From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 31 Oct 2017 18:12:36 +0000 (+0000)
Subject: Merge branch 'bug/JAL-2791selectVisibleFeatures' into
X-Git-Tag: Release_2_11_0~164
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d2fbfb17ae43c983123e18a0ef1074c2aba907ff;hp=19bf96b1bcedc7c00f97e1947d889c24fec48ae7;p=jalview.git

Merge branch 'bug/JAL-2791selectVisibleFeatures' into
features/JAL-1793VCF

Conflicts:
	src/jalview/controller/AlignViewController.java
---

diff --git a/.classpath b/.classpath
index c4a2832..441ba60 100644
--- a/.classpath
+++ b/.classpath
@@ -48,11 +48,9 @@
 	<classpathentry kind="lib" path="lib/VARNAv3-93.jar"/>
 	<classpathentry kind="lib" path="lib/jfreesvg-2.1.jar"/>
 	<classpathentry kind="lib" path="lib/quaqua-filechooser-only-8.0.jar"/>
-	<classpathentry kind="lib" path="lib/htsjdk-1.133.jar"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin"/>
 	<classpathentry kind="lib" path="lib/xml-apis.jar"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Plugin.jar"/>
 	<classpathentry kind="lib" path="lib/jersey-client-1.19.jar"/>
 	<classpathentry kind="lib" path="lib/jersey-core-1.19.jar"/>
@@ -69,5 +67,7 @@
 	<classpathentry kind="lib" path="lib/biojava-core-4.1.0.jar"/>
 	<classpathentry kind="lib" path="lib/biojava-ontology-4.1.0.jar"/>
 	<classpathentry kind="lib" path="lib/groovy-all-2.4.6-indy.jar"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
+	<classpathentry kind="lib" path="lib/htsjdk-2.12.0.jar"/>
 	<classpathentry kind="output" path="classes"/>
 </classpath>
diff --git a/.settings/org.eclipse.jdt.core.prefs b/.settings/org.eclipse.jdt.core.prefs
index 8a5e7a7..5908bb2 100644
--- a/.settings/org.eclipse.jdt.core.prefs
+++ b/.settings/org.eclipse.jdt.core.prefs
@@ -1,15 +1,15 @@
 eclipse.preferences.version=1
 org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
 org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
 org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
-org.eclipse.jdt.core.compiler.compliance=1.7
+org.eclipse.jdt.core.compiler.compliance=1.8
 org.eclipse.jdt.core.compiler.debug.lineNumber=generate
 org.eclipse.jdt.core.compiler.debug.localVariable=generate
 org.eclipse.jdt.core.compiler.debug.sourceFile=generate
 org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
 org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
-org.eclipse.jdt.core.compiler.source=1.7
+org.eclipse.jdt.core.compiler.source=1.8
 org.eclipse.jdt.core.formatter.align_type_members_on_columns=false
 org.eclipse.jdt.core.formatter.alignment_for_arguments_in_allocation_expression=16
 org.eclipse.jdt.core.formatter.alignment_for_arguments_in_annotation=52
diff --git a/build.xml b/build.xml
index f39fdf3..436148a 100755
--- a/build.xml
+++ b/build.xml
@@ -106,8 +106,8 @@
     <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
     <property name="j2sev" value="1.7+" />
     <!-- Java Compilation settings - source and target javac version -->
-    <property name="javac.source" value="1.7" />
-    <property name="javac.target" value="1.7" />
+    <property name="javac.source" value="1.8" />
+    <property name="javac.target" value="1.8" />
 
     <!-- Permissions for running Java applets and applications. -->
     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
@@ -425,7 +425,7 @@
           <offline_allowed />
         </information>
         <resources>
-          <j2se version="1.7+" />
+          <j2se version="1.8+" />
           <jar main="true" href="jalview.jar"/>
           <fileset dir="${packageDir}">
             <exclude name="jalview.jar" />
@@ -451,8 +451,8 @@
 
     <jnlpf toFile="${jnlpFile}" />
     <!-- add the add-modules j2se attribute for java 9 -->
-    <replace file="${jnlpFile}" value="j2se version=&quot;1.7+&quot; initial-heap-size=&quot;${inih}&quot; max-heap-size=&quot;${maxh}&quot; java-vm-args=&quot;--add-modules=java.se.ee&quot;">
-          <replacetoken>j2se version="1.7+"</replacetoken>
+    <replace file="${jnlpFile}" value="j2se version=&quot;1.8+&quot; initial-heap-size=&quot;${inih}&quot; max-heap-size=&quot;${maxh}&quot; java-vm-args=&quot;--add-modules=java.se.ee&quot;">
+          <replacetoken>j2se version="1.8+"</replacetoken>
            
         </replace>
   </target>
@@ -624,7 +624,7 @@
       <include name="plugin.jar" />
     </fileset>
   </path>
-  <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
+  <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard_5.3.3.jar" />
 
   <proguard verbose="true" >
     <injar file="in.jar" />
diff --git a/lib/htsjdk-2.12.0.jar b/lib/htsjdk-2.12.0.jar
new file mode 100644
index 0000000..1df12b2
Binary files /dev/null and b/lib/htsjdk-2.12.0.jar differ
diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 5d9bdff..c950bbc 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -490,6 +490,10 @@ label.settings_for_type = Settings for {0}
 label.view_full_application = View in Full Application
 label.load_associated_tree = Load Associated Tree...
 label.load_features_annotations = Load Features/Annotations...
+label.load_vcf = Load SNP variants from plain text or indexed VCF data
+label.load_vcf_file = Load VCF File
+label.searching_vcf = Loading VCF variants...
+label.added_vcf = Added {0} VCF variants to {1} sequence(s)
 label.export_features = Export Features...
 label.export_annotations = Export Annotations...
 label.to_upper_case = To Upper Case
@@ -1319,3 +1323,14 @@ label.select_hidden_colour = Select hidden colour
 label.overview = Overview
 label.reset_to_defaults = Reset to defaults
 label.oview_calc = Recalculating overview...
+label.feature_details = Feature details
+label.matchCondition_contains = Contains
+label.matchCondition_notcontains = Does not contain
+label.matchCondition_matches = Matches
+label.matchCondition_notmatches = Does not match
+label.matchCondition_eq = =
+label.matchCondition_ne = not =
+label.matchCondition_lt = <
+label.matchCondition_le = <=
+label.matchCondition_gt = >
+label.matchCondition_ge = >=
diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 90d9197..bef667d 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -29,6 +29,7 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.GeneLociI;
 import jalview.datamodel.IncompleteCodonException;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
@@ -36,6 +37,7 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.features.SequenceFeatures;
+import jalview.io.gff.Gff3Helper;
 import jalview.io.gff.SequenceOntologyI;
 import jalview.schemes.ResidueProperties;
 import jalview.util.Comparison;
@@ -105,6 +107,15 @@ public class AlignmentUtils
     {
       return variant == null ? null : variant.getFeatureGroup();
     }
+
+    /**
+     * toString for aid in the debugger only
+     */
+    @Override
+    public String toString()
+    {
+      return base + ":" + (variant == null ? "" : variant.getDescription());
+    }
   }
 
   /**
@@ -384,7 +395,7 @@ public class AlignmentUtils
    * Answers true if the mappings include one between the given (dataset)
    * sequences.
    */
-  public static boolean mappingExists(List<AlignedCodonFrame> mappings,
+  protected static boolean mappingExists(List<AlignedCodonFrame> mappings,
           SequenceI aaSeq, SequenceI cdnaSeq)
   {
     if (mappings != null)
@@ -1636,8 +1647,8 @@ public class AlignmentUtils
       productSeqs = new HashSet<SequenceI>();
       for (SequenceI seq : products)
       {
-        productSeqs.add(seq.getDatasetSequence() == null ? seq
-                : seq.getDatasetSequence());
+        productSeqs.add(seq.getDatasetSequence() == null ? seq : seq
+                .getDatasetSequence());
       }
     }
 
@@ -1730,9 +1741,8 @@ public class AlignmentUtils
           /*
            * add a mapping from CDS to the (unchanged) mapped to range
            */
-          List<int[]> cdsRange = Collections
-                  .singletonList(new int[]
-                  { 1, cdsSeq.getLength() });
+          List<int[]> cdsRange = Collections.singletonList(new int[] { 1,
+              cdsSeq.getLength() });
           MapList cdsToProteinMap = new MapList(cdsRange,
                   mapList.getToRanges(), mapList.getFromRatio(),
                   mapList.getToRatio());
@@ -1754,7 +1764,7 @@ public class AlignmentUtils
            * add another mapping from original 'from' range to CDS
            */
           AlignedCodonFrame dnaToCdsMapping = new AlignedCodonFrame();
-          MapList dnaToCdsMap = new MapList(mapList.getFromRanges(),
+          final MapList dnaToCdsMap = new MapList(mapList.getFromRanges(),
                   cdsRange, 1, 1);
           dnaToCdsMapping.addMap(dnaSeq.getDatasetSequence(), cdsSeqDss,
                   dnaToCdsMap);
@@ -1764,6 +1774,13 @@ public class AlignmentUtils
           }
 
           /*
+           * transfer dna chromosomal loci (if known) to the CDS
+           * sequence (via the mapping)
+           */
+          final MapList cdsToDnaMap = dnaToCdsMap.getInverse();
+          transferGeneLoci(dnaSeq, cdsToDnaMap, cdsSeq);
+
+          /*
            * add DBRef with mapping from protein to CDS
            * (this enables Get Cross-References from protein alignment)
            * This is tricky because we can't have two DBRefs with the
@@ -1782,26 +1799,30 @@ public class AlignmentUtils
 
           for (DBRefEntry primRef : dnaDss.getPrimaryDBRefs())
           {
-            // creates a complementary cross-reference to the source sequence's
-            // primary reference.
-
-            DBRefEntry cdsCrossRef = new DBRefEntry(primRef.getSource(),
-                    primRef.getSource() + ":" + primRef.getVersion(),
-                    primRef.getAccessionId());
-            cdsCrossRef
-                    .setMap(new Mapping(dnaDss, new MapList(dnaToCdsMap)));
+            /*
+             * create a cross-reference from CDS to the source sequence's
+             * primary reference and vice versa
+             */
+            String source = primRef.getSource();
+            String version = primRef.getVersion();
+            DBRefEntry cdsCrossRef = new DBRefEntry(source, source + ":"
+                    + version, primRef.getAccessionId());
+            cdsCrossRef.setMap(new Mapping(dnaDss, new MapList(cdsToDnaMap)));
             cdsSeqDss.addDBRef(cdsCrossRef);
 
+            dnaSeq.addDBRef(new DBRefEntry(source, version, cdsSeq
+                    .getName(), new Mapping(cdsSeqDss, dnaToCdsMap)));
+
             // problem here is that the cross-reference is synthesized -
             // cdsSeq.getName() may be like 'CDS|dnaaccession' or
             // 'CDS|emblcdsacc'
             // assuming cds version same as dna ?!?
 
-            DBRefEntry proteinToCdsRef = new DBRefEntry(primRef.getSource(),
-                    primRef.getVersion(), cdsSeq.getName());
+            DBRefEntry proteinToCdsRef = new DBRefEntry(source, version,
+                    cdsSeq.getName());
             //
-            proteinToCdsRef.setMap(
-                    new Mapping(cdsSeqDss, cdsToProteinMap.getInverse()));
+            proteinToCdsRef.setMap(new Mapping(cdsSeqDss, cdsToProteinMap
+                    .getInverse()));
             proteinProduct.addDBRef(proteinToCdsRef);
           }
 
@@ -1814,14 +1835,46 @@ public class AlignmentUtils
       }
     }
 
-    AlignmentI cds = new Alignment(
-            cdsSeqs.toArray(new SequenceI[cdsSeqs.size()]));
+    AlignmentI cds = new Alignment(cdsSeqs.toArray(new SequenceI[cdsSeqs
+            .size()]));
     cds.setDataset(dataset);
 
     return cds;
   }
 
   /**
+   * Tries to transfer gene loci (dbref to chromosome positions) from fromSeq to
+   * toSeq, mediated by the given mapping between the sequences
+   * 
+   * @param fromSeq
+   * @param targetToFrom
+   *          Map
+   * @param targetSeq
+   */
+  protected static void transferGeneLoci(SequenceI fromSeq,
+          MapList targetToFrom, SequenceI targetSeq)
+  {
+    if (targetSeq.getGeneLoci() != null)
+    {
+      // already have - don't override
+      return;
+    }
+    GeneLociI fromLoci = fromSeq.getGeneLoci();
+    if (fromLoci == null)
+    {
+      return;
+    }
+
+    MapList newMap = targetToFrom.traverse(fromLoci.getMap());
+
+    if (newMap != null)
+    {
+      targetSeq.setGeneLoci(fromLoci.getSpeciesId(),
+              fromLoci.getAssemblyId(), fromLoci.getChromosomeId(), newMap);
+    }
+  }
+
+  /**
    * A helper method that finds a CDS sequence in the alignment dataset that is
    * mapped to the given protein sequence, and either is, or has a mapping from,
    * the given dna sequence.
@@ -1989,19 +2042,19 @@ public class AlignmentUtils
   }
 
   /**
-   * add any DBRefEntrys to cdsSeq from contig that have a Mapping congruent to
+   * Adds any DBRefEntrys to cdsSeq from contig that have a Mapping congruent to
    * the given mapping.
    * 
    * @param cdsSeq
    * @param contig
+   * @param proteinProduct
    * @param mapping
-   * @return list of DBRefEntrys added.
+   * @return list of DBRefEntrys added
    */
-  public static List<DBRefEntry> propagateDBRefsToCDS(SequenceI cdsSeq,
+  protected static List<DBRefEntry> propagateDBRefsToCDS(SequenceI cdsSeq,
           SequenceI contig, SequenceI proteinProduct, Mapping mapping)
   {
-
-    // gather direct refs from contig congrent with mapping
+    // gather direct refs from contig congruent with mapping
     List<DBRefEntry> direct = new ArrayList<DBRefEntry>();
     HashSet<String> directSources = new HashSet<String>();
     if (contig.getDBRefs() != null)
@@ -2081,7 +2134,7 @@ public class AlignmentUtils
    *          subtypes in the Sequence Ontology)
    * @param omitting
    */
-  public static int transferFeatures(SequenceI fromSeq, SequenceI toSeq,
+  protected static int transferFeatures(SequenceI fromSeq, SequenceI toSeq,
           MapList mapping, String select, String... omitting)
   {
     SequenceI copyTo = toSeq;
@@ -2235,7 +2288,7 @@ public class AlignmentUtils
    * @param dnaSeq
    * @return
    */
-  public static List<int[]> findCdsPositions(SequenceI dnaSeq)
+  protected static List<int[]> findCdsPositions(SequenceI dnaSeq)
   {
     List<int[]> result = new ArrayList<int[]>();
 
@@ -2370,7 +2423,7 @@ public class AlignmentUtils
     {
       if (var.variant != null)
       {
-        String alleles = (String) var.variant.getValue("alleles");
+        String alleles = (String) var.variant.getValue(Gff3Helper.ALLELES);
         if (alleles != null)
         {
           for (String base : alleles.split(","))
@@ -2392,7 +2445,7 @@ public class AlignmentUtils
     {
       if (var.variant != null)
       {
-        String alleles = (String) var.variant.getValue("alleles");
+        String alleles = (String) var.variant.getValue(Gff3Helper.ALLELES);
         if (alleles != null)
         {
           for (String base : alleles.split(","))
@@ -2414,7 +2467,7 @@ public class AlignmentUtils
     {
       if (var.variant != null)
       {
-        String alleles = (String) var.variant.getValue("alleles");
+        String alleles = (String) var.variant.getValue(Gff3Helper.ALLELES);
         if (alleles != null)
         {
           for (String base : alleles.split(","))
@@ -2509,7 +2562,10 @@ public class AlignmentUtils
 
   /**
    * Builds a map whose key is position in the protein sequence, and value is a
-   * list of the base and all variants for each corresponding codon position
+   * list of the base and all variants for each corresponding codon position.
+   * <p>
+   * This depends on dna variants being held as a comma-separated list as
+   * property "alleles" on variant features.
    * 
    * @param dnaSeq
    * @param dnaToProtein
@@ -2547,6 +2603,30 @@ public class AlignmentUtils
         // not handling multi-locus variant features
         continue;
       }
+
+      /*
+       * ignore variant if not a SNP
+       */
+      String alls = (String) sf.getValue(Gff3Helper.ALLELES);
+      if (alls == null)
+      {
+        continue; // non-SNP VCF variant perhaps - can't process this
+      }
+
+      String[] alleles = alls.toUpperCase().split(",");
+      boolean isSnp = true;
+      for (String allele : alleles)
+      {
+        if (allele.trim().length() > 1)
+        {
+          isSnp = false;
+        }
+      }
+      if (!isSnp)
+      {
+        continue;
+      }
+
       int[] mapsTo = dnaToProtein.locateInTo(dnaCol, dnaCol);
       if (mapsTo == null)
       {
@@ -2565,21 +2645,6 @@ public class AlignmentUtils
       }
 
       /*
-       * extract dna variants to a string array
-       */
-      String alls = (String) sf.getValue("alleles");
-      if (alls == null)
-      {
-        continue;
-      }
-      String[] alleles = alls.toUpperCase().split(",");
-      int i = 0;
-      for (String allele : alleles)
-      {
-        alleles[i++] = allele.trim(); // lose any space characters "A, G"
-      }
-
-      /*
        * get this peptide's codon positions e.g. [3, 4, 5] or [4, 7, 10]
        */
       int[] codon = peptidePosition == lastPeptidePostion ? lastCodon
diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index a10b037..f3088ea 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -851,6 +851,23 @@ public class Dna
   }
 
   /**
+   * Answers the reverse complement of the input string
+   * 
+   * @see #getComplement(char)
+   * @param s
+   * @return
+   */
+  public static String reverseComplement(String s)
+  {
+    StringBuilder sb = new StringBuilder(s.length());
+    for (int i = s.length() - 1; i >= 0; i--)
+    {
+      sb.append(Dna.getComplement(s.charAt(i)));
+    }
+    return sb.toString();
+  }
+
+  /**
    * Returns dna complement (preserving case) for aAcCgGtTuU. Ambiguity codes
    * are treated as on http://reverse-complement.com/. Anything else is left
    * unchanged.
diff --git a/src/jalview/api/FeatureColourI.java b/src/jalview/api/FeatureColourI.java
index 0ded079..3b2313d 100644
--- a/src/jalview/api/FeatureColourI.java
+++ b/src/jalview/api/FeatureColourI.java
@@ -21,6 +21,7 @@
 package jalview.api;
 
 import jalview.datamodel.SequenceFeature;
+import jalview.util.matcher.KeyedMatcherSetI;
 
 import java.awt.Color;
 
