
 public abstract class FeatureRendererModel
         implements jalview.api.FeatureRenderer
 {
@@ -1162,8 +1162,8 @@ public abstract class FeatureRendererModel
   }
 
   @Override
-  public MappedFeatures findComplementFeaturesAtResidue(SequenceI sequence,
-          int pos)
+  public MappedFeatures findComplementFeaturesAtResidue(
+          final SequenceI sequence, final int pos)
   {
     SequenceI ds = sequence.getDatasetSequence();
     if (ds == null)
@@ -1232,9 +1232,12 @@ public abstract class FeatureRendererModel
     }
 
     /*
-     * sort by renderorder, inefficiently
+     * sort by renderorder (inefficiently but ok for small scale);
+     * NB this sorts 'on top' feature to end, for rendering
      */
     List<SequenceFeature> result = new ArrayList<>();
+    final int toAdd = found.size();
+    int added = 0;
     for (String type : renderOrder)
     {
       for (SequenceFeature sf : found)
@@ -1242,11 +1245,15 @@ public abstract class FeatureRendererModel
         if (type.equals(sf.getType()))
         {
           result.add(sf);
-          if (result.size() == found.size())
-          {
-            return new MappedFeatures(mapping, mapFrom, pos, residue,
-                    result);
-          }
+          added++;
+        }
+        if (added == toAdd)
+        {
+          break;
+        }
+        if (added == toAdd)
+        {
+          break;
         }
       }
     }
diff --git a/test/jalview/datamodel/SequenceFeatureTest.java b/test/jalview/datamodel/SequenceFeatureTest.java
index cd8f9eb..673ea29 100644
--- a/test/jalview/datamodel/SequenceFeatureTest.java
+++ b/test/jalview/datamodel/SequenceFeatureTest.java
@@ -26,11 +26,11 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.gui.JvOptionPane;
-
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import jalview.gui.JvOptionPane;
+
 public class SequenceFeatureTest
 {
 
@@ -285,7 +285,7 @@ public class SequenceFeatureTest
     String expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>22</td></tr>"
             + "<tr><td>Type</td><td>variant</td><td></td></tr>"
             + "<tr><td>Description</td><td>G,C</td><td></td></tr></table>";
-    assertEquals(expected, sf.getDetailsReport(seqName));
+    assertEquals(expected, sf.getDetailsReport(seqName, null));
 
     // contact feature
     sf = new SequenceFeature("Disulphide Bond", "a description", 28, 31,
@@ -293,7 +293,7 @@ public class SequenceFeatureTest
     expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>28:31</td></tr>"
             + "<tr><td>Type</td><td>Disulphide Bond</td><td></td></tr>"
             + "<tr><td>Description</td><td>a description</td><td></td></tr></table>";
-    assertEquals(expected, sf.getDetailsReport(seqName));
+    assertEquals(expected, sf.getDetailsReport(seqName, null));
 
     sf = new SequenceFeature("variant", "G,C", 22, 33,
             12.5f, "group");
@@ -306,7 +306,7 @@ public class SequenceFeatureTest
             + "<tr><td>Group</td><td>group</td><td></td></tr>"
             + "<tr><td>Child</td><td></td><td>ENSP002</td></tr>"
             + "<tr><td>Parent</td><td></td><td>ENSG001</td></tr></table>";
-    assertEquals(expected, sf.getDetailsReport(seqName));
+    assertEquals(expected, sf.getDetailsReport(seqName, null));
 
     /*
      * feature with embedded html link in description
@@ -317,6 +317,6 @@ public class SequenceFeatureTest
             + "<tr><td>Type</td><td>Pfam</td><td></td></tr>"
             + "<tr><td>Description</td><td>Fer2 Status: True Positive <a href=\"http://pfam.xfam.org/family/PF00111\">Pfam 8_8</a></td><td></td></tr>"
             + "<tr><td>Group</td><td>Uniprot</td><td></td></tr></table>";
-    assertEquals(expected, sf.getDetailsReport(seqName));
+    assertEquals(expected, sf.getDetailsReport(seqName, null));
   }
 }
diff --git a/test/jalview/io/SequenceAnnotationReportTest.java b/test/jalview/io/SequenceAnnotationReportTest.java
index 42183ca..7e00caa 100644
--- a/test/jalview/io/SequenceAnnotationReportTest.java
+++ b/test/jalview/io/SequenceAnnotationReportTest.java
@@ -23,6 +23,14 @@ package jalview.io;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
 