@@ -169,4 +170,20 @@ public interface FeatureColourI
    * @return
    */
   String toJalviewFormat(String featureType);
+
+  /**
+   * Sets the attribute filter conditions, or removes them if the argument is
+   * null
+   * 
+   * @param filter
+   */
+  public void setAttributeFilters(KeyedMatcherSetI filter);
+
+  /**
+   * Answers the attribute value filters for the colour scheme, or null if no
+   * filters are set
+   * 
+   * @return
+   */
+  public KeyedMatcherSetI getAttributeFilters();
 }
diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 7bb295e..8b001b3 100644
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -247,12 +247,11 @@ public class AlignViewController implements AlignViewControllerI
         boolean found = false;
         for (SequenceFeature sf : sfs)
         {
-          {
-            if (!visibleFeatures.contains(sf.getType())
-                    || fr.getColour(sf) == null) // could pull up getColour to
-                                                 // FeatureRenderer interface
-            {
-              continue;
+          { 
+            if (!visibleFeatures.contains(sf.getType()) 
+                    || fr.getColour(sf) == null) // could pull up getColour to FeatureRenderer interface 
+            { 
+              continue; 
             }
           }
           if (!found)
@@ -260,6 +259,7 @@ public class AlignViewController implements AlignViewControllerI
             nseq++;
           }
           found = true;
+
           int sfStartCol = sq.findIndex(sf.getBegin());
           int sfEndCol = sq.findIndex(sf.getEnd());
 
diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index f7837f7..98868ce 100755
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -27,7 +27,20 @@ import java.util.List;
 
 public class DBRefEntry implements DBRefEntryI
 {
-  String source = "", version = "", accessionId = "";
+  /*
+   * the mapping to chromosome (genome) is held as an instance with
+   * source = speciesId
+   * version = assemblyId
+   * accessionId = "chromosome:" + chromosomeId
+   * map = mapping from sequence to reference assembly
+   */
+  public static final String CHROMOSOME = "chromosome";
+
+  String source = "";
+
+  String version = "";
+
+  String accessionId = "";
 
   /**
    * maps from associated sequence to the database sequence's coordinate system
@@ -331,4 +344,14 @@ public class DBRefEntry implements DBRefEntryI
     }
     return true;
   }
+
+  /**
+   * Mappings to chromosome are held with accessionId as "chromosome:id"
+   * 
+   * @return
+   */
+  public boolean isChromosome()
+  {
+    return accessionId != null && accessionId.startsWith(CHROMOSOME + ":");
+  }
 }
diff --git a/src/jalview/datamodel/GeneLociI.java b/src/jalview/datamodel/GeneLociI.java
new file mode 100644
index 0000000..f8c7ec5
--- /dev/null
+++ b/src/jalview/datamodel/GeneLociI.java
@@ -0,0 +1,38 @@
+package jalview.datamodel;
+
+import jalview.util.MapList;
+
+/**
+ * An interface to model one or more contiguous regions on one chromosome
+ */
+public interface GeneLociI
+{
+  /**
+   * Answers the species identifier
+   * 
+   * @return
+   */
+  String getSpeciesId();
+
+  /**
+   * Answers the reference assembly identifier
+   * 
+   * @return
+   */
+  String getAssemblyId();
+
+  /**
+   * Answers the chromosome identifier e.g. "2", "Y", "II"
+   * 
+   * @return
+   */
+  String getChromosomeId();
+
+  /**
+   * Answers the mapping from sequence to chromosome loci. For a reverse strand
+   * mapping, the chromosomal ranges will have start > end.
+   * 
+   * @return
+   */
+  MapList getMap();
+}
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 96b0757..1905f42 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -662,10 +662,10 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   /**
-   * DOCUMENT ME!
+   * Sets the sequence description, and also parses out any special formats of
+   * interest
    * 
    * @param desc
-   *          DOCUMENT ME!
    */
   @Override
   public void setDescription(String desc)
@@ -673,10 +673,67 @@ public class Sequence extends ASequence implements SequenceI
     this.description = desc;
   }
 
+  @Override
+  public void setGeneLoci(String speciesId, String assemblyId,
+          String chromosomeId, MapList map)
+  {
+    addDBRef(new DBRefEntry(speciesId, assemblyId, DBRefEntry.CHROMOSOME
+            + ":" + chromosomeId, new Mapping(map)));
+  }
+
   /**
-   * DOCUMENT ME!
+   * Returns the gene loci mapping for the sequence (may be null)
    * 
-   * @return DOCUMENT ME!
+   * @return
+   */
+  @Override
+  public GeneLociI getGeneLoci()
+  {
+    DBRefEntry[] refs = getDBRefs();
+    if (refs != null)
+    {
+      for (final DBRefEntry ref : refs)
+      {
+        if (ref.isChromosome())
+        {
+          return new GeneLociI()
+          {
+            @Override
+            public String getSpeciesId()
+            {
+              return ref.getSource();
+            }
+
+            @Override
+            public String getAssemblyId()
+            {
+              return ref.getVersion();
+            }
+
+            @Override
+            public String getChromosomeId()
+            {
+              // strip off "chromosome:" prefix to chrId
+              return ref.getAccessionId().substring(
+                      DBRefEntry.CHROMOSOME.length() + 1);
+            }
+
+            @Override
+            public MapList getMap()
+            {
+              return ref.getMap().getMap();
+            }
+          };
+        }
+      }
+    }
+    return null;
+  }
+
+  /**
+   * Answers the description
+   * 
+   * @return
    */
   @Override
   public String getDescription()
diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 9c4087e..5029da5 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -20,18 +20,23 @@
  */
 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.HashMap;
 import java.util.Map;
 import java.util.Map.Entry;
+import java.util.TreeMap;
 import java.util.Vector;
 
 /**
- * DOCUMENT ME!
- * 
- * @author $author$
- * @version $Revision$
+ * A class that models a single contiguous feature on a sequence. If flag
+ * 'contactFeature' is true, the start and end positions are interpreted instead
+ * as two contact points.
  */
 public class SequenceFeature implements FeatureLocationI
 {
@@ -51,6 +56,20 @@ public class SequenceFeature implements FeatureLocationI
   // private key for ENA location designed not to conflict with real GFF data
   private static final String LOCATION = "!Location";
 
+  private static final String ROW_DATA = "<tr><td>%s</td><td>%s</td><td>%s</td></tr>";
+
+  /*
+   * map of otherDetails special keys, and their value fields' delimiter
+   */
+  private static final Map<String, String> INFO_KEYS = new HashMap<>();
+
+  static
+  {
+    INFO_KEYS.put("CSQ", ",");
+    // todo capture second level metadata (CSQ FORMAT)
+    // and delimiter "|" so as to report in a table within a table?
+  }
+
   /*
    * ATTRIBUTES is reserved for the GFF 'column 9' data, formatted as
    * name1=value1;name2=value2,value3;...etc
@@ -84,6 +103,12 @@ public class SequenceFeature implements FeatureLocationI
 
   public Vector<String> links;
 
+  /*
+   * the identifier (if known) for the FeatureSource held in FeatureSources,
+   * as a provider of metadata about feature attributes 
+   */
+  private String source;
+
   /**
    * Constructs a duplicate feature. Note: Uses makes a shallow copy of the
    * otherDetails map, so the new and original SequenceFeature may reference the
@@ -155,6 +180,8 @@ public class SequenceFeature implements FeatureLocationI
     this(newType, sf.getDescription(), newBegin, newEnd, newScore,
             newGroup);
 
+    this.source = sf.source;
+
     if (sf.otherDetails != null)
     {
       otherDetails = new HashMap<String, Object>();
@@ -398,6 +425,7 @@ public class SequenceFeature implements FeatureLocationI
       }
 
       otherDetails.put(key, value);
+      FeatureAttributes.getInstance().addAttribute(this.type, key);
     }
   }
 
@@ -535,4 +563,135 @@ public class SequenceFeature implements FeatureLocationI
   {
     return begin == 0 && end == 0;
   }
+
+  /**
+   * Answers an html-formatted report of feature details
+   * 
+   * @return
+   */
+  public String getDetailsReport()
+  {
+    FeatureSourceI metadata = FeatureSources.getInstance()
+            .getSource(source);
+
+    StringBuilder sb = new StringBuilder(128);
+    sb.append("<br>");
+    sb.append("<table>");
+    sb.append(String.format(ROW_DATA, "Type", type, ""));
+    sb.append(String.format(ROW_DATA, "Start/end", begin == end ? begin
+            : begin + (isContactFeature() ? ":" : "-") + end, ""));
+    String desc = StringUtils.stripHtmlTags(description);
+    sb.append(String.format(ROW_DATA, "Description", desc, ""));
+    if (!Float.isNaN(score) && score != 0f)
+    {
+      sb.append(String.format(ROW_DATA, "Score", score, ""));
+    }
+    if (featureGroup != null)
+    {
+      sb.append(String.format(ROW_DATA, "Group", featureGroup, ""));
+    }
+
+    if (otherDetails != null)
+    {
+      TreeMap<String, Object> ordered = new TreeMap<>(
+              String.CASE_INSENSITIVE_ORDER);
+      ordered.putAll(otherDetails);
+
+      for (Entry<String, Object> entry : ordered.entrySet())
+      {
+        String key = entry.getKey();
+        if (ATTRIBUTES.equals(key))
+        {
+          continue; // to avoid double reporting
+        }
+        if (INFO_KEYS.containsKey(key))
+        {
+          /*
+           * split selected INFO data by delimiter over multiple lines
+           */
+          String delimiter = INFO_KEYS.get(key);
+          String[] values = entry.getValue().toString().split(delimiter);
+          for (String value : values)
+          {
+            sb.append(String.format(ROW_DATA, key, "", value));
+          }
+        }
+        else
+        { // tried <td title="key"> but it failed to provide a tooltip :-(
+          String attDesc = null;
+          if (metadata != null)
+          {
+            attDesc = metadata.getAttributeName(key);
+          }
+          String value = entry.getValue().toString();
+          if (isValueInteresting(key, value, metadata))
+          {
+            sb.append(String.format(ROW_DATA, key, attDesc == null ? ""
+                    : attDesc, value));
+          }
+        }
+      }
+    }
+    sb.append("</table>");
+
+    String text = sb.toString();
+    return text;
+  }
+
+  /**
+   * Answers true if we judge the value is worth displaying, by some heuristic
+   * rules, else false
+   * 
+   * @param key
+   * @param value
+   * @param metadata
+   * @return
+   */
+  boolean isValueInteresting(String key, String value,
+          FeatureSourceI metadata)
+  {
+    /*
+     * currently suppressing zero values as well as null or empty
+     */
+    if (value == null || "".equals(value) || ".".equals(value)
+            || "0".equals(value))
+    {
+      return false;
+    }
+
+    if (metadata == null)
+    {
+      return true;
+    }
+
+    FeatureAttributeType attType = metadata.getAttributeType(key);
+    if (attType != null
+            && (attType == FeatureAttributeType.Float || attType
+                    .equals(FeatureAttributeType.Integer)))
+    {
+      try
+      {
+        float fval = Float.valueOf(value);
+        if (fval == 0f)
+        {
+          return false;
+        }
+      } catch (NumberFormatException e)
+      {
+        // ignore
+      }
+    }
+
+    return true; // default to interesting
+  }
+
+  /**
+   * Sets the feature source identifier
+   * 
+   * @param theSource
+   */
+  public void setSource(String theSource)
+  {
+    source = theSource;
+  }
 }
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 6e6d1aa..28be85f 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -21,6 +21,7 @@
 package jalview.datamodel;
 
 import jalview.datamodel.features.SequenceFeaturesI;
+import jalview.util.MapList;
 
 import java.util.BitSet;
 import java.util.List;
@@ -534,4 +535,22 @@ public interface SequenceI extends ASequenceI
    * @param c2
    */
   public int replace(char c1, char c2);
+
+  /**
+   * Answers the GeneLociI, or null if not known
+   * 
+   * @return
+   */
+  GeneLociI getGeneLoci();
+
+  /**
+   * Sets the mapping to gene loci for the sequence
+   * 
+   * @param speciesId
+   * @param assemblyId
+   * @param chromosomeId
+   * @param map
+   */
+  void setGeneLoci(String speciesId, String assemblyId,
+          String chromosomeId, MapList map);
 }
diff --git a/src/jalview/datamodel/features/FeatureAttributeType.java b/src/jalview/datamodel/features/FeatureAttributeType.java
new file mode 100644
index 0000000..fd3069d
--- /dev/null
+++ b/src/jalview/datamodel/features/FeatureAttributeType.java
@@ -0,0 +1,12 @@
+package jalview.datamodel.features;
+
+/**
+ * A class to model the datatype of feature attributes.
+ * 
+ * @author gmcarstairs
+ *
+ */
+public enum FeatureAttributeType
+{
+  String, Integer, Float, Character, Flag;
+}
diff --git a/src/jalview/datamodel/features/FeatureAttributes.java b/src/jalview/datamodel/features/FeatureAttributes.java
new file mode 100644
index 0000000..7990f6b
--- /dev/null
+++ b/src/jalview/datamodel/features/FeatureAttributes.java
@@ -0,0 +1,71 @@
+package jalview.datamodel.features;
+
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeSet;
+
+/**
+ * A singleton class to hold the set of attributes known for each feature type
+ */
+public class FeatureAttributes
+{
+  private static FeatureAttributes instance = new FeatureAttributes();
+
+  private Map<String, Set<String>> attributes;
+
+  /**
+   * Answers the singleton instance of this class
+   * 
+   * @return
+   */
+  public static FeatureAttributes getInstance()
+  {
+    return instance;
+  }
+
+  private FeatureAttributes()
+  {
+    attributes = new HashMap<>();
+  }
+
+  /**
+   * Answers the attributes known for the given feature type, in alphabetical
+   * order (not case sensitive), or an empty set if no attributes are known
+   * 
+   * @param featureType
+   * @return
+   */
+  public Iterable<String> getAttributes(String featureType)
+  {
+    if (!attributes.containsKey(featureType))
+    {
+      return Collections.emptySet();
+    }
+
+    return attributes.get(featureType);
+  }
+
+  /**
+   * Records the given attribute name for the given feature type
+   * 
+   * @param featureType
+   * @param attName
+   */
+  public void addAttribute(String featureType, String attName)
+  {
+    if (featureType == null || attName == null)
+    {
+      return;
+    }
+
+    if (!attributes.containsKey(featureType))
+    {
+      attributes.put(featureType, new TreeSet<String>(
+              String.CASE_INSENSITIVE_ORDER));
+    }
+
+    attributes.get(featureType).add(attName);
+  }
+}
diff --git a/src/jalview/datamodel/features/FeatureSource.java b/src/jalview/datamodel/features/FeatureSource.java
new file mode 100644
index 0000000..a1be1dc
--- /dev/null
+++ b/src/jalview/datamodel/features/FeatureSource.java
@@ -0,0 +1,78 @@
+package jalview.datamodel.features;
+
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * A class to model one source of feature data, including metadata about
+ * attributes of features
+ * 
+ * @author gmcarstairs
+ *
+ */
+public class FeatureSource implements FeatureSourceI
+{
+  private String name;
+
+  private Map<String, String> attributeNames;
+  
+  private Map<String, FeatureAttributeType> attributeTypes;
+  
+  /**
+   * Constructor
+   * 
+   * @param theName
+   */
+  public FeatureSource(String theName)
+  {
+    this.name = theName;
+    attributeNames = new HashMap<>();
+    attributeTypes = new HashMap<>();
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public String getName()
+  {
+    return name;
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public String getAttributeName(String attributeId)
+  {
+    return attributeNames.get(attributeId);
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public FeatureAttributeType getAttributeType(String attributeId)
+  {
+    return attributeTypes.get(attributeId);
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public void setAttributeName(String id, String attName)
+  {
+    attributeNames.put(id, attName);
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public void setAttributeType(String id, FeatureAttributeType type)
+  {
+    attributeTypes.put(id, type);
+  }
+
+}
diff --git a/src/jalview/datamodel/features/FeatureSourceI.java b/src/jalview/datamodel/features/FeatureSourceI.java
new file mode 100644
index 0000000..c873593
--- /dev/null
+++ b/src/jalview/datamodel/features/FeatureSourceI.java
@@ -0,0 +1,45 @@
+package jalview.datamodel.features;
+
+public interface FeatureSourceI
+{
+  /**
+   * Answers a name for the feature source (not necessarily unique)
+   * 
+   * @return
+   */
+  String getName();
+
+  /**
+   * Answers the 'long name' of an attribute given its id (short name or
+   * abbreviation), or null if not known
+   * 
+   * @param attributeId
+   * @return
+   */
+  String getAttributeName(String attributeId);
+
+  /**
+   * Sets the 'long name' of an attribute given its id (short name or
+   * abbreviation).
+   * 
+   * @param id
+   * @param name
+   */
+  void setAttributeName(String id, String name);
+
+  /**
+   * Answers the datatype of the attribute with given id, or null if not known
+   * 
+   * @param attributeId
+   * @return
+   */
+  FeatureAttributeType getAttributeType(String attributeId);
+
+  /**
+   * Sets the datatype of the attribute with given id
+   * 
+   * @param id
+   * @param type
+   */
+  void setAttributeType(String id, FeatureAttributeType type);
+}
diff --git a/src/jalview/datamodel/features/FeatureSources.java b/src/jalview/datamodel/features/FeatureSources.java
new file mode 100644
index 0000000..1be1b82
--- /dev/null
+++ b/src/jalview/datamodel/features/FeatureSources.java
@@ -0,0 +1,58 @@
+package jalview.datamodel.features;
+
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * A singleton to hold metadata about feature attributes, keyed by a unique
+ * feature source identifier
+ * 
+ * @author gmcarstairs
+ *
+ */
+public class FeatureSources
+{
+  private static FeatureSources instance = new FeatureSources();
+
+  private Map<String, FeatureSourceI> sources;
+
+  /**
+   * Answers the singleton instance of this class
+   * 
+   * @return
+   */
+  public static FeatureSources getInstance()
+  {
+    return instance;
+  }
+
+  private FeatureSources()
+  {
+    sources = new HashMap<>();
+  }
+
+  /**
+   * Answers the FeatureSource with the given unique identifier, or null if not
+   * known
+   * 
+   * @param sourceId
+   * @return
+   */
+  public FeatureSourceI getSource(String sourceId)
+  {
+    return sources.get(sourceId);
+  }
+
+  /**
+   * Adds the given source under the given key. This will replace any existing
+   * source with the same id, it is the caller's responsibility to ensure keys
+   * are unique if necessary.
+   * 
+   * @param sourceId
+   * @param source
+   */
+  public void addSource(String sourceId, FeatureSource source)
+  {
+    sources.put(sourceId, source);
+  }
+}
diff --git a/src/jalview/ext/ensembl/EnsemblData.java b/src/jalview/ext/ensembl/EnsemblData.java
new file mode 100644
index 0000000..47fe0fc
--- /dev/null
+++ b/src/jalview/ext/ensembl/EnsemblData.java
@@ -0,0 +1,91 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ext.ensembl;
+
+/**
+ * A data class to model the data and rest version of one Ensembl domain,
+ * currently for rest.ensembl.org and rest.ensemblgenomes.org
+ * 
+ * @author gmcarstairs
+ */
+class EnsemblData
+{
+  /*
+   * The http domain this object is holding data values for
+   */
+  String domain;
+
+  /*
+   * The latest version Jalview has tested for, e.g. "4.5"; a minor version change should be
+   * ok, a major version change may break stuff 
+   */
+  String expectedRestVersion;
+
+  /*
+   * Major / minor / point version e.g. "4.5.1"
+   * @see http://rest.ensembl.org/info/rest/?content-type=application/json
+   */
+  String restVersion;
+
+  /*
+   * data version
+   * @see http://rest.ensembl.org/info/data/?content-type=application/json
+   */
+  String dataVersion;
+
+  /*
+   * true when http://rest.ensembl.org/info/ping/?content-type=application/json
+   * returns response code 200 and not {"error":"Database is unavailable"}
+   */
+  boolean restAvailable;
+
+  /*
+   * absolute time when availability was last checked
+   */
+  long lastAvailableCheckTime;
+
+  /*
+   * absolute time when version numbers were last checked
+   */
+  long lastVersionCheckTime;
+
+  // flag set to true if REST major version is not the one expected
+  boolean restMajorVersionMismatch;
+
+  /*
+   * absolute time to wait till if we overloaded the REST service
+   */
+  long retryAfter;
+
+  /**
+   * Constructor given expected REST version number e.g 4.5 or 3.4.3
+   * 
+   * @param restExpected
+   */
+  EnsemblData(String theDomain, String restExpected)
+  {
+    domain = theDomain;
+    expectedRestVersion = restExpected;
+    lastAvailableCheckTime = -1;
+    lastVersionCheckTime = -1;
+  }
+
+}
diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index 50dfa90..cdcfa96 100644
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -23,6 +23,8 @@ package jalview.ext.ensembl;
 import jalview.api.FeatureColourI;
 import jalview.api.FeatureSettingsModelI;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.GeneLociI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
@@ -144,8 +146,10 @@ public class EnsemblGene extends EnsemblSeqProxy
       {
         continue;
       }
+      
       if (geneAlignment.getHeight() == 1)
       {
+        findGeneLoci(geneAlignment.getSequenceAt(0), geneId);
         getTranscripts(geneAlignment, geneId);
       }
       if (al == null)
@@ -161,6 +165,67 @@ public class EnsemblGene extends EnsemblSeqProxy
   }
 
   /**
+   * Calls the /lookup/id REST service, parses the response for gene
+   * coordinates, and if successful, adds these to the sequence. If this fails,
+   * fall back on trying to parse the sequence description in case it is in
+   * Ensembl-gene format e.g. chromosome:GRCh38:17:45051610:45109016:1.
+   * 
+   * @param seq
+   * @param geneId
+   */
+  void findGeneLoci(SequenceI seq, String geneId)
+  {
+    GeneLociI geneLoci = new EnsemblLookup(getDomain()).getGeneLoci(geneId);
+    if (geneLoci != null)
+    {
+      seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
+              geneLoci.getChromosomeId(), geneLoci.getMap());
+    }
+    else
+    {
+      parseChromosomeLocations(seq);
+    }
+  }
+
+  /**
+   * Parses and saves fields of an Ensembl-style description e.g.
+   * chromosome:GRCh38:17:45051610:45109016:1
+   * 
+   * @param seq
+   */
+  boolean parseChromosomeLocations(SequenceI seq)
+  {
+    String description = seq.getDescription();
+    if (description == null)
+    {
+      return false;
+    }
+    String[] tokens = description.split(":");
+    if (tokens.length == 6 && tokens[0].startsWith(DBRefEntry.CHROMOSOME))
+    {
+      String ref = tokens[1];
+      String chrom = tokens[2];
+      try
+      {
+        int chStart = Integer.parseInt(tokens[3]);
+        int chEnd = Integer.parseInt(tokens[4]);
+        boolean forwardStrand = "1".equals(tokens[5]);
+        String species = ""; // not known here
+        int[] from = new int[] { seq.getStart(), seq.getEnd() };
+        int[] to = new int[] { forwardStrand ? chStart : chEnd,
+            forwardStrand ? chEnd : chStart };
+        MapList map = new MapList(from, to, 1, 1);
+        seq.setGeneLoci(species, ref, chrom, map);
+        return true;
+      } catch (NumberFormatException e)
+      {
+        System.err.println("Bad integers in description " + description);
+      }
+    }
+    return false;
+  }
+
+  /**
    * Converts a query, which may contain one or more gene, transcript, or
    * external (to Ensembl) identifiers, into a non-redundant list of gene
    * identifiers.
@@ -354,6 +419,8 @@ public class EnsemblGene extends EnsemblSeqProxy
     cdna.transferFeatures(gene.getFeatures().getPositionalFeatures(),
             transcript.getDatasetSequence(), mapping, parentId);
 
+    mapTranscriptToChromosome(transcript, gene, mapping);
+
     /*
      * fetch and save cross-references
      */
@@ -368,6 +435,42 @@ public class EnsemblGene extends EnsemblSeqProxy
   }
 
   /**
+   * If the gene has a mapping to chromosome coordinates, derive the transcript
+   * chromosome regions and save on the transcript sequence
+   * 
+   * @param transcript
+   * @param gene
+   * @param mapping
+   *          the mapping from gene to transcript positions
+   */
+  protected void mapTranscriptToChromosome(SequenceI transcript,
+          SequenceI gene, MapList mapping)
+  {
+    GeneLociI loci = gene.getGeneLoci();
+    if (loci == null)
+    {
+      return;
+    }
+
+    MapList geneMapping = loci.getMap();
+
+    List<int[]> exons = mapping.getFromRanges();
+    List<int[]> transcriptLoci = new ArrayList<>();
+
+    for (int[] exon : exons)
+    {
+      transcriptLoci.add(geneMapping.locateInTo(exon[0], exon[1]));
+    }
+
+    List<int[]> transcriptRange = Arrays.asList(new int[] {
+        transcript.getStart(), transcript.getEnd() });
+    MapList mapList = new MapList(transcriptRange, transcriptLoci, 1, 1);
+
+    transcript.setGeneLoci(loci.getSpeciesId(), loci.getAssemblyId(),
+            loci.getChromosomeId(), mapList);
+  }
+
+  /**
    * Returns the 'transcript_id' property of the sequence feature (or null)
    * 
    * @param feature
diff --git a/src/jalview/ext/ensembl/EnsemblInfo.java b/src/jalview/ext/ensembl/EnsemblInfo.java
index 7668941..de55a53 100644
--- a/src/jalview/ext/ensembl/EnsemblInfo.java
+++ b/src/jalview/ext/ensembl/EnsemblInfo.java
@@ -1,86 +1,185 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ 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.
- *  
- * 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/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
 package jalview.ext.ensembl;
 
-/**
- * A data class to model the data and rest version of one Ensembl domain,
- * currently for rest.ensembl.org and rest.ensemblgenomes.org
- * 
- * @author gmcarstairs
- */
-class EnsemblInfo
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefSource;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.json.simple.JSONArray;
+import org.json.simple.parser.JSONParser;
+import org.json.simple.parser.ParseException;
+
+public class EnsemblInfo extends EnsemblRestClient
 {
-  /*
-   * The http domain this object is holding data values for
-   */
-  String domain;
 
   /*
-   * The latest version Jalview has tested for, e.g. "4.5"; a minor version change should be
-   * ok, a major version change may break stuff 
+   * cached results of REST /info/divisions service, currently
+   * <pre>
+   * { 
+   *  { "ENSEMBLFUNGI", "http://rest.ensemblgenomes.org"},
+   *    "ENSEMBLBACTERIA", "http://rest.ensemblgenomes.org"},
+   *    "ENSEMBLPROTISTS", "http://rest.ensemblgenomes.org"},
+   *    "ENSEMBLMETAZOA", "http://rest.ensemblgenomes.org"},
+   *    "ENSEMBLPLANTS",  "http://rest.ensemblgenomes.org"},
+   *    "ENSEMBL", "http://rest.ensembl.org" }
+   *  }
+   * </pre>
+   * The values for EnsemblGenomes are retrieved by a REST call, that for
+   * Ensembl is added programmatically for convenience of lookup
    */
-  String expectedRestVersion;
+  private static Map<String, String> divisions;
 
-  /*
-   * Major / minor / point version e.g. "4.5.1"
-   * @see http://rest.ensembl.org/info/rest/?content-type=application/json
-   */
-  String restVersion;
+  @Override
+  public String getDbName()
+  {
+    return "ENSEMBL";
+  }
 
-  /*
-   * data version
-   * @see http://rest.ensembl.org/info/data/?content-type=application/json
-   */
-  String dataVersion;
+  @Override
+  public AlignmentI getSequenceRecords(String queries) throws Exception
+  {
+    return null;
+  }
 
-  /*
-   * true when http://rest.ensembl.org/info/ping/?content-type=application/json
-   * returns response code 200 and not {"error":"Database is unavailable"}
+  @Override
+  protected URL getUrl(List<String> ids) throws MalformedURLException
+  {
+    return null;
+  }
+
+  @Override
+  protected boolean useGetRequest()
+  {
+    return true;
+  }
+
+  @Override
+  protected String getRequestMimeType(boolean multipleIds)
+  {
+    return "application/json";
+  }
+
+  @Override
+  protected String getResponseMimeType()
+  {
+    return "application/json";
+  }
+
+  /**
+   * Answers the domain (http://rest.ensembl.org or
+   * http://rest.ensemblgenomes.org) for the given division, or null if not
+   * recognised by Ensembl.
+   * 
+   * @param division
+   * @return
    */
-  boolean restAvailable;
+  public String getDomain(String division)
+  {
+    if (divisions == null)
+    {
+      fetchDivisions();
+    }
+    return divisions.get(division.toUpperCase());
+  }
 
-  /*
-   * absolute time when availability was last checked
+  /**
+   * On first request only, populate the lookup map by fetching the list of
+   * divisions known to EnsemblGenomes.
    */
-  long lastAvailableCheckTime;
+  void fetchDivisions()
+  {
+    divisions = new HashMap<>();
 
-  /*
-   * absolute time when version numbers were last checked
+    /*
+     * for convenience, pre-fill ensembl.org as the domain for "ENSEMBL"
+     */
+    divisions.put(DBRefSource.ENSEMBL.toUpperCase(), ENSEMBL_REST);
+
+    BufferedReader br = null;
+    try
+    {
+      URL url = getDivisionsUrl(ENSEMBL_GENOMES_REST);
+      if (url != null)
+      {
+        br = getHttpResponse(url, null);
+      }
+      parseResponse(br, ENSEMBL_GENOMES_REST);
+    } catch (IOException e)
+    {
+      // ignore
+    } finally
+    {
+      if (br != null)
+      {
+        try
+        {
+          br.close();
+        } catch (IOException e)
+        {
+          // ignore
+        }
+      }
+    }
+  }
+
+  /**
+   * Parses the JSON response to /info/divisions, and add each to the lookup map
+   * 
+   * @param br
+   * @param domain
    */
-  long lastVersionCheckTime;
+  void parseResponse(BufferedReader br, String domain)
+  {
+    JSONParser jp = new JSONParser();
+
+    try
+    {
+      JSONArray parsed = (JSONArray) jp.parse(br);
 
-  // flag set to true if REST major version is not the one expected
-  boolean restMajorVersionMismatch;
+      Iterator rvals = parsed.iterator();
+      while (rvals.hasNext())
+      {
+        String division = rvals.next().toString();
+        divisions.put(division.toUpperCase(), domain);
+      }
+    } catch (IOException | ParseException | NumberFormatException e)
+    {
+      // ignore
+    }
+  }
 
   /**
-   * Constructor given expected REST version number e.g 4.5 or 3.4.3
+   * Constructs the URL for the EnsemblGenomes /info/divisions REST service
+   * @param domain TODO
    * 
-   * @param restExpected
+   * @return
+   * @throws MalformedURLException
    */
-  EnsemblInfo(String theDomain, String restExpected)
+  URL getDivisionsUrl(String domain) throws MalformedURLException
   {
-    domain = theDomain;
-    expectedRestVersion = restExpected;
-    lastAvailableCheckTime = -1;
-    lastVersionCheckTime = -1;
+    return new URL(domain
+            + "/info/divisions?content-type=application/json");
   }
 
+  /**
+   * Returns the set of 'divisions' recognised by Ensembl or EnsemblGenomes
+   * 
+   * @return
+   */
+  public Set<String> getDivisions() {
+    if (divisions == null)
+    {
+      fetchDivisions();
+    }
+
+    return divisions.keySet();
+  }
 }
diff --git a/src/jalview/ext/ensembl/EnsemblLookup.java b/src/jalview/ext/ensembl/EnsemblLookup.java
index 31da9c0..0d1b554 100644
--- a/src/jalview/ext/ensembl/EnsemblLookup.java
+++ b/src/jalview/ext/ensembl/EnsemblLookup.java
@@ -20,31 +20,36 @@
  */
 package jalview.ext.ensembl;
 
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.GeneLociI;
+import jalview.util.MapList;
 
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
+import java.util.function.Function;
 
 import org.json.simple.JSONObject;
 import org.json.simple.parser.JSONParser;
 import org.json.simple.parser.ParseException;
 
 /**
- * A client for the Ensembl lookup REST endpoint; used to find the Parent gene
- * identifier given a transcript identifier.
+ * A client for the Ensembl lookup REST endpoint
  * 
  * @author gmcarstairs
- *
  */
 public class EnsemblLookup extends EnsemblRestClient
 {
+  private static final String SPECIES = "species";
 
-  private static final String OBJECT_TYPE_TRANSLATION = "Translation";
   private static final String PARENT = "Parent";
+
+  private static final String OBJECT_TYPE_TRANSLATION = "Translation";
   private static final String OBJECT_TYPE_TRANSCRIPT = "Transcript";
   private static final String ID = "id";
   private static final String OBJECT_TYPE_GENE = "Gene";
@@ -123,14 +128,45 @@ public class EnsemblLookup extends EnsemblRestClient
   }
 
   /**
-   * Calls the Ensembl lookup REST endpoint and retrieves the 'Parent' for the
-   * given identifier, or null if not found
+   * Calls the Ensembl lookup REST endpoint and returns
+   * <ul>
+   * <li>the 'id' for the identifier if its type is "Gene"</li>
+   * <li>the 'Parent' if its type is 'Transcript'</li>
+   * <ul>
+   * If the type is 'Translation', does a recursive call to this method, passing
+   * in the 'Parent' (transcript id).
    * 
    * @param identifier
    * @return
    */
   public String getGeneId(String identifier)
   {
+    return (String) getResult(identifier, br -> parseGeneId(br));
+  }
+
+  /**
+   * Calls the Ensembl lookup REST endpoint and retrieves the 'species' for the
+   * given identifier, or null if not found
+   * 
+   * @param identifier
+   * @return
+   */
+  public String getSpecies(String identifier)
+  {
+    return (String) getResult(identifier, br -> getAttribute(br, SPECIES));
+  }
+
+  /**
+   * Calls the /lookup/id rest service and delegates parsing of the JSON
+   * response to the supplied parser
+   * 
+   * @param identifier
+   * @param parser
+   * @return
+   */
+  protected Object getResult(String identifier,
+          Function<BufferedReader, Object> parser)
+  {
     List<String> ids = Arrays.asList(new String[] { identifier });
 
     BufferedReader br = null;
@@ -141,7 +177,7 @@ public class EnsemblLookup extends EnsemblRestClient
       {
         br = getHttpResponse(url, ids);
       }
-      return br == null ? null : parseResponse(br);
+      return br == null ? null : parser.apply(br);
     } catch (IOException e)
     {
       // ignore
@@ -162,6 +198,29 @@ public class EnsemblLookup extends EnsemblRestClient
   }
 
   /**
+   * Answers the value of 'attribute' from the JSON response, or null if not
+   * found
+   * 
+   * @param br
+   * @param attribute
+   * @return
+   */
+  protected String getAttribute(BufferedReader br, String attribute)
+  {
+    String value = null;
+    JSONParser jp = new JSONParser();
+    try
+    {
+      JSONObject val = (JSONObject) jp.parse(br);
+      value = val.get(attribute).toString();
+    } catch (ParseException | NullPointerException | IOException e)
+    {
+      // ignore
+    }
+    return value;
+  }
+
+  /**
    * Parses the JSON response and returns the gene identifier, or null if not
    * found. If the returned object_type is Gene, returns the id, if Transcript
    * returns the Parent. If it is Translation (peptide identifier), then the
@@ -169,9 +228,8 @@ public class EnsemblLookup extends EnsemblRestClient
    * 
    * @param br
    * @return
-   * @throws IOException
    */
-  protected String parseResponse(BufferedReader br) throws IOException
+  protected String parseGeneId(BufferedReader br)
   {
     String geneId = null;
     JSONParser jp = new JSONParser();
@@ -204,11 +262,87 @@ public class EnsemblLookup extends EnsemblRestClient
                           + " looping on Parent!");
         }
       }
-    } catch (ParseException e)
+    } catch (ParseException | IOException e)
     {
       // ignore
     }
     return geneId;
   }
 