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
 import jalview.api.FeatureColourI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.Sequence;
@@ -33,15 +41,6 @@ import jalview.io.gff.GffConstants;
 import jalview.renderer.seqfeatures.FeatureRenderer;
 import jalview.schemes.FeatureColour;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
-
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
 import junit.extensions.PA;
 
 public class SequenceAnnotationReportTest
@@ -57,24 +56,24 @@ public class SequenceAnnotationReportTest
   @Test(groups = "Functional")
   public void testAppendFeature_disulfideBond()
   {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
     StringBuilder sb = new StringBuilder();
     sb.append("123456");
     SequenceFeature sf = new SequenceFeature("disulfide bond", "desc", 1,
             3, 1.2f, "group");
 
     // residuePos == 2 does not match start or end of feature, nothing done:
-    sar.appendFeature(sb, 2, null, sf, null);
+    sar.appendFeature(sb, 2, null, sf, null, 0);
     assertEquals("123456", sb.toString());
 
     // residuePos == 1 matches start of feature, text appended (but no <br/>)
     // feature score is not included
-    sar.appendFeature(sb, 1, null, sf, null);
+    sar.appendFeature(sb, 1, null, sf, null, 0);
     assertEquals("123456disulfide bond 1:3", sb.toString());
 
     // residuePos == 3 matches end of feature, text appended
     // <br/> is prefixed once sb.length() > 6
-    sar.appendFeature(sb, 3, null, sf, null);
+    sar.appendFeature(sb, 3, null, sf, null, 0);
     assertEquals("123456disulfide bond 1:3<br/>disulfide bond 1:3",
             sb.toString());
   }
@@ -82,13 +81,13 @@ public class SequenceAnnotationReportTest
   @Test(groups = "Functional")
   public void testAppendFeatures_longText()
   {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
     StringBuilder sb = new StringBuilder();
     String longString = "Abcd".repeat(50);
     SequenceFeature sf = new SequenceFeature("sequence", longString, 1, 3,
             "group");
 
-    sar.appendFeature(sb, 1, null, sf, null);
+    sar.appendFeature(sb, 1, null, sf, null, 0);
     assertTrue(sb.length() < 100);
 
     List<SequenceFeature> sfl = new ArrayList<>();
@@ -103,7 +102,7 @@ public class SequenceAnnotationReportTest
     sfl.add(sf);
     sfl.add(sf);
     sfl.add(sf);
-    int n = sar.appendFeaturesLengthLimit(sb, 1, sfl,
+    int n = sar.appendFeatures(sb, 1, sfl,
             new FeatureRenderer(null), 200); // text should terminate before 200 characters
     String s = sb.toString();
     assertTrue(s.length() < 200);
@@ -114,27 +113,27 @@ public class SequenceAnnotationReportTest
   @Test(groups = "Functional")
   public void testAppendFeature_status()
   {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
     StringBuilder sb = new StringBuilder();
     SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
             Float.NaN, "group");
     sf.setStatus("Confirmed");
 
-    sar.appendFeature(sb, 1, null, sf, null);
+    sar.appendFeature(sb, 1, null, sf, null, 0);
     assertEquals("METAL 1 3; Fe2-S; (Confirmed)", sb.toString());
   }
 
   @Test(groups = "Functional")
   public void testAppendFeature_withScore()
   {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
     StringBuilder sb = new StringBuilder();
     SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f,
             "group");
 
     FeatureRendererModel fr = new FeatureRenderer(null);
     Map<String, float[][]> minmax = fr.getMinMax();
-    sar.appendFeature(sb, 1, fr, sf, null);
+    sar.appendFeature(sb, 1, fr, sf, null, 0);
     /*
      * map has no entry for this feature type - score is not shown:
      */
@@ -144,7 +143,7 @@ public class SequenceAnnotationReportTest
      * map has entry for this feature type - score is shown:
      */
     minmax.put("METAL", new float[][] { { 0f, 1f }, null });
-    sar.appendFeature(sb, 1, fr, sf, null);
+    sar.appendFeature(sb, 1, fr, sf, null, 0);
     // <br/> is appended to a buffer > 6 in length
     assertEquals("METAL 1 3; Fe2-S<br/>METAL 1 3; Fe2-S Score=1.3",
             sb.toString());
@@ -154,19 +153,19 @@ public class SequenceAnnotationReportTest
      */
     minmax.put("METAL", new float[][] { { 2f, 2f }, null });
     sb.setLength(0);
-    sar.appendFeature(sb, 1, fr, sf, null);
+    sar.appendFeature(sb, 1, fr, sf, null, 0);
     assertEquals("METAL 1 3; Fe2-S", sb.toString());
   }
 
   @Test(groups = "Functional")
   public void testAppendFeature_noScore()
   {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
     StringBuilder sb = new StringBuilder();
     SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
             Float.NaN, "group");
 
-    sar.appendFeature(sb, 1, null, sf, null);
+    sar.appendFeature(sb, 1, null, sf, null, 0);
     assertEquals("METAL 1 3; Fe2-S", sb.toString());
   }
 