+  /**
+   * Calls the /lookup/id rest service for the given id, and if successful,
+   * parses and returns the gene's chromosomal coordinates
+   * 
+   * @param geneId
+   * @return
+   */
+  public GeneLociI getGeneLoci(String geneId)
+  {
+    return (GeneLociI) getResult(geneId, br -> parseGeneLoci(br));
+  }
+
+  /**
+   * Parses the /lookup/id response for species, asssembly_name,
+   * seq_region_name, start, end and returns an object that wraps them, or null
+   * if unsuccessful
+   * 
+   * @param br
+   * @return
+   */
+  GeneLociI parseGeneLoci(BufferedReader br)
+  {
+    JSONParser jp = new JSONParser();
+    try
+    {
+      JSONObject val = (JSONObject) jp.parse(br);
+      final String species = val.get("species").toString();
+      final String assembly = val.get("assembly_name").toString();
+      final String chromosome = val.get("seq_region_name").toString();
+      String strand = val.get("strand").toString();
+      int start = Integer.parseInt(val.get("start").toString());
+      int end = Integer.parseInt(val.get("end").toString());
+      int fromEnd = end - start + 1;
+      boolean reverseStrand = "-1".equals(strand);
+      int toStart = reverseStrand ? end : start;
+      int toEnd = reverseStrand ? start : end;
+      List<int[]> fromRange = Collections.singletonList(new int[] { 1,
+          fromEnd });
+      List<int[]> toRange = Collections.singletonList(new int[] { toStart,
+          toEnd });
+      final MapList map = new MapList(fromRange, toRange, 1, 1);
+      return new GeneLociI()
+      {
+
+        @Override
+        public String getSpeciesId()
+        {
+          return species == null ? "" : species;
+        }
+
+        @Override
+        public String getAssemblyId()
+        {
+          return assembly;
+        }
+
+        @Override
+        public String getChromosomeId()
+        {
+          return chromosome;
+        }
+
+        @Override
+        public MapList getMap()
+        {
+          return map;
+        }
+      };
+    } catch (ParseException | NullPointerException | IOException
+            | NumberFormatException | ClassCastException e)
+    {
+      Cache.log.error("Error looking up gene loci: " + e.getMessage());
+    }
+    return null;
+  }
+
 }
diff --git a/src/jalview/ext/ensembl/EnsemblMap.java b/src/jalview/ext/ensembl/EnsemblMap.java
new file mode 100644
index 0000000..56657e0
--- /dev/null
+++ b/src/jalview/ext/ensembl/EnsemblMap.java
@@ -0,0 +1,422 @@
+package jalview.ext.ensembl;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.GeneLociI;
+import jalview.util.MapList;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Iterator;
+import java.util.List;
+
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+import org.json.simple.parser.ParseException;
+
+public class EnsemblMap extends EnsemblRestClient
+{
+  private static final String MAPPED = "mapped";
+
+  private static final String MAPPINGS = "mappings";
+
+  private static final String CDS = "cds";
+
+  private static final String CDNA = "cdna";
+
+  /**
+   * Default constructor (to use rest.ensembl.org)
+   */
+  public EnsemblMap()
+  {
+    super();
+  }
+
+  /**
+   * Constructor given the target domain to fetch data from
+   * 
+   * @param
+   */
+  public EnsemblMap(String domain)
+  {
+    super(domain);
+  }
+
+  @Override
+  public String getDbName()
+  {
+    return DBRefSource.ENSEMBL;
+  }
+
+  @Override
+  public AlignmentI getSequenceRecords(String queries) throws Exception
+  {
+    return null; // not used
+  }
+
+  /**
+   * Constructs a URL of the format <code>
+   * http://rest.ensembl.org/map/human/GRCh38/17:45051610..45109016:1/GRCh37?content-type=application/json
+   * </code>
+   * 
+   * @param species
+   * @param chromosome
+   * @param fromRef
+   * @param toRef
+   * @param startPos
+   * @param endPos
+   * @return
+   * @throws MalformedURLException
+   */
+  protected URL getAssemblyMapUrl(String species, String chromosome, String fromRef,
+          String toRef, int startPos, int endPos)
+          throws MalformedURLException
+  {
+    /*
+     * start-end might be reverse strand - present forwards to the service
+     */
+    boolean forward = startPos <= endPos;
+    int start = forward ? startPos : endPos;
+    int end = forward ? endPos : startPos;
+    String strand = forward ? "1" : "-1";
+    String url = String.format(
+            "%s/map/%s/%s/%s:%d..%d:%s/%s?content-type=application/json",
+            getDomain(), species, fromRef, chromosome, start, end, strand,
+            toRef);
+    return new URL(url);
+  }
+
+  @Override
+  protected boolean useGetRequest()
+  {
+    return true;
+  }
+
+  @Override
+  protected String getRequestMimeType(boolean multipleIds)
+  {
+    return "application/json";
+  }
+
+  @Override
+  protected String getResponseMimeType()
+  {
+    return "application/json";
+  }
+
+  @Override
+  protected URL getUrl(List<String> ids) throws MalformedURLException
+  {
+    return null; // not used
+  }
+
+  /**
+   * Calls the REST /map service to get the chromosomal coordinates (start/end)
+   * in 'toRef' that corresponding to the (start/end) queryRange in 'fromRef'
+   * 
+   * @param species
+   * @param chromosome
+   * @param fromRef
+   * @param toRef
+   * @param queryRange
+   * @return
+   * @see http://rest.ensemblgenomes.org/documentation/info/assembly_map
+   */
+  public int[] getAssemblyMapping(String species, String chromosome,
+          String fromRef, String toRef, int[] queryRange)
+  {
+    URL url = null;
+    BufferedReader br = null;
+
+    try
+    {
+      url = getAssemblyMapUrl(species, chromosome, fromRef, toRef, queryRange[0],
+              queryRange[1]);
+      br = getHttpResponse(url, null);
+      return (parseAssemblyMappingResponse(br));
+    } catch (Throwable t)
+    {
+      System.out.println("Error calling " + url + ": " + t.getMessage());
+      return null;
+    } finally
+    {
+      if (br != null)
+      {
+        try
+        {
+          br.close();
+        } catch (IOException e)
+        {
+          // ignore
+        }
+      }
+    }
+  }
+
+  /**
+   * Parses the JSON response from the /map/&lt;species&gt;/ REST service. The
+   * format is (with some fields omitted)
+   * 
+   * <pre>
+   *  {"mappings": 
+   *    [{
+   *       "original": {"end":45109016,"start":45051610},
+   *       "mapped"  : {"end":43186384,"start":43128978} 
+   *  }] }
+   * </pre>
+   * 
+   * @param br
+   * @return
+   */
+  protected int[] parseAssemblyMappingResponse(BufferedReader br)
+  {
+    int[] result = null;
+    JSONParser jp = new JSONParser();
+
+    try
+    {
+      JSONObject parsed = (JSONObject) jp.parse(br);
+      JSONArray mappings = (JSONArray) parsed.get(MAPPINGS);
+
+      Iterator rvals = mappings.iterator();
+      while (rvals.hasNext())
+      {
+        // todo check for "mapped"
+        JSONObject val = (JSONObject) rvals.next();
+        JSONObject mapped = (JSONObject) val.get(MAPPED);
+        int start = Integer.parseInt(mapped.get("start").toString());
+        int end = Integer.parseInt(mapped.get("end").toString());
+        String strand = mapped.get("strand").toString();
+        if ("1".equals(strand))
+        {
+          result = new int[] { start, end };
+        }
+        else
+        {
+          result = new int[] { end, start };
+        }
+      }
+    } catch (IOException | ParseException | NumberFormatException e)
+    {
+      // ignore
+    }
+    return result;
+  }
+
+  /**
+   * Calls the REST /map/cds/id service, and returns a DBRefEntry holding the
+   * returned chromosomal coordinates, or returns null if the call fails
+   * 
+   * @param division
+   *          e.g. Ensembl, EnsemblMetazoa
+   * @param accession
+   *          e.g. ENST00000592782, Y55B1AR.1.1
+   * @param start
+   * @param end
+   * @return
+   */
+  public GeneLociI getCdsMapping(String division, String accession,
+          int start, int end)
+  {
+    return getIdMapping(division, accession, start, end, CDS);
+  }
+
+  /**
+   * Calls the REST /map/cdna/id service, and returns a DBRefEntry holding the
+   * returned chromosomal coordinates, or returns null if the call fails
+   * 
+   * @param division
+   *          e.g. Ensembl, EnsemblMetazoa
+   * @param accession
+   *          e.g. ENST00000592782, Y55B1AR.1.1
+   * @param start
+   * @param end
+   * @return
+   */
+  public GeneLociI getCdnaMapping(String division, String accession,
+          int start, int end)
+  {
+    return getIdMapping(division, accession, start, end, CDNA);
+  }
+
+  GeneLociI getIdMapping(String division, String accession, int start,
+          int end, String cdsOrCdna)
+  {
+    URL url = null;
+    BufferedReader br = null;
+
+    try
+    {
+      String domain = new EnsemblInfo().getDomain(division);
+      if (domain != null)
+      {
+        url = getIdMapUrl(domain, accession, start, end, cdsOrCdna);
+        br = getHttpResponse(url, null);
+        return (parseIdMappingResponse(br, accession, domain));
+      }
+      return null;
+    } catch (Throwable t)
+    {
+      System.out.println("Error calling " + url + ": " + t.getMessage());
+      return null;
+    } finally
+    {
+      if (br != null)
+      {
+        try
+        {
+          br.close();
+        } catch (IOException e)
+        {
+          // ignore
+        }
+      }
+    }
+  }
+
+  /**
+   * Constructs a URL to the /map/cds/<id> or /map/cdna/<id> REST service. The
+   * REST call is to either ensembl or ensemblgenomes, as determined from the
+   * division, e.g. Ensembl or EnsemblProtists.
+   * 
+   * @param domain
+   * @param accession
+   * @param start
+   * @param end
+   * @param cdsOrCdna
+   * @return
+   * @throws MalformedURLException
+   */
+  URL getIdMapUrl(String domain, String accession, int start, int end,
+          String cdsOrCdna) throws MalformedURLException
+  {
+    String url = String
+            .format("%s/map/%s/%s/%d..%d?include_original_region=1&content-type=application/json",
+                    domain, cdsOrCdna, accession, start, end);
+    return new URL(url);
+  }
+
+  /**
+   * Parses the JSON response from the /map/cds/ or /map/cdna REST service. The
+   * format is
+   * 
+   * <pre>
+   * {"mappings":
+   *   [
+   *    {"assembly_name":"TAIR10","end":2501311,"seq_region_name":"1","gap":0,
+   *     "strand":-1,"coord_system":"chromosome","rank":0,"start":2501114},
+   *    {"assembly_name":"TAIR10","end":2500815,"seq_region_name":"1","gap":0,
+   *     "strand":-1,"coord_system":"chromosome","rank":0,"start":2500714}
+   *   ]
+   * }
+   * </pre>
+   * 
+   * @param br
+   * @param accession
+   * @param domain
+   * @return
+   */
+  GeneLociI parseIdMappingResponse(BufferedReader br, String accession,
+          String domain)
+  {
+    JSONParser jp = new JSONParser();
+
+    try
+    {
+      JSONObject parsed = (JSONObject) jp.parse(br);
+      JSONArray mappings = (JSONArray) parsed.get(MAPPINGS);
+
+      Iterator rvals = mappings.iterator();
+      String assembly = null;
+      String chromosome = null;
+      int fromEnd = 0;
+      List<int[]> regions = new ArrayList<>();
+
+      while (rvals.hasNext())
+      {
+        JSONObject val = (JSONObject) rvals.next();
+        JSONObject original = (JSONObject) val.get("original");
+        fromEnd = Integer.parseInt(original.get("end").toString());
+
+        JSONObject mapped = (JSONObject) val.get(MAPPED);
+        int start = Integer.parseInt(mapped.get("start").toString());
+        int end = Integer.parseInt(mapped.get("end").toString());
+        String ass = mapped.get("assembly_name").toString();
+        if (assembly != null && !assembly.equals(ass))
+        {
+          System.err
+                  .println("EnsemblMap found multiple assemblies - can't resolve");
+          return null;
+        }
+        assembly = ass;
+        String chr = mapped.get("seq_region_name").toString();
+        if (chromosome != null && !chromosome.equals(chr))
+        {
+          System.err
+                  .println("EnsemblMap found multiple chromosomes - can't resolve");
+          return null;
+        }
+        chromosome = chr;
+        String strand = mapped.get("strand").toString();
+        if ("-1".equals(strand))
+        {
+          regions.add(new int[] { end, start });
+        }
+        else
+        {
+          regions.add(new int[] { start, end });
+        }
+      }
+
+      /*
+       * processed all mapped regions on chromosome, assemble the result,
+       * having first fetched the species id for the accession
+       */
+      final String species = new EnsemblLookup(domain)
+              .getSpecies(accession);
+      final String as = assembly;
+      final String chr = chromosome;
+      List<int[]> fromRange = Collections.singletonList(new int[] { 1,
+          fromEnd });
+      final MapList map = new MapList(fromRange, regions, 1, 1);
+      return new GeneLociI()
+      {
+
+        @Override
+        public String getSpeciesId()
+        {
+          return species == null ? "" : species;
+        }
+
+        @Override
+        public String getAssemblyId()
+        {
+          return as;
+        }
+
+        @Override
+        public String getChromosomeId()
+        {
+          return chr;
+        }
+
+        @Override
+        public MapList getMap()
+        {
+          return map;
+        }
+      };
+    } catch (IOException | ParseException | NumberFormatException e)
+    {
+      // ignore
+    }
+
+    return null;
+  }
+
+}
diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java
index b1bc8e5..e3d1215 100644
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -72,7 +72,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
 
   private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
 
-  private static Map<String, EnsemblInfo> domainData;
+  private static Map<String, EnsemblData> domainData;
 
   // @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats
   private static final String PING_URL = "http://rest.ensembl.org/info/ping.json";
@@ -87,8 +87,8 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   {
     domainData = new HashMap<>();
     domainData.put(ENSEMBL_REST,
-            new EnsemblInfo(ENSEMBL_REST, LATEST_ENSEMBL_REST_VERSION));
-    domainData.put(ENSEMBL_GENOMES_REST, new EnsemblInfo(
+            new EnsemblData(ENSEMBL_REST, LATEST_ENSEMBL_REST_VERSION));
+    domainData.put(ENSEMBL_GENOMES_REST, new EnsemblData(
             ENSEMBL_GENOMES_REST, LATEST_ENSEMBLGENOMES_REST_VERSION));
   }
 
@@ -381,7 +381,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
    */
   protected boolean isEnsemblAvailable()
   {
-    EnsemblInfo info = domainData.get(getDomain());
+    EnsemblData info = domainData.get(getDomain());
 
     long now = System.currentTimeMillis();
 
@@ -455,7 +455,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
    */
   private void checkEnsemblRestVersion()
   {
-    EnsemblInfo info = domainData.get(getDomain());
+    EnsemblData info = domainData.get(getDomain());
 
     JSONParser jp = new JSONParser();
     URL url = null;
diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index 577111e..35ceea3 100644
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -34,6 +34,7 @@ import jalview.datamodel.features.SequenceFeatures;
 import jalview.exceptions.JalviewException;
 import jalview.io.FastaFile;
 import jalview.io.FileParse;
+import jalview.io.gff.Gff3Helper;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyI;
 import jalview.util.Comparison;
@@ -59,8 +60,6 @@ import java.util.Map.Entry;
  */
 public abstract class EnsemblSeqProxy extends EnsemblRestClient
 {
-  private static final String ALLELES = "alleles";
-
   protected static final String PARENT = "Parent";
 
   protected static final String ID = "ID";
@@ -717,7 +716,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
    */
   static void reverseComplementAlleles(SequenceFeature sf)
   {
-    final String alleles = (String) sf.getValue(ALLELES);
+    final String alleles = (String) sf.getValue(Gff3Helper.ALLELES);
     if (alleles == null)
     {
       return;
@@ -728,7 +727,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       reverseComplementAllele(complement, allele);
     }
     String comp = complement.toString();
-    sf.setValue(ALLELES, comp);
+    sf.setValue(Gff3Helper.ALLELES, comp);
     sf.setDescription(comp);
 
     /*
@@ -738,7 +737,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     String atts = sf.getAttributes();
     if (atts != null)
     {
-      atts = atts.replace(ALLELES + "=" + alleles, ALLELES + "=" + comp);
+      atts = atts.replace(Gff3Helper.ALLELES + "=" + alleles,
+              Gff3Helper.ALLELES + "=" + comp);
       sf.setAttributes(atts);
     }
   }
diff --git a/src/jalview/ext/ensembl/EnsemblSymbol.java b/src/jalview/ext/ensembl/EnsemblSymbol.java
index 75598a0..65be906 100644
--- a/src/jalview/ext/ensembl/EnsemblSymbol.java
+++ b/src/jalview/ext/ensembl/EnsemblSymbol.java
@@ -152,7 +152,6 @@ public class EnsemblSymbol extends EnsemblXref
             if (br != null)
             {
               String geneId = parseSymbolResponse(br);
-              System.out.println(url + " returned " + geneId);
               if (geneId != null && !result.contains(geneId))
               {
                 result.add(geneId);
diff --git a/src/jalview/ext/htsjdk/VCFReader.java b/src/jalview/ext/htsjdk/VCFReader.java
new file mode 100644
index 0000000..14c057f
--- /dev/null
+++ b/src/jalview/ext/htsjdk/VCFReader.java
@@ -0,0 +1,214 @@
+package jalview.ext.htsjdk;
+
+import htsjdk.samtools.util.CloseableIterator;
+import htsjdk.variant.variantcontext.VariantContext;
+import htsjdk.variant.vcf.VCFFileReader;
+import htsjdk.variant.vcf.VCFHeader;
+
+import java.io.Closeable;
+import java.io.File;
+import java.io.IOException;
+
+/**
+ * A thin wrapper for htsjdk classes to read either plain, or compressed, or
+ * compressed and indexed VCF files
+ */
+public class VCFReader implements Closeable, Iterable<VariantContext>
+{
+  private static final String GZ = "gz";
+
+  private static final String TBI_EXTENSION = ".tbi";
+
+  private boolean indexed;
+
+  private VCFFileReader reader;
+
+  /**
+   * Constructor given a raw or compressed VCF file or a (tabix) index file
+   * <p>
+   * For now, file type is inferred from its suffix: .gz or .bgz for compressed
+   * data, .tbi for an index file, anything else is assumed to be plain text
+   * VCF.
+   * 
+   * @param f
+   * @throws IOException
+   */
+  public VCFReader(String filePath) throws IOException
+  {
+    if (filePath.endsWith(GZ))
+    {
+      if (new File(filePath + TBI_EXTENSION).exists())
+      {
+        indexed = true;
+      }
+    }
+    else if (filePath.endsWith(TBI_EXTENSION))
+    {
+      indexed = true;
+      filePath = filePath.substring(0, filePath.length() - 4);
+    }
+
+    reader = new VCFFileReader(new File(filePath), indexed);
+  }
+
+  @Override
+  public void close() throws IOException
+  {
+    if (reader != null)
+    {
+      reader.close();
+    }
+  }
+
+  /**
+   * Returns an iterator over VCF variants in the file. The client should call
+   * close() on the iterator when finished with it.
+   */
+  @Override
+  public CloseableIterator<VariantContext> iterator()
+  {
+    return reader == null ? null : reader.iterator();
+  }
+
+  /**
+   * Queries for records overlapping the region specified. Note that this method
+   * is performant if the VCF file is indexed, and may be very slow if it is
+   * not.
+   * <p>
+   * Client code should call close() on the iterator when finished with it.
+   * 
+   * @param chrom
+   *          the chromosome to query
+   * @param start
+   *          query interval start
+   * @param end
+   *          query interval end
+   * @return
+   */
+  public CloseableIterator<VariantContext> query(final String chrom,
+          final int start, final int end)
+  {
+   if (reader == null) {
+     return null;
+   }
+    if (indexed)
+    {
+      return reader.query(chrom, start, end);
+    }
+    else
+    {
+      return queryUnindexed(chrom, start, end);
+    }
+  }
+
+  /**
+   * Returns an iterator over variant records read from a flat file which
+   * overlap the specified chromosomal positions. Call close() on the iterator
+   * when finished with it!
+   * 
+   * @param chrom
+   * @param start
+   * @param end
+   * @return
+   */
+  protected CloseableIterator<VariantContext> queryUnindexed(
+          final String chrom, final int start, final int end)
+  {
+    final CloseableIterator<VariantContext> it = reader.iterator();
+    
+    return new CloseableIterator<VariantContext>()
+    {
+      boolean atEnd = false;
+
+      // prime look-ahead buffer with next matching record
+      private VariantContext next = findNext();
+
+      private VariantContext findNext()
+      {
+        if (atEnd)
+        {
+          return null;
+        }
+        VariantContext variant = null;
+        while (it.hasNext())
+        {
+          variant = it.next();
+          int vstart = variant.getStart();
+
+          if (vstart > end)
+          {
+            atEnd = true;
+            close();
+            return null;
+          }
+
+          int vend = variant.getEnd();
+          // todo what is the undeprecated way to get
+          // the chromosome for the variant?
+          if (chrom.equals(variant.getChr()) && (vstart <= end)
+                  && (vend >= start))
+          {
+            return variant;
+          }
+        }
+        return null;
+      }
+
+      @Override
+      public boolean hasNext()
+      {
+        boolean hasNext = !atEnd && (next != null);
+        if (!hasNext)
+        {
+          close();
+        }
+        return hasNext;
+      }
+
+      @Override
+      public VariantContext next()
+      {
+        /*
+         * return the next match, and then re-prime
+         * it with the following one (if any)
+         */
+        VariantContext temp = next;
+        next = findNext();
+        return temp;
+      }
+
+      @Override
+      public void remove()
+      {
+        // not implemented
+      }
+
+      @Override
+      public void close()
+      {
+        it.close();
+      }
+    };
+  }
+
+  /**
+   * Returns an object that models the VCF file headers
+   * 
+   * @return
+   */
+  public VCFHeader getFileHeader()
+  {
+    return reader == null ? null : reader.getFileHeader();
+  }
+
+  /**
+   * Answers true if we are processing a tab-indexed VCF file, false if it is a
+   * plain text (uncompressed) file.
+   * 
+   * @return
+   */
+  public boolean isIndex()
+  {
+    return indexed;
+  }
+}
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 298688b..5b812c2 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -81,6 +81,7 @@ import jalview.io.JnetAnnotationMaker;
 import jalview.io.NewickFile;
 import jalview.io.ScoreMatrixFile;
 import jalview.io.TCoffeeScoreFile;
+import jalview.io.vcf.VCFLoader;
 import jalview.jbgui.GAlignFrame;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
@@ -839,6 +840,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     AlignmentI al = getViewport().getAlignment();
     boolean nucleotide = al.isNucleotide();
 
+    loadVcf.setVisible(nucleotide);
     showTranslation.setVisible(nucleotide);
     showReverse.setVisible(nucleotide);
     showReverseComplement.setVisible(nucleotide);
@@ -4258,7 +4260,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
           final String source)
   {
-    new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
+    new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
             .start();
   }
 
@@ -5585,6 +5587,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       new CalculationChooser(AlignFrame.this);
     }
   }
+
+  @Override
+  protected void loadVcf_actionPerformed()
+  {
+    JalviewFileChooser chooser = new JalviewFileChooser(
+            Cache.getProperty("LAST_DIRECTORY"));
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
+    chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
+
+    int value = chooser.showOpenDialog(null);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      String choice = chooser.getSelectedFile().getPath();
+      Cache.setProperty("LAST_DIRECTORY", choice);
+      new VCFLoader(viewport.getAlignment()).loadVCF(choice, this);
+    }
+
+  }
 }
 
 class PrintThread extends Thread
diff --git a/src/jalview/gui/AquaInternalFrameManager.java b/src/jalview/gui/AquaInternalFrameManager.java
index ea809eb..829135b 100644
--- a/src/jalview/gui/AquaInternalFrameManager.java
+++ b/src/jalview/gui/AquaInternalFrameManager.java
@@ -60,7 +60,6 @@ import javax.swing.JInternalFrame;
  * around to the bottom of the window stack (as the original implementation
  * does)
  * 
- * @see com.sun.java.swing.plaf.windows.WindowsDesktopManager
  */
 public class AquaInternalFrameManager extends DefaultDesktopManager
 {
diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java
index 2d1dfd4..285e574 100644
--- a/src/jalview/gui/CrossRefAction.java
+++ b/src/jalview/gui/CrossRefAction.java
@@ -27,17 +27,25 @@ import jalview.api.FeatureSettingsModelI;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
+import jalview.datamodel.GeneLociI;
 import jalview.datamodel.SequenceI;
+import jalview.ext.ensembl.EnsemblInfo;
+import jalview.ext.ensembl.EnsemblMap;
 import jalview.io.gff.SequenceOntologyI;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.DBRefUtils;
+import jalview.util.MapList;
+import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.ws.SequenceFetcher;
 
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
-
-import javax.swing.JOptionPane;
+import java.util.Map;
+import java.util.Set;
 
 /**
  * Factory constructor and runnable for discovering and displaying
@@ -52,13 +60,13 @@ public class CrossRefAction implements Runnable
 
   private SequenceI[] sel;
 
-  private boolean _odna;
+  private final boolean _odna;
 
   private String source;
 
-  List<AlignmentViewPanel> xrefViews = new ArrayList<AlignmentViewPanel>();
+  List<AlignmentViewPanel> xrefViews = new ArrayList<>();
 
-  public List<jalview.api.AlignmentViewPanel> getXrefViews()
+  List<AlignmentViewPanel> getXrefViews()
   {
     return xrefViews;
   }
@@ -90,6 +98,13 @@ public class CrossRefAction implements Runnable
       {
         return;
       }
+
+      /*
+       * try to look up chromosomal coordinates for nucleotide
+       * sequences (if not already retrieved)
+       */
+      findGeneLoci(xrefs.getSequences());
+
       /*
        * get display scheme (if any) to apply to features
        */
@@ -113,75 +128,14 @@ public class CrossRefAction implements Runnable
 
       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
       {
-        boolean copyAlignmentIsAligned = false;
-        if (dna)
-        {
-          copyAlignment = AlignmentUtils.makeCdsAlignment(sel, dataset,
-                  xrefsAlignment.getSequencesArray());
-          if (copyAlignment.getHeight() == 0)
-          {
-            JvOptionPane.showMessageDialog(alignFrame,
-                    MessageManager.getString("label.cant_map_cds"),
-                    MessageManager.getString("label.operation_failed"),
-                    JvOptionPane.OK_OPTION);
-            System.err.println("Failed to make CDS alignment");
-          }
-
-          /*
-           * pending getting Embl transcripts to 'align', 
-           * we are only doing this for Ensembl
-           */
-          // TODO proper criteria for 'can align as cdna'
-          if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
-                  || AlignmentUtils.looksLikeEnsembl(alignment))
-          {
-            copyAlignment.alignAs(alignment);
-            copyAlignmentIsAligned = true;
-          }
-        }
-        else
+        copyAlignment = copyAlignmentForSplitFrame(alignment, dataset, dna,
+                xrefs, xrefsAlignment);
+        if (copyAlignment == null)
         {
-          copyAlignment = AlignmentUtils.makeCopyAlignment(sel,
-                  xrefs.getSequencesArray(), dataset);
-        }
-        copyAlignment
-                .setGapCharacter(alignFrame.viewport.getGapCharacter());
-
-        StructureSelectionManager ssm = StructureSelectionManager
-                .getStructureSelectionManager(Desktop.instance);
-
-        /*
-         * register any new mappings for sequence mouseover etc
-         * (will not duplicate any previously registered mappings)
-         */
-        ssm.registerMappings(dataset.getCodonFrames());
-
-        if (copyAlignment.getHeight() <= 0)
-        {
-          System.err.println(
-                  "No Sequences generated for xRef type " + source);
-          return;
-        }
-        /*
-         * align protein to dna
-         */
-        if (dna && copyAlignmentIsAligned)
-        {
-          xrefsAlignment.alignAs(copyAlignment);
-        }
-        else
-        {
-          /*
-           * align cdna to protein - currently only if 
-           * fetching and aligning Ensembl transcripts!
-           */
-          // TODO: generalise for other sources of locus/transcript/cds data
-          if (dna && DBRefSource.ENSEMBL.equalsIgnoreCase(source))
-          {
-            copyAlignment.alignAs(xrefsAlignment);
-          }
+          return; // failed
         }
       }
+
       /*
        * build AlignFrame(s) according to available alignment data
        */
@@ -207,6 +161,7 @@ public class CrossRefAction implements Runnable
         xrefViews.add(newFrame.alignPanel);
         return; // via finally clause
       }
+
       AlignFrame copyThis = new AlignFrame(copyAlignment,
               AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
       copyThis.setTitle(alignFrame.getTitle());
@@ -263,6 +218,260 @@ public class CrossRefAction implements Runnable
   }
 
   /**
+   * Tries to add chromosomal coordinates to any nucleotide sequence which does
+   * not already have them. Coordinates are retrieved from Ensembl given an
+   * Ensembl identifier, either on the sequence itself or on a peptide sequence
+   * it has a reference to.
+   * 
+   * <pre>
+   * Example (human):
+   * - fetch EMBLCDS cross-references for Uniprot entry P30419
+   * - the EMBL sequences do not have xrefs to Ensembl
+   * - the Uniprot entry has xrefs to 
+   *    ENSP00000258960, ENSP00000468424, ENST00000258960, ENST00000592782
+   * - either of the transcript ids can be used to retrieve gene loci e.g.
+   *    http://rest.ensembl.org/map/cds/ENST00000592782/1..100000
+   * Example (invertebrate):
+   * - fetch EMBLCDS cross-references for Uniprot entry Q43517 (FER1_SOLLC)
+   * - the Uniprot entry has an xref to ENSEMBLPLANTS Solyc10g044520.1.1
+   * - can retrieve gene loci with
+   *    http://rest.ensemblgenomes.org/map/cds/Solyc10g044520.1.1/1..100000
+   * </pre>
+   * 
+   * @param sequences
+   */
+  public static void findGeneLoci(List<SequenceI> sequences)
+  {
+    Map<DBRefEntry, GeneLociI> retrievedLoci = new HashMap<>();
+    for (SequenceI seq : sequences)
+    {
+      findGeneLoci(seq, retrievedLoci);
+    }
+  }
+
+  /**
+   * Tres to find chromosomal coordinates for the sequence, by searching its
+   * direct and indirect cross-references for Ensembl. If the loci have already
+   * been retrieved, just reads them out of the map of retrievedLoci; this is
+   * the case of an alternative transcript for the same protein. Otherwise calls
+   * a REST service to retrieve the loci, and if successful, adds them to the
+   * sequence and to the retrievedLoci.
+   * 
+   * @param seq
+   * @param retrievedLoci
+   */
+  static void findGeneLoci(SequenceI seq,
+          Map<DBRefEntry, GeneLociI> retrievedLoci)
+  {
+    /*
+     * don't replace any existing chromosomal coordinates
+     */
+    if (seq == null || seq.isProtein() || seq.getGeneLoci() != null
+            || seq.getDBRefs() == null)
+    {
+      return;
+    }
+    
+    Set<String> ensemblDivisions = new EnsemblInfo().getDivisions();
+    
+    /*
+     * first look for direct dbrefs from sequence to Ensembl
+     */
+    String[] divisionsArray = ensemblDivisions
+            .toArray(new String[ensemblDivisions.size()]);
+    DBRefEntry[] seqRefs = seq.getDBRefs();
+    DBRefEntry[] directEnsemblRefs = DBRefUtils.selectRefs(seqRefs,
+            divisionsArray);
+    if (directEnsemblRefs != null)
+    {
+      for (DBRefEntry ensemblRef : directEnsemblRefs)
+      {
+        if (fetchGeneLoci(seq, ensemblRef, retrievedLoci))
+        {
+          return;
+        }
+      }
+    }
+
+    /*
+     * else look for indirect dbrefs from sequence to Ensembl
+     */
+    for (DBRefEntry dbref : seq.getDBRefs())
+    {
+      if (dbref.getMap() != null && dbref.getMap().getTo() != null)
+      {
+        DBRefEntry[] dbrefs = dbref.getMap().getTo().getDBRefs();
+        DBRefEntry[] indirectEnsemblRefs = DBRefUtils.selectRefs(dbrefs,
+                divisionsArray);
+        if (indirectEnsemblRefs != null)
+        {
+          for (DBRefEntry ensemblRef : indirectEnsemblRefs)
+          {
+            if (fetchGeneLoci(seq, ensemblRef, retrievedLoci))
+            {
+              return;
+            }
+          }
+        }
+      }
+    }
+  }
+
+  /**
+   * Retrieves chromosomal coordinates for the Ensembl (or EnsemblGenomes)
+   * identifier in dbref. If successful, and the sequence length matches gene
+   * loci length, then add it to the sequence, and to the retrievedLoci map.
+   * Answers true if successful, else false.
+   * 
+   * @param seq
+   * @param dbref
+   * @param retrievedLoci
+   * @return
+   */
+  static boolean fetchGeneLoci(SequenceI seq, DBRefEntry dbref,
+          Map<DBRefEntry, GeneLociI> retrievedLoci)
+  {
+    String accession = dbref.getAccessionId();
+    String division = dbref.getSource();
+
+    /*
+     * hack: ignore cross-references to Ensembl protein ids
+     * (or use map/translation perhaps?)
+     * todo: is there an equivalent in EnsemblGenomes?
+     */
+    if (accession.startsWith("ENSP"))
+    {
+      return false;
+    }
+    EnsemblMap mapper = new EnsemblMap();
+
+    /*
+     * try CDS mapping first
+     */
+    GeneLociI geneLoci = mapper.getCdsMapping(division, accession, 1,
+            seq.getLength());
+    if (geneLoci != null)
+    {
+      MapList map = geneLoci.getMap();
+      int mappedFromLength = MappingUtils.getLength(map.getFromRanges());
+      if (mappedFromLength == seq.getLength())
+      {
+        seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
+                geneLoci.getChromosomeId(), geneLoci.getMap());
+        retrievedLoci.put(dbref, geneLoci);
+        return true;
+      }
+    }
+
+    /*
+     * else try CDNA mapping
+     */
+    geneLoci = mapper.getCdnaMapping(division, accession, 1,
+            seq.getLength());
+    if (geneLoci != null)
+    {
+      MapList map = geneLoci.getMap();
+      int mappedFromLength = MappingUtils.getLength(map.getFromRanges());
+      if (mappedFromLength == seq.getLength())
+      {
+        seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
+                geneLoci.getChromosomeId(), geneLoci.getMap());
+        retrievedLoci.put(dbref, geneLoci);
+        return true;
+      }
+    }
+
+    return false;
+  }
+
+  /**
+   * @param alignment
+   * @param dataset
+   * @param dna
+   * @param xrefs
+   * @param xrefsAlignment
+   * @return
+   */
+  protected AlignmentI copyAlignmentForSplitFrame(AlignmentI alignment,
+          AlignmentI dataset, boolean dna, AlignmentI xrefs,
+          AlignmentI xrefsAlignment)
+  {
+    AlignmentI copyAlignment;
+    boolean copyAlignmentIsAligned = false;
+    if (dna)
+    {
+      copyAlignment = AlignmentUtils.makeCdsAlignment(sel, dataset,
+              xrefsAlignment.getSequencesArray());
+      if (copyAlignment.getHeight() == 0)
+      {
+        JvOptionPane.showMessageDialog(alignFrame,
+                MessageManager.getString("label.cant_map_cds"),
+                MessageManager.getString("label.operation_failed"),
+                JvOptionPane.OK_OPTION);
+        System.err.println("Failed to make CDS alignment");
+        return null;
+      }
+
+      /*
+       * pending getting Embl transcripts to 'align', 
+       * we are only doing this for Ensembl
+       */
+      // TODO proper criteria for 'can align as cdna'
+      if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
+              || AlignmentUtils.looksLikeEnsembl(alignment))
+      {
+        copyAlignment.alignAs(alignment);
+        copyAlignmentIsAligned = true;
+      }
+    }
+    else
+    {
+      copyAlignment = AlignmentUtils.makeCopyAlignment(sel,
+              xrefs.getSequencesArray(), dataset);
+    }
+    copyAlignment
+            .setGapCharacter(alignFrame.viewport.getGapCharacter());
+
+    StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(Desktop.instance);
+
+    /*
+     * register any new mappings for sequence mouseover etc
+     * (will not duplicate any previously registered mappings)
+     */
+    ssm.registerMappings(dataset.getCodonFrames());
+
+    if (copyAlignment.getHeight() <= 0)
+    {
+      System.err.println(
+              "No Sequences generated for xRef type " + source);
+      return null;
+    }
+
+    /*
+     * align protein to dna
+     */
+    if (dna && copyAlignmentIsAligned)
+    {
+      xrefsAlignment.alignAs(copyAlignment);
+    }
+    else
+    {
+      /*
+       * align cdna to protein - currently only if 
+       * fetching and aligning Ensembl transcripts!
+       */
+      // TODO: generalise for other sources of locus/transcript/cds data
+      if (dna && DBRefSource.ENSEMBL.equalsIgnoreCase(source))
+      {
+        copyAlignment.alignAs(xrefsAlignment);
+      }
+    }
+
+    return copyAlignment;
+  }
+
+  /**
    * Makes an alignment containing the given sequences, and adds them to the
    * given dataset, which is also set as the dataset for the new alignment
    * 
@@ -291,20 +500,28 @@ public class CrossRefAction implements Runnable
     return al;
   }
 