@@ -176,7 +175,7 @@ public class SequenceAnnotationReportTest
   @Test(groups = "Functional")
   public void testAppendFeature_colouredByAttribute()
   {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
     StringBuilder sb = new StringBuilder();
     SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
             Float.NaN, "group");
@@ -186,7 +185,7 @@ public class SequenceAnnotationReportTest
      * first with no colour by attribute
      */
     FeatureRendererModel fr = new FeatureRenderer(null);
-    sar.appendFeature(sb, 1, fr, sf, null);
+    sar.appendFeature(sb, 1, fr, sf, null, 0);
     assertEquals("METAL 1 3; Fe2-S", sb.toString());
 
     /*
@@ -197,7 +196,7 @@ public class SequenceAnnotationReportTest
     fc.setAttributeName("Pfam");
     fr.setColour("METAL", fc);
     sb.setLength(0);
-    sar.appendFeature(sb, 1, fr, sf, null);
+    sar.appendFeature(sb, 1, fr, sf, null, 0);
     assertEquals("METAL 1 3; Fe2-S", sb.toString()); // no change
 
     /*
@@ -205,7 +204,7 @@ public class SequenceAnnotationReportTest
      */
     fc.setAttributeName("clinical_significance");
     sb.setLength(0);
-    sar.appendFeature(sb, 1, fr, sf, null);
+    sar.appendFeature(sb, 1, fr, sf, null, 0);
     assertEquals("METAL 1 3; Fe2-S; clinical_significance=Benign",
             sb.toString());
   }
@@ -213,7 +212,7 @@ public class SequenceAnnotationReportTest
   @Test(groups = "Functional")
   public void testAppendFeature_withScoreStatusAttribute()
   {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
     StringBuilder sb = new StringBuilder();
     SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f,
             "group");
@@ -227,7 +226,7 @@ public class SequenceAnnotationReportTest
     fc.setAttributeName("clinical_significance");
     fr.setColour("METAL", fc);
     minmax.put("METAL", new float[][] { { 0f, 1f }, null });
-    sar.appendFeature(sb, 1, fr, sf, null);
+    sar.appendFeature(sb, 1, fr, sf, null, 0);
 
     assertEquals(
             "METAL 1 3; Fe2-S Score=1.3; (Confirmed); clinical_significance=Benign",
@@ -237,38 +236,38 @@ public class SequenceAnnotationReportTest
   @Test(groups = "Functional")
   public void testAppendFeature_DescEqualsType()
   {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
     StringBuilder sb = new StringBuilder();
     SequenceFeature sf = new SequenceFeature("METAL", "METAL", 1, 3,
             Float.NaN, "group");
 
     // description is not included if it duplicates type:
-    sar.appendFeature(sb, 1, null, sf, null);
+    sar.appendFeature(sb, 1, null, sf, null, 0);
     assertEquals("METAL 1 3", sb.toString());
 
     sb.setLength(0);
     sf.setDescription("Metal");
     // test is case-sensitive:
-    sar.appendFeature(sb, 1, null, sf, null);
+    sar.appendFeature(sb, 1, null, sf, null, 0);
     assertEquals("METAL 1 3; Metal", sb.toString());
   }
 
   @Test(groups = "Functional")
   public void testAppendFeature_stripHtml()
   {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
     StringBuilder sb = new StringBuilder();
     SequenceFeature sf = new SequenceFeature("METAL",
             "<html><body>hello<em>world</em></body></html>", 1, 3,
             Float.NaN, "group");
 
-    sar.appendFeature(sb, 1, null, sf, null);
+    sar.appendFeature(sb, 1, null, sf, null, 0);
     // !! strips off </body> but not <body> ??
     assertEquals("METAL 1 3; <body>hello<em>world</em>", sb.toString());
 
     sb.setLength(0);
     sf.setDescription("<br>&kHD>6");
-    sar.appendFeature(sb, 1, null, sf, null);
+    sar.appendFeature(sb, 1, null, sf, null, 0);
     // if no <html> tag, html-encodes > and < (only):
     assertEquals("METAL 1 3; &lt;br&gt;&kHD&gt;6", sb.toString());
   }
@@ -276,7 +275,7 @@ public class SequenceAnnotationReportTest
   @Test(groups = "Functional")
   public void testCreateSequenceAnnotationReport()
   {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
     StringBuilder sb = new StringBuilder();
 
     SequenceI seq = new Sequence("s1", "MAKLKRFQSSTLL");
@@ -398,7 +397,7 @@ public class SequenceAnnotationReportTest
   @Test(groups = "Functional")
   public void testCreateSequenceAnnotationReport_withEllipsis()
   {
-    SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
+    SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
     StringBuilder sb = new StringBuilder();
   
     SequenceI seq = new Sequence("s1", "ABC");