-  public CrossRefAction(AlignFrame alignFrame, SequenceI[] sel,
-          boolean _odna, String source)
+  /**
+   * Constructor
+   * 
+   * @param af
+   * @param seqs
+   * @param fromDna
+   * @param dbSource
+   */
+  CrossRefAction(AlignFrame af, SequenceI[] seqs, boolean fromDna,
+          String dbSource)
   {
-    this.alignFrame = alignFrame;
-    this.sel = sel;
-    this._odna = _odna;
-    this.source = source;
+    this.alignFrame = af;
+    this.sel = seqs;
+    this._odna = fromDna;
+    this.source = dbSource;
   }
 
-  public static CrossRefAction showProductsFor(final SequenceI[] sel,
-          final boolean _odna, final String source,
+  public static CrossRefAction getHandlerFor(final SequenceI[] sel,
+          final boolean fromDna, final String source,
           final AlignFrame alignFrame)
   {
-    return new CrossRefAction(alignFrame, sel, _odna, source);
+    return new CrossRefAction(alignFrame, sel, fromDna, source);
   }
 
 }
diff --git a/src/jalview/gui/CutAndPasteHtmlTransfer.java b/src/jalview/gui/CutAndPasteHtmlTransfer.java
index 71a1520..2e51bce 100644
--- a/src/jalview/gui/CutAndPasteHtmlTransfer.java
+++ b/src/jalview/gui/CutAndPasteHtmlTransfer.java
@@ -141,6 +141,7 @@ public class CutAndPasteHtmlTransfer extends GCutAndPasteHtmlTransfer
    */
   public void setText(String text)
   {
+    textarea.setDocument(textarea.getEditorKit().createDefaultDocument());
     textarea.setText(text);
   }
 
diff --git a/src/jalview/gui/FeatureColourChooser.java b/src/jalview/gui/FeatureColourChooser.java
index d8db546..fbe8437 100644
--- a/src/jalview/gui/FeatureColourChooser.java
+++ b/src/jalview/gui/FeatureColourChooser.java
@@ -22,19 +22,29 @@ package jalview.gui;
 
 import jalview.api.FeatureColourI;
 import jalview.datamodel.GraphLine;
+import jalview.datamodel.features.FeatureAttributes;
 import jalview.schemes.FeatureColour;
 import jalview.util.MessageManager;
+import jalview.util.matcher.Condition;
+import jalview.util.matcher.KeyedMatcher;
+import jalview.util.matcher.KeyedMatcherI;
+import jalview.util.matcher.KeyedMatcherSet;
+import jalview.util.matcher.KeyedMatcherSetI;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Dimension;
 import java.awt.FlowLayout;
+import java.awt.GridLayout;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.FocusAdapter;
 import java.awt.event.FocusEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
+import java.util.Iterator;
 
 import javax.swing.BorderFactory;
 import javax.swing.JCheckBox;
@@ -94,6 +104,18 @@ public class FeatureColourChooser extends JalviewDialog
 
   private ActionListener colourEditor = null;
 
+  private JComboBox<String> filterAttribute;
+
+  private JComboBox<Condition> filterCondition;
+
+  private JTextField filterValue;
+
+  private JComboBox<String> filterAttribute2;
+
+  private JComboBox<Condition> filterCondition2;
+
+  private JTextField filterValue2;
+
   /**
    * Constructor
    * 
@@ -213,62 +235,90 @@ public class FeatureColourChooser extends JalviewDialog
       threshline.value = cs.getThreshold();
     }
 
+    setInitialFilters(cs.getAttributeFilters());
+
     adjusting = false;
 
     changeColour(false);
     waitForInput();
   }
 
-  private void jbInit() throws Exception
+  /**
+   * Populates the attribute filter fields for the initial display
+   * 
+   * @param filters
+   */
+  void setInitialFilters(KeyedMatcherSetI filters)
   {
+    // todo generalise to populate N conditions
 
-    minColour.setFont(JvSwingUtils.getLabelFont());
-    minColour.setBorder(BorderFactory.createLineBorder(Color.black));
-    minColour.setPreferredSize(new Dimension(40, 20));
-    minColour.setToolTipText(MessageManager.getString("label.min_colour"));
-    minColour.addMouseListener(new MouseAdapter()
+    if (filters == null)
     {
-      @Override
-      public void mousePressed(MouseEvent e)
-      {
-        if (minColour.isEnabled())
-        {
-          minColour_actionPerformed();
-        }
-      }
-    });
-    maxColour.setFont(JvSwingUtils.getLabelFont());
-    maxColour.setBorder(BorderFactory.createLineBorder(Color.black));
-    maxColour.setPreferredSize(new Dimension(40, 20));
-    maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
-    maxColour.addMouseListener(new MouseAdapter()
+      return;
+    }
+
+    Iterator<KeyedMatcherI> theFilters = filters.getMatchers();
+    if (theFilters.hasNext())
     {
-      @Override
-      public void mousePressed(MouseEvent e)
-      {
-        if (maxColour.isEnabled())
-        {
-          maxColour_actionPerformed();
-        }
-      }
-    });
-    maxColour.setBorder(new LineBorder(Color.black));
-    JLabel minText = new JLabel(MessageManager.getString("label.min"));
-    minText.setFont(JvSwingUtils.getLabelFont());
-    JLabel maxText = new JLabel(MessageManager.getString("label.max"));
-    maxText.setFont(JvSwingUtils.getLabelFont());
-    this.setLayout(new BorderLayout());
-    JPanel jPanel1 = new JPanel();
-    jPanel1.setBackground(Color.white);
-    JPanel jPanel2 = new JPanel();
-    jPanel2.setLayout(new FlowLayout());
-    jPanel2.setBackground(Color.white);
+      KeyedMatcherI filter = theFilters.next();
+      filterAttribute.setSelectedItem(filter.getKey());
+      filterCondition.setSelectedItem(filter.getMatcher().getCondition());
+      filterValue.setText(filter.getMatcher().getPattern());
+    }
+    if (theFilters.hasNext())
+    {
+      KeyedMatcherI filter = theFilters.next();
+      boolean anded = filters.isAnded();
+      // todo add OR/AND condition to gui
+      // - user choice for the second condition, fixed thereafter
+      filterAttribute2.setSelectedItem(filter.getKey());
+      filterCondition2.setSelectedItem(filter.getMatcher().getCondition());
+      filterValue2.setText(filter.getMatcher().getPattern());
+    }
+  }
+
+  private void jbInit() throws Exception
+  {
+    this.setLayout(new GridLayout(4, 1));
+
+    JPanel colourByPanel = initColoursPanel();
+
+    JPanel thresholdPanel = initThresholdPanel();
+
+    JPanel okCancelPanel = initOkCancelPanel();
+
+    this.add(colourByPanel);
+    this.add(thresholdPanel);
+
+    /*
+     * add filter by attributes options only if we know any attributes
+     */
+    Iterator<String> attributes = FeatureAttributes.getInstance()
+            .getAttributes(type).iterator();
+    if (attributes.hasNext())
+    {
+      JPanel filtersPanel = initFiltersPanel(attributes);
+      this.add(filtersPanel);
+    }
+
+    this.add(okCancelPanel);
+  }
+
+  /**
+   * Lay out fields for threshold options
+   * 
+   * @return
+   */
+  protected JPanel initThresholdPanel()
+  {
+    JPanel thresholdPanel = new JPanel();
+    thresholdPanel.setLayout(new FlowLayout());
     threshold.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        threshold_actionPerformed();
+        changeColour(true);
       }
     });
     threshold.setToolTipText(MessageManager
@@ -280,8 +330,6 @@ public class FeatureColourChooser extends JalviewDialog
     threshold.addItem(MessageManager
             .getString("label.threshold_feature_below_threshold")); // index 2
 
-    JPanel jPanel3 = new JPanel();
-    jPanel3.setLayout(new FlowLayout());
     thresholdValue.addActionListener(new ActionListener()
     {
       @Override
@@ -308,7 +356,7 @@ public class FeatureColourChooser extends JalviewDialog
             MessageManager.getString("label.adjust_threshold"));
     thresholdValue.setEnabled(false);
     thresholdValue.setColumns(7);
-    jPanel3.setBackground(Color.white);
+    thresholdPanel.setBackground(Color.white);
     thresholdIsMin.setBackground(Color.white);
     thresholdIsMin
             .setText(MessageManager.getString("label.threshold_minmax"));
@@ -319,40 +367,101 @@ public class FeatureColourChooser extends JalviewDialog
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        thresholdIsMin_actionPerformed();
+        changeColour(true);
       }
     });
-    colourByLabel.setBackground(Color.white);
-    colourByLabel
-            .setText(MessageManager.getString("label.colour_by_label"));
-    colourByLabel.setToolTipText(MessageManager.getString(
-            "label.display_features_same_type_different_label_using_different_colour"));
-    colourByLabel.addActionListener(new ActionListener()
+    thresholdPanel.add(threshold);
+    thresholdPanel.add(slider);
+    thresholdPanel.add(thresholdValue);
+    thresholdPanel.add(thresholdIsMin);
+    return thresholdPanel;
+  }
+
+  /**
+   * Lay out OK and Cancel buttons
+   * 
+   * @return
+   */
+  protected JPanel initOkCancelPanel()
+  {
+    JPanel okCancelPanel = new JPanel();
+    okCancelPanel.setBackground(Color.white);
+    okCancelPanel.add(ok);
+    okCancelPanel.add(cancel);
+    return okCancelPanel;
+  }
+
+  /**
+   * Lay out Colour by Label and min/max colour widgets
+   * 
+   * @return
+   */
+  protected JPanel initColoursPanel()
+  {
+    JPanel colourByPanel = new JPanel();
+    colourByPanel.setLayout(new FlowLayout());
+    colourByPanel.setBackground(Color.white);
+    minColour.setFont(JvSwingUtils.getLabelFont());
+    minColour.setBorder(BorderFactory.createLineBorder(Color.black));
+    minColour.setPreferredSize(new Dimension(40, 20));
+    minColour.setToolTipText(MessageManager.getString("label.min_colour"));
+    minColour.addMouseListener(new MouseAdapter()
     {
       @Override
-      public void actionPerformed(ActionEvent actionEvent)
+      public void mousePressed(MouseEvent e)
       {
-        colourByLabel_actionPerformed();
+        if (minColour.isEnabled())
+        {
+          minColour_actionPerformed();
+        }
       }
     });
+    maxColour.setFont(JvSwingUtils.getLabelFont());
+    maxColour.setBorder(BorderFactory.createLineBorder(Color.black));
+    maxColour.setPreferredSize(new Dimension(40, 20));
+    maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
+    maxColour.addMouseListener(new MouseAdapter()
+    {
+      @Override
+      public void mousePressed(MouseEvent e)
+      {
+        if (maxColour.isEnabled())
+        {
+          maxColour_actionPerformed();
+        }
+      }
+    });
+    maxColour.setBorder(new LineBorder(Color.black));
+    JLabel minText = new JLabel(MessageManager.getString("label.min"));
+    minText.setFont(JvSwingUtils.getLabelFont());
+    JLabel maxText = new JLabel(MessageManager.getString("label.max"));
+    maxText.setFont(JvSwingUtils.getLabelFont());
 
     JPanel colourPanel = new JPanel();
     colourPanel.setBackground(Color.white);
-    jPanel1.add(ok);
-    jPanel1.add(cancel);
-    jPanel2.add(colourByLabel, BorderLayout.WEST);
-    jPanel2.add(colourPanel, BorderLayout.EAST);
     colourPanel.add(minText);
     colourPanel.add(minColour);
     colourPanel.add(maxText);
     colourPanel.add(maxColour);
-    this.add(jPanel3, BorderLayout.CENTER);
-    jPanel3.add(threshold);
-    jPanel3.add(slider);
-    jPanel3.add(thresholdValue);
-    jPanel3.add(thresholdIsMin);
-    this.add(jPanel1, BorderLayout.SOUTH);
-    this.add(jPanel2, BorderLayout.NORTH);
+    colourByPanel.add(colourByLabel, BorderLayout.WEST);
+    colourByPanel.add(colourPanel, BorderLayout.EAST);
+
+    colourByLabel.setBackground(Color.white);
+    colourByLabel
+            .setText(MessageManager.getString("label.colour_by_label"));
+    colourByLabel
+            .setToolTipText(MessageManager
+                    .getString("label.display_features_same_type_different_label_using_different_colour"));
+    colourByLabel.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        changeColour(true);
+      }
+    });
+
+    return colourByPanel;
   }
 
   /**
@@ -406,6 +515,11 @@ public class FeatureColourChooser extends JalviewDialog
       return;
     }
 
+    if (!validateInputs())
+    {
+      return;
+    }
+
     boolean aboveThreshold = false;
     boolean belowThreshold = false;
     if (threshold.getSelectedIndex() == 1)
@@ -505,11 +619,101 @@ public class FeatureColourChooser extends JalviewDialog
       maxColour.setForeground(oldmaxColour);
       minColour.setForeground(oldminColour);
     }
+
+    /*
+     * add attribute filters if entered
+     */
+    if (filterAttribute != null)
+    {
+      setAttributeFilters(acg);
+    }
+
     fr.setColour(type, acg);
     cs = acg;
     ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview);
   }
 
+  /**
+   * Checks inputs are valid, and answers true if they are, else false. Also
+   * sets the colour of invalid inputs to red.
+   * 
+   * @return
+   */
+  boolean validateInputs()
+  {
+    // todo generalise to N filters
+    return isValidFilter(filterValue, filterCondition)
+            || isValidFilter(filterValue2, filterCondition2);
+  }
+
+  /**
+   * Answers true unless a numeric condition has been selected with a
+   * non-numeric value
+   * 
+   * @param value
+   * @param condition
+   */
+  protected boolean isValidFilter(JTextField value, JComboBox<Condition> condition)
+  {
+    if (value == null || condition == null)
+    {
+      return true; // fields not populated
+    }
+
+    value.setBackground(Color.white);
+    String v1 = value.getText().trim();
+    if (v1.length() > 0)
+    {
+      Condition c1 = (Condition) condition.getSelectedItem();
+      if (c1.isNumeric())
+      {
+        try
+        {
+          Float.valueOf(v1);
+        } catch (NumberFormatException e)
+        {
+          value.setBackground(Color.red);
+          return false;
+        }
+      }
+    }
+
+    return true;
+  }
+
+  /**
+   * Sets any attribute value filters entered in the dialog as filters on the
+   * colour scheme
+   * 
+   * @param acg
+   */
+  protected void setAttributeFilters(FeatureColourI acg)
+  {
+    String attribute = (String) filterAttribute.getSelectedItem();
+    Condition cond = (Condition) filterCondition.getSelectedItem();
+    String pattern = filterValue.getText().trim();
+    if (pattern.length() > 0)
+    {
+      KeyedMatcherSetI filters = new KeyedMatcherSet();
+      KeyedMatcherI km = new KeyedMatcher(attribute, cond, pattern);
+      filters.and(km);
+
+      /*
+       * is there a second condition?
+       * todo: allow N conditions with choice of AND or OR (but not both!)
+       */
+      pattern = filterValue2.getText().trim();
+      if (pattern.length() > 1)
+      {
+        attribute = (String) filterAttribute2.getSelectedItem();
+        cond = (Condition) filterCondition2.getSelectedItem();
+        KeyedMatcherI km2 = new KeyedMatcher(attribute, cond, pattern);
+        filters.and(km2);
+      }
+      acg.setAttributeFilters(filters);
+    }
+  }
+
   @Override
   protected void raiseClosed()
   {
@@ -544,14 +748,6 @@ public class FeatureColourChooser extends JalviewDialog
   }
 
   /**
-   * Action on change of choice of No / Above / Below Threshold
-   */
-  protected void threshold_actionPerformed()
-  {
-    changeColour(true);
-  }
-
-  /**
    * Action on text entry of a threshold value
    */
   protected void thresholdValue_actionPerformed()
@@ -594,16 +790,6 @@ public class FeatureColourChooser extends JalviewDialog
     changeColour(false);
   }
 
-  protected void thresholdIsMin_actionPerformed()
-  {
-    changeColour(true);
-  }
-
-  protected void colourByLabel_actionPerformed()
-  {
-    changeColour(true);
-  }
-
   void addActionListener(ActionListener graduatedColorEditor)
   {
     if (colourEditor != null)
@@ -629,4 +815,130 @@ public class FeatureColourChooser extends JalviewDialog
     return cs;
   }
 
+  /**
+   * Lay out fields for attribute value filters
+   * 
+   * @param attNames
+   * 
+   * @return
+   */
+  protected JPanel initFiltersPanel(Iterator<String> attNames)
+  {
+    JPanel filtersPanel = new JPanel();
+    filtersPanel.setLayout(new GridLayout(2, 3));
+    filtersPanel.setBackground(Color.white);
+
+    /*
+     * drop-down choice of attribute
+     */
+    filterAttribute = new JComboBox<>();
+    filterAttribute2 = new JComboBox<>();
+    while (attNames.hasNext())
+    {
+      String attName = attNames.next();
+      filterAttribute.addItem(attName);
+      filterAttribute2.addItem(attName);
+    }
+    filterAttribute.addItemListener(new ItemListener()
+    {
+      @Override
+      public void itemStateChanged(ItemEvent e)
+      {
+        changeColour(true);
+      }
+    });
+
+    /*
+     * drop-down choice of test condition
+     */
+    filterCondition = new JComboBox<>();
+    for (Condition cond : Condition.values())
+    {
+      filterCondition.addItem(cond);
+    }
+    filterCondition.addItemListener(new ItemListener()
+    {
+      @Override
+      public void itemStateChanged(ItemEvent e)
+      {
+        changeColour(true);
+      }
+    });
+
+    filterValue = new JTextField(12);
+    filterValue.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        changeColour(true);
+      }
+    });
+    filterValue.addFocusListener(new FocusAdapter()
+    {
+      @Override
+      public void focusLost(FocusEvent e)
+      {
+        changeColour(true);
+      }
+    });
+
+    /*
+     * repeat for a second filter
+     * todo: generalise to N filters
+     */
+    filterAttribute2.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        changeColour(true);
+      }
+    });
+
+    /*
+     * drop-down choice of test condition
+     */
+    filterCondition2 = new JComboBox<>();
+    for (Condition cond : Condition.values())
+    {
+      filterCondition2.addItem(cond);
+    }
+    filterCondition2.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        changeColour(true);
+      }
+    });
+
+    filterValue2 = new JTextField(12);
+    filterValue2.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        changeColour(true);
+      }
+    });
+    filterValue2.addFocusListener(new FocusAdapter()
+    {
+      @Override
+      public void focusLost(FocusEvent e)
+      {
+        changeColour(true);
+      }
+    });
+
+    filtersPanel.add(filterAttribute);
+    filtersPanel.add(filterCondition);
+    filtersPanel.add(filterValue);
+    filtersPanel.add(filterAttribute2);
+    filtersPanel.add(filterCondition2);
+    filtersPanel.add(filterValue2);
+
+    return filtersPanel;
+  }
+
 }
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 1f2a3ad..a4f79c2 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -331,7 +331,8 @@ public class IdPanel extends JPanel
      *  and any non-positional features
      */
     List<String> nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
-    for (SequenceFeature sf : sq.getFeatures().getNonPositionalFeatures())
+    List<SequenceFeature> features = sq.getFeatures().getNonPositionalFeatures();
+    for (SequenceFeature sf : features)
     {
       if (sf.links != null)
       {
@@ -342,7 +343,7 @@ public class IdPanel extends JPanel
       }
     }
 
-    PopupMenu pop = new PopupMenu(alignPanel, sq, nlinks,
+    PopupMenu pop = new PopupMenu(alignPanel, sq, features,
             Preferences.getGroupURLLinks());
     pop.show(this, e.getX(), e.getY());
   }
diff --git a/src/jalview/gui/JalviewDialog.java b/src/jalview/gui/JalviewDialog.java
index 05f5ffc..1008203 100644
--- a/src/jalview/gui/JalviewDialog.java
+++ b/src/jalview/gui/JalviewDialog.java
@@ -27,8 +27,8 @@ import java.awt.Dimension;
 import java.awt.Rectangle;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
-import java.awt.event.WindowListener;
 
 import javax.swing.JButton;
 import javax.swing.JDialog;
@@ -118,55 +118,14 @@ public abstract class JalviewDialog extends JPanel
         closeDialog();
       }
     });
-    frame.addWindowListener(new WindowListener()
+    frame.addWindowListener(new WindowAdapter()
     {
-
-      @Override
-      public void windowOpened(WindowEvent e)
-      {
-        // TODO Auto-generated method stub
-
-      }
-
-      @Override
-      public void windowIconified(WindowEvent e)
-      {
-        // TODO Auto-generated method stub
-
-      }
-
-      @Override
-      public void windowDeiconified(WindowEvent e)
-      {
-        // TODO Auto-generated method stub
-
-      }
-
-      @Override
-      public void windowDeactivated(WindowEvent e)
-      {
-        // TODO Auto-generated method stub
-
-      }
-
       @Override
       public void windowClosing(WindowEvent e)
       {
         // user has cancelled the dialog
         closeDialog();
       }
-
-      @Override
-      public void windowClosed(WindowEvent e)
-      {
-      }
-
-      @Override
-      public void windowActivated(WindowEvent e)
-      {
-        // TODO Auto-generated method stub
-
-      }
     });
   }
 
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 850a09a..6da7d4f 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -34,7 +34,6 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -50,6 +49,7 @@ import jalview.schemes.PIDColourScheme;
 import jalview.util.GroupUrlLink;
 import jalview.util.GroupUrlLink.UrlStringTooLongException;
 import jalview.util.MessageManager;
+import jalview.util.StringUtils;
 import jalview.util.UrlLink;
 
 import java.awt.Color;
@@ -176,25 +176,31 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
    * Creates a new PopupMenu object.
    * 
    * @param ap
-   *          DOCUMENT ME!
    * @param seq
-   *          DOCUMENT ME!
+   * @param features
+   *          non-positional features (for seq not null), or positional features
+   *          at residue (for seq equal to null)
    */
-  public PopupMenu(final AlignmentPanel ap, Sequence seq,
-          List<String> links)
+  public PopupMenu(final AlignmentPanel ap, SequenceI seq,
+          List<SequenceFeature> features)
   {
-    this(ap, seq, links, null);
+    this(ap, seq, features, null);
   }
 
   /**
+   * Constructor
    * 
-   * @param ap
+   * @param alignPanel
    * @param seq
-   * @param links
+   *          the sequence under the cursor if in the Id panel, null if in the
+   *          sequence panel
+   * @param features
+   *          non-positional features if in the Id panel, features at the
+   *          clicked residue if in the sequence panel
    * @param groupLinks
    */
-  public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
-          List<String> links, List<String> groupLinks)
+  public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,
+          List<SequenceFeature> features, List<String> groupLinks)
   {
     // /////////////////////////////////////////////////////////
     // If this is activated from the sequence panel, the user may want to
@@ -202,7 +208,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     //
     // If from the IDPanel, we must display the sequence menu
     // ////////////////////////////////////////////////////////
-    this.ap = ap;
+    this.ap = alignPanel;
     sequence = seq;
 
     for (String ff : FileFormats.getInstance().getWritableFormats(true))
@@ -237,9 +243,9 @@ 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
+    final List<SequenceI> selectedGroup = (alignPanel.av.getSelectionGroup() == null
             ? Collections.<SequenceI> emptyList()
-            : ap.av.getSelectionGroup().getSequences());
+            : alignPanel.av.getSelectionGroup().getSequences());
     buildAnnotationTypesMenus(groupShowAnnotationsMenu,
             groupHideAnnotationsMenu, selectedGroup);
     configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
@@ -257,7 +263,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     if (seq != null)
     {
       sequenceMenu.setText(sequence.getName());
-      if (seq == ap.av.getAlignment().getSeqrep())
+      if (seq == alignPanel.av.getAlignment().getSeqrep())
       {
         makeReferenceSeq.setText(
                 MessageManager.getString("action.unmark_as_reference"));
@@ -268,7 +274,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
                 MessageManager.getString("action.set_as_reference"));
       }
 
-      if (!ap.av.getAlignment().isNucleotide())
+      if (!alignPanel.av.getAlignment().isNucleotide())
       {
         remove(rnaStructureMenu);
       }
@@ -279,7 +285,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
          * add menu items to 2D-render any alignment or sequence secondary
          * structure annotation
          */
-        AlignmentAnnotation[] aas = ap.av.getAlignment()
+        AlignmentAnnotation[] aas = alignPanel.av.getAlignment()
                 .getAlignmentAnnotation();
         if (aas != null)
         {
@@ -299,7 +305,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
                 @Override
                 public void actionPerformed(ActionEvent e)
                 {
-                  new AppVarna(seq, aa, ap);
+                  new AppVarna(seq, aa, alignPanel);
                 }
               });
               rnaStructureMenu.add(menuItem);
@@ -328,7 +334,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
                 public void actionPerformed(ActionEvent e)
                 {
                   // TODO: VARNA does'nt print gaps in the sequence
-                  new AppVarna(seq, aa, ap);
+                  new AppVarna(seq, aa, alignPanel);
                 }
               });
               rnaStructureMenu.add(menuItem);
@@ -353,8 +359,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       });
       add(menuItem);
 
-      if (ap.av.getSelectionGroup() != null
-              && ap.av.getSelectionGroup().getSize() > 1)
+      if (alignPanel.av.getSelectionGroup() != null
+              && alignPanel.av.getSelectionGroup().getSize() > 1)
       {
         menuItem = new JMenuItem(MessageManager
                 .formatMessage("label.represent_group_with", new Object[]
@@ -370,12 +376,12 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         sequenceMenu.add(menuItem);
       }
 
-      if (ap.av.hasHiddenRows())
+      if (alignPanel.av.hasHiddenRows())
       {
-        final int index = ap.av.getAlignment().findIndex(seq);
+        final int index = alignPanel.av.getAlignment().findIndex(seq);
 
-        if (ap.av.adjustForHiddenSeqs(index)
-                - ap.av.adjustForHiddenSeqs(index - 1) > 1)
+        if (alignPanel.av.adjustForHiddenSeqs(index)
+                - alignPanel.av.adjustForHiddenSeqs(index - 1) > 1)
         {
           menuItem = new JMenuItem(
                   MessageManager.getString("action.reveal_sequences"));
@@ -384,10 +390,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
             @Override
             public void actionPerformed(ActionEvent e)
             {
-              ap.av.showSequence(index);
-              if (ap.overviewPanel != null)
+              alignPanel.av.showSequence(index);
+              if (alignPanel.overviewPanel != null)
               {
-                ap.overviewPanel.updateOverviewImage();
+                alignPanel.overviewPanel.updateOverviewImage();
               }
             }
           });
@@ -396,7 +402,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       }
     }
     // for the case when no sequences are even visible
-    if (ap.av.hasHiddenRows())
+    if (alignPanel.av.hasHiddenRows())
     {
       {
         menuItem = new JMenuItem(
@@ -406,10 +412,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
           @Override
           public void actionPerformed(ActionEvent e)
           {
-            ap.av.showAllHiddenSeqs();
-            if (ap.overviewPanel != null)
+            alignPanel.av.showAllHiddenSeqs();
+            if (alignPanel.overviewPanel != null)
             {
-              ap.overviewPanel.updateOverviewImage();
+              alignPanel.overviewPanel.updateOverviewImage();
             }
           }
         });
@@ -418,9 +424,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       }
     }
 
-    SequenceGroup sg = ap.av.getSelectionGroup();
+    SequenceGroup sg = alignPanel.av.getSelectionGroup();
     boolean isDefinedGroup = (sg != null)
-            ? ap.av.getAlignment().getGroups().contains(sg)
+            ? alignPanel.av.getAlignment().getGroups().contains(sg)
             : false;
 
     if (sg != null && sg.getSize() > 0)
@@ -458,7 +464,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
 
       SequenceI sqass = null;
-      for (SequenceI sq : ap.av.getSequenceSelection())
+      for (SequenceI sq : alignPanel.av.getSequenceSelection())
       {
         Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
         if (pes != null && pes.size() > 0)
@@ -508,24 +514,130 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       rnaStructureMenu.setVisible(false);
     }
 
-    if (links != null && links.size() > 0)
+    addLinks(seq, features);
+
+    if (seq == null)
+    {
+      addFeatureDetails(features);
+    }
+  }
+
+  /**
+   * Add a link to show feature details for each sequence feature
+   * 
+   * @param features
+   */
+  protected void addFeatureDetails(List<SequenceFeature> features)
+  {
+    if (features == null || features.isEmpty())
+    {
+      return;
+    }
+    JMenu details = new JMenu(
+            MessageManager.getString("label.feature_details"));
+    add(details);
+
+    for (final SequenceFeature sf : features)
     {
-      addFeatureLinks(seq, links);
+      int start = sf.getBegin();
+      int end = sf.getEnd();
+      String desc = null;
+      if (start == end)
+      {
+        desc = String.format("%s %d", sf.getType(), start);
+      }
+      else
+      {
+        desc = String.format("%s %d-%d", sf.getType(), start, end);
+      }
+      String description = sf.getDescription();
+      if (description != null)
+      {
+        description = StringUtils.stripHtmlTags(description);
+        if (description.length() <= 6)
+        {
+          desc = desc + " " + description;
+        }
+        else
+        {
+          desc = desc + " " + description.substring(0, 6) + "..";
+        }
+      }
+      if (sf.getFeatureGroup() != null)
+      {
+        desc = desc + " (" + sf.getFeatureGroup() + ")";
+      }
+      JMenuItem item = new JMenuItem(desc);
+      item.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          showFeatureDetails(sf);
+        }
+      });
+      details.add(item);
     }
   }
 
   /**
+   * Opens a panel showing a text report of feature dteails
+   * 
+   * @param sf
+   */
+  protected void showFeatureDetails(SequenceFeature sf)
+  {
+    CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
+    // it appears Java's CSS does not support border-collaps :-(
+    cap.addStylesheetRule("table { border-collapse: collapse;}");
+    cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
+    cap.setText(sf.getDetailsReport());
+
+    Desktop.addInternalFrame(cap,
+            MessageManager.getString("label.feature_details"), 500, 500);
+  }
+
+  /**
    * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
+   * When seq is not null, these are links for the sequence id, which may be to
+   * external web sites for the sequence accession, and/or links embedded in
+   * non-positional features. When seq is null, only links embedded in the
+   * provided features are added.
    * 
    * @param seq
-   * @param links
+   * @param features
    */
-  void addFeatureLinks(final SequenceI seq, List<String> links)
+  void addLinks(final SequenceI seq, List<SequenceFeature> features)
   {
     JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
+
+    List<String> nlinks = null;
+    if (seq != null)
+    {
+      nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
+    }
+    else
+    {
+      nlinks = new ArrayList<>();
+    }
+
+    if (features != null)
+    {
+      for (SequenceFeature sf : features)
+      {
+        if (sf.links != null)
+        {
+          for (String link : sf.links)
+          {
+            nlinks.add(link);
+          }
+        }
+      }
+    }
+
     Map<String, List<String>> linkset = new LinkedHashMap<>();
 
-    for (String link : links)
+    for (String link : nlinks)
     {
       UrlLink urlLink = null;
       try
@@ -548,25 +660,18 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
     addshowLinks(linkMenu, linkset.values());
 
-    // disable link menu if there are no valid entries
+    // only add link menu if it has entries
     if (linkMenu.getItemCount() > 0)
     {
-      linkMenu.setEnabled(true);
-    }
-    else
-    {
-      linkMenu.setEnabled(false);
-    }
-
-    if (sequence != null)
-    {
-      sequenceMenu.add(linkMenu);
-    }
-    else
-    {
-      add(linkMenu);
+      if (sequence != null)
+      {
+        sequenceMenu.add(linkMenu);
+      }
+      else
+      {
+        add(linkMenu);
+      }
     }
-
   }
 
   /**
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 2223ee5..6148a2e 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -59,7 +59,6 @@ import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.awt.event.MouseWheelEvent;
 import java.awt.event.MouseWheelListener;
-import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 
@@ -1792,21 +1791,10 @@ public class SeqPanel extends JPanel
     final int column = findColumn(evt);
     final int seq = findSeq(evt);
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
-    List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
+    List<SequenceFeature> features = ap.getFeatureRenderer()
             .findFeaturesAtColumn(sequence, column + 1);
-    List<String> links = new ArrayList<>();
-    for (SequenceFeature sf : allFeatures)
-    {
-      if (sf.links != null)
-      {
-        for (String link : sf.links)
-        {
-          links.add(link);
-        }
-      }
-    }
 
-    PopupMenu pop = new PopupMenu(ap, null, links);
+    PopupMenu pop = new PopupMenu(ap, null, features);
     pop.show(this, evt.getX(), evt.getY());
   }
 
diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index f1ebcac..6d819d3 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -26,6 +26,7 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.io.gff.GffConstants;
 import jalview.util.MessageManager;
+import jalview.util.StringUtils;
 import jalview.util.UrlLink;
 
 import java.util.Arrays;
@@ -58,7 +59,7 @@ public class SequenceAnnotationReport
 
   /*
    * Comparator to order DBRefEntry by Source + accession id (case-insensitive),
-   * with 'Primary' sources placed before others
+   * with 'Primary' sources placed before others, and 'chromosome' first of all
    */
   private static Comparator<DBRefEntry> comparator = new Comparator<DBRefEntry>()
   {
@@ -66,6 +67,14 @@ public class SequenceAnnotationReport
     @Override
     public int compare(DBRefEntry ref1, DBRefEntry ref2)
     {
+      if (ref1.isChromosome())
+      {
+        return -1;
+      }
+      if (ref2.isChromosome())
+      {
+        return 1;
+      }
       String s1 = ref1.getSource();
       String s2 = ref2.getSource();
       boolean s1Primary = isPrimarySource(s1);
@@ -175,50 +184,11 @@ public class SequenceAnnotationReport
           sb.append(" ").append(feature.end);
         }
 
-        if (feature.getDescription() != null
-                && !feature.description.equals(feature.getType()))
+        String description = feature.getDescription();
+        if (description != null && !description.equals(feature.getType()))
         {
-          String tmpString = feature.getDescription();
-          String tmp2up = tmpString.toUpperCase();
-          int startTag = tmp2up.indexOf("<HTML>");
-          if (startTag > -1)
-          {
-            tmpString = tmpString.substring(startTag + 6);
-            tmp2up = tmp2up.substring(startTag + 6);
-          }
-          int endTag = tmp2up.indexOf("</BODY>");
-          if (endTag > -1)
-          {
-            tmpString = tmpString.substring(0, endTag);
-            tmp2up = tmp2up.substring(0, endTag);
-          }
-          endTag = tmp2up.indexOf("</HTML>");
-          if (endTag > -1)
-          {
-            tmpString = tmpString.substring(0, endTag);
-          }
-
-          if (startTag > -1)
-          {
-            sb.append("; ").append(tmpString);
-          }
-          else
-          {
-            if (tmpString.indexOf("<") > -1 || tmpString.indexOf(">") > -1)
-            {
-              // The description does not specify html is to
-              // be used, so we must remove < > symbols
-              tmpString = tmpString.replaceAll("<", "&lt;");
-              tmpString = tmpString.replaceAll(">", "&gt;");
-
-              sb.append("; ");
-              sb.append(tmpString);
-            }
-            else
-            {
-              sb.append("; ").append(tmpString);
-            }
-          }
+          description = StringUtils.stripHtmlTags(description);
+          sb.append("; ").append(description);
         }
         // check score should be shown
         if (!Float.isNaN(feature.getScore()))
diff --git a/src/jalview/io/gff/Gff3Helper.java b/src/jalview/io/gff/Gff3Helper.java
index c7e1d7a..a25a014 100644
--- a/src/jalview/io/gff/Gff3Helper.java
+++ b/src/jalview/io/gff/Gff3Helper.java
@@ -39,6 +39,8 @@ import java.util.Map;
  */
 public class Gff3Helper extends GffHelperBase
 {
+  public static final String ALLELES = "alleles";
+
   protected static final String TARGET = "Target";
 
   protected static final String ID = "ID";
@@ -399,7 +401,7 @@ public class Gff3Helper extends GffHelperBase
       /*
        * Ensembl returns dna variants as 'alleles'
        */
-      desc = StringUtils.listToDelimitedString(attributes.get("alleles"),
+      desc = StringUtils.listToDelimitedString(attributes.get(ALLELES),
               ",");
     }
 
diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
new file mode 100644
index 0000000..5adc55c
--- /dev/null
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -0,0 +1,1070 @@
+package jalview.io.vcf;
+
+import htsjdk.samtools.util.CloseableIterator;
+import htsjdk.variant.variantcontext.Allele;
+import htsjdk.variant.variantcontext.VariantContext;
+import htsjdk.variant.vcf.VCFHeader;
+import htsjdk.variant.vcf.VCFHeaderLine;
+import htsjdk.variant.vcf.VCFHeaderLineCount;
+import htsjdk.variant.vcf.VCFHeaderLineType;
+import htsjdk.variant.vcf.VCFInfoHeaderLine;
+
+import jalview.analysis.AlignmentUtils;
+import jalview.analysis.Dna;
+import jalview.api.AlignViewControllerGuiI;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.GeneLociI;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureAttributeType;
+import jalview.datamodel.features.FeatureSource;
+import jalview.datamodel.features.FeatureSources;
+import jalview.ext.ensembl.EnsemblMap;
+import jalview.ext.htsjdk.VCFReader;
+import jalview.io.gff.Gff3Helper;
+import jalview.io.gff.SequenceOntologyI;
+import jalview.util.MapList;
+import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+
+/**
+ * A class to read VCF data (using the htsjdk) and add variants as sequence
+ * features on dna and any related protein product sequences
+ * 
+ * @author gmcarstairs
+ */
+public class VCFLoader
+{
+  /*
+   * keys to fields of VEP CSQ consequence data
+   * see https://www.ensembl.org/info/docs/tools/vep/vep_formats.html
+   */
+  private static final String ALLELE_KEY = "Allele";
+
+  private static final String ALLELE_NUM_KEY = "ALLELE_NUM"; // 0 (ref), 1...
+  private static final String FEATURE_KEY = "Feature"; // Ensembl stable id
+
+  /*
+   * what comes before column headings in CSQ Description field
+   */
+  private static final String FORMAT = "Format: ";
+
+  /*
+   * default VCF INFO key for VEP consequence data
+   * NB this can be overridden running VEP with --vcf_info_field
+   * - we don't handle this case (require CSQ identifier)
+   */
+  private static final String CSQ = "CSQ";
+
+  /*
+   * separator for fields in consequence data
+   */
+  private static final String PIPE = "|";
+
+  private static final String PIPE_REGEX = "\\" + PIPE;
+
+  /*
+   * key for Allele Frequency output by VEP
+   * see http://www.ensembl.org/info/docs/tools/vep/vep_formats.html
+   */
+  private static final String ALLELE_FREQUENCY_KEY = "AF";
+
+  /*
+   * delimiter that separates multiple consequence data blocks
+   */
+  private static final String COMMA = ",";
+
+  /*
+   * the feature group assigned to a VCF variant in Jalview
+   */
+  private static final String FEATURE_GROUP_VCF = "VCF";
+
+  /*
+   * internal delimiter used to build keys for assemblyMappings
+   * 
+   */
+  private static final String EXCL = "!";
+
+  /*
+   * the alignment we are associating VCF data with
+   */
+  private AlignmentI al;
+
+  /*
+   * mappings between VCF and sequence reference assembly regions, as 
+   * key = "species!chromosome!fromAssembly!toAssembly
+   * value = Map{fromRange, toRange}
+   */
+  private Map<String, Map<int[], int[]>> assemblyMappings;
+
+  /*
+   * holds details of the VCF header lines (metadata)
+   */
+  private VCFHeader header;
+
+  /*
+   * the position (0...) of field in each block of
+   * CSQ (consequence) data (if declared in the VCF INFO header for CSQ)
+   * see http://www.ensembl.org/info/docs/tools/vep/vep_formats.html
+   */
+  private int csqAlleleFieldIndex = -1;
+  private int csqAlleleNumberFieldIndex = -1;
+  private int csqFeatureFieldIndex = -1;
+
+  /*
+   * a unique identifier under which to save metadata about feature
+   * attributes (selected INFO field data)
+   */
+  private String sourceId;
+
+  /**
+   * Constructor given an alignment context
+   * 
+   * @param alignment
+   */
+  public VCFLoader(AlignmentI alignment)
+  {
+    al = alignment;
+
+    // map of species!chromosome!fromAssembly!toAssembly to {fromRange, toRange}
+    assemblyMappings = new HashMap<String, Map<int[], int[]>>();
+  }
+
+  /**
+   * Starts a new thread to query and load VCF variant data on to the alignment
+   * <p>
+   * This method is not thread safe - concurrent threads should use separate
+   * instances of this class.
+   * 
+   * @param filePath
+   * @param gui
+   */
+  public void loadVCF(final String filePath,
+          final AlignViewControllerGuiI gui)
+  {
+    if (gui != null)
+    {
+      gui.setStatus(MessageManager.getString("label.searching_vcf"));
+    }
+
+    new Thread()
+    {
+
+      @Override
+      public void run()
+      {
+        VCFLoader.this.doLoad(filePath, gui);
+      }
+
+    }.start();
+  }
+
+  /**
+   * Loads VCF on to an alignment - provided it can be related to one or more
+   * sequence's chromosomal coordinates
+   * 
+   * @param filePath
+   * @param gui
+   *          optional callback handler for messages
+   */
+  protected void doLoad(String filePath, AlignViewControllerGuiI gui)
+  {
+    VCFReader reader = null;
+    try
+    {
+      // long start = System.currentTimeMillis();
+      reader = new VCFReader(filePath);
+
+      header = reader.getFileHeader();
+
+      sourceId = filePath;
+
+      saveMetadata(sourceId);
+
+      /*
+       * get offset of CSQ ALLELE_NUM and Feature if declared
+       */
+      locateCsqFields();
+
+      VCFHeaderLine ref = header
+              .getOtherHeaderLine(VCFHeader.REFERENCE_KEY);
+      String vcfAssembly = ref.getValue();
+
+      int varCount = 0;
+      int seqCount = 0;
+
+      /*
+       * query for VCF overlapping each sequence in turn
+       */
+      for (SequenceI seq : al.getSequences())
+      {
+        int added = loadSequenceVCF(seq, reader, vcfAssembly);
+        if (added > 0)
+        {
+          seqCount++;
+          varCount += added;
+          transferAddedFeatures(seq);
+        }
+      }
+      if (gui != null)
+      {
+        // long elapsed = System.currentTimeMillis() - start;
+        String msg = MessageManager.formatMessage("label.added_vcf",
+                varCount, seqCount);
+        gui.setStatus(msg);
+        if (gui.getFeatureSettingsUI() != null)
+        {
+          gui.getFeatureSettingsUI().discoverAllFeatureData();
+        }
+      }
+    } catch (Throwable e)
+    {
+      System.err.println("Error processing VCF: " + e.getMessage());
+      e.printStackTrace();
+      if (gui != null)
+      {
+        gui.setStatus("Error occurred - see console for details");
+      }
+    } finally
+    {
+      if (reader != null)
+      {
+        try
+        {
+          reader.close();
+        } catch (IOException e)
+        {
+          // ignore
+        }
+      }
+    }
+  }
+
+  /**
+   * Reads metadata (such as INFO field descriptions and datatypes) and saves
+   * them for future reference
+   * 
+   * @param sourceId
+   */
+  void saveMetadata(String sourceId)
+  {
+    FeatureSource metadata = new FeatureSource(sourceId);
+
+    for (VCFInfoHeaderLine info : header.getInfoHeaderLines())
+    {
+      String attributeId = info.getID();
+      String desc = info.getDescription();
+      VCFHeaderLineType type = info.getType();
+      FeatureAttributeType attType = null;
+      switch (type)
+      {
+      case Character:
+        attType = FeatureAttributeType.Character;
+        break;
+      case Flag:
+        attType = FeatureAttributeType.Flag;
+        break;
+      case Float:
+        attType = FeatureAttributeType.Float;
+        break;
+      case Integer:
+        attType = FeatureAttributeType.Integer;
+        break;
+      case String:
+        attType = FeatureAttributeType.String;
+        break;
+      }
+      metadata.setAttributeName(attributeId, desc);
+      metadata.setAttributeType(attributeId, attType);
+    }
+
+    FeatureSources.getInstance().addSource(sourceId, metadata);
+  }
+
+  /**
+   * Records the position of selected fields defined in the CSQ INFO header (if
+   * there is one). CSQ fields are declared in the CSQ INFO Description e.g.
+   * <p>
+   * Description="Consequence ...from ... VEP. Format: Allele|Consequence|...
+   */
+  protected void locateCsqFields()
+  {
+    VCFInfoHeaderLine csqInfo = header.getInfoHeaderLine(CSQ);
+    if (csqInfo == null)
+    {
+      return;
+    }
+
+    String desc = csqInfo.getDescription();
+    int formatPos = desc.indexOf(FORMAT);
+    if (formatPos == -1)
+    {
+      System.err.println("Parse error, failed to find " + FORMAT
+              + " in " + desc);
+      return;
+    }
+    desc = desc.substring(formatPos + FORMAT.length());
+
+    if (desc != null)
+    {
+      String[] format = desc.split(PIPE_REGEX);
+      int index = 0;
+      for (String field : format)
+      {
+        if (ALLELE_NUM_KEY.equals(field))
+        {
+          csqAlleleNumberFieldIndex = index;
+        }
+        if (ALLELE_KEY.equals(field))
+        {
+          csqAlleleFieldIndex = index;
+        }
+        if (FEATURE_KEY.equals(field))
+        {
+          csqFeatureFieldIndex = index;
+        }
+        index++;
+      }
+    }
+  }
+
+  /**
+   * Transfers VCF features to sequences to which this sequence has a mapping.
+   * If the mapping is 3:1, computes peptide variants from nucleotide variants.
+   * 
+   * @param seq
+   */
+  protected void transferAddedFeatures(SequenceI seq)
+  {
+    DBRefEntry[] dbrefs = seq.getDBRefs();
+    if (dbrefs == null)
+    {
+      return;
+    }
+    for (DBRefEntry dbref : dbrefs)
+    {
+      Mapping mapping = dbref.getMap();
+      if (mapping == null || mapping.getTo() == null)
+      {
+        continue;
+      }
+
+      SequenceI mapTo = mapping.getTo();
+      MapList map = mapping.getMap();
+      if (map.getFromRatio() == 3)
+      {
+        /*
+         * dna-to-peptide product mapping
+         */
+        AlignmentUtils.computeProteinFeatures(seq, mapTo, map);
+      }
+      else
+      {
+        /*
+         * nucleotide-to-nucleotide mapping e.g. transcript to CDS
+         */
+        List<SequenceFeature> features = seq.getFeatures()
+                .getPositionalFeatures(SequenceOntologyI.SEQUENCE_VARIANT);
+        for (SequenceFeature sf : features)
+        {
+          if (FEATURE_GROUP_VCF.equals(sf.getFeatureGroup()))
+          {
+            transferFeature(sf, mapTo, map);
+          }
+        }
+      }
+    }
+  }
+
+  /**
+   * Tries to add overlapping variants read from a VCF file to the given
+   * sequence, and returns the number of variant features added. Note that this
+   * requires the sequence to hold information as to its species, chromosomal
+   * positions and reference assembly, in order to be able to map the VCF
+   * variants to the sequence (or not)
+   * 
+   * @param seq
+   * @param reader
+   * @param vcfAssembly
+   * @return
+   */
+  protected int loadSequenceVCF(SequenceI seq, VCFReader reader,
+          String vcfAssembly)
+  {
+    int count = 0;
+    GeneLociI seqCoords = seq.getGeneLoci();
+    if (seqCoords == null)
+    {
+      System.out.println(String.format(
+              "Can't query VCF for %s as chromosome coordinates not known",
+              seq.getName()));
+      return 0;
+    }
+
+    if (!vcfSpeciesMatchesSequence(vcfAssembly, seqCoords.getSpeciesId()))
+    {
+      return 0;
+    }
+
+    List<int[]> seqChromosomalContigs = seqCoords.getMap().getToRanges();
+    for (int[] range : seqChromosomalContigs)
+    {
+      count += addVcfVariants(seq, reader, range, vcfAssembly);
+    }
+
+    return count;
+  }
+
+  /**
+   * Answers true if the species inferred from the VCF reference identifier
+   * matches that for the sequence
+   * 
+   * @param vcfAssembly
+   * @param speciesId
+   * @return
+   */
+  boolean vcfSpeciesMatchesSequence(String vcfAssembly, String speciesId)
+  {
+    // PROBLEM 1
+    // there are many aliases for species - how to equate one with another?
+    // PROBLEM 2
+    // VCF ##reference header is an unstructured URI - how to extract species?
+    // perhaps check if ref includes any (Ensembl) alias of speciesId??
+    // TODO ask the user to confirm this??
+
+    if (vcfAssembly.contains("Homo_sapiens") // gnomAD exome data example
+            && "HOMO_SAPIENS".equals(speciesId)) // Ensembl species id
+    {
+      return true;
+    }
+
+    if (vcfAssembly.contains("c_elegans") // VEP VCF response example
+            && "CAENORHABDITIS_ELEGANS".equals(speciesId)) // Ensembl
+    {
+      return true;
+    }
+
+    // this is not a sustainable solution...
+
+    return false;
+  }
+
+  /**
+   * Queries the VCF reader for any variants that overlap the given chromosome
+   * region of the sequence, and adds as variant features. Returns the number of
+   * overlapping variants found.
+   * 
+   * @param seq
+   * @param reader
+   * @param range
+   *          start-end range of a sequence region in its chromosomal
+   *          coordinates
+   * @param vcfAssembly
+   *          the '##reference' identifier for the VCF reference assembly
+   * @return
+   */
+  protected int addVcfVariants(SequenceI seq, VCFReader reader,
+          int[] range, String vcfAssembly)
+  {
+    GeneLociI seqCoords = seq.getGeneLoci();
+
+    String chromosome = seqCoords.getChromosomeId();
+    String seqRef = seqCoords.getAssemblyId();
+    String species = seqCoords.getSpeciesId();
+
+    /*
+     * map chromosomal coordinates from sequence to VCF if the VCF
+     * data has a different reference assembly to the sequence
+     */
+    // TODO generalise for non-human species
+    // - or get the user to choose in a dialog
+
+    int offset = 0;
+    if ("GRCh38".equalsIgnoreCase(seqRef) // Ensembl
+            && vcfAssembly.contains("Homo_sapiens_assembly19")) // gnomAD
+    {
+      String toRef = "GRCh37";
+      int[] newRange = mapReferenceRange(range, chromosome, "human",
+              seqRef, toRef);
+      if (newRange == null)
+      {
+        System.err.println(String.format(
+                "Failed to map %s:%s:%s:%d:%d to %s", species, chromosome,
+                seqRef, range[0], range[1], toRef));
+        return 0;
+      }
+      offset = newRange[0] - range[0];
+      range = newRange;
+    }
+
+    boolean forwardStrand = range[0] <= range[1];
+
+    /*
+     * query the VCF for overlaps
+     * (convert a reverse strand range to forwards)
+     */
+    int count = 0;
+    MapList mapping = seqCoords.getMap();
+
+    int fromLocus = Math.min(range[0], range[1]);
+    int toLocus = Math.max(range[0], range[1]);
+    CloseableIterator<VariantContext> variants = reader.query(chromosome,
+            fromLocus, toLocus);
+    while (variants.hasNext())
+    {
+      /*
+       * get variant location in sequence chromosomal coordinates
+       */
+      VariantContext variant = variants.next();
+
+      int start = variant.getStart() - offset;
+      int end = variant.getEnd() - offset;
+
+      /*
+       * convert chromosomal location to sequence coordinates
+       * - may be reverse strand (convert to forward for sequence feature)
+       * - null if a partially overlapping feature
+       */
+      int[] seqLocation = mapping.locateInFrom(start, end);
+      if (seqLocation != null)
+      {
+        int featureStart = Math.min(seqLocation[0], seqLocation[1]);
+        int featureEnd = Math.max(seqLocation[0], seqLocation[1]);
+        count += addAlleleFeatures(seq, variant, featureStart, featureEnd,
+                forwardStrand);
+      }
+    }
+
+    variants.close();
+
+    return count;
+  }
+
+  /**
+   * A convenience method to get the AF value for the given alternate allele
+   * index
+   * 
+   * @param variant
+   * @param alleleIndex
+   * @return
+   */
+  protected float getAlleleFrequency(VariantContext variant, int alleleIndex)
+  {
+    float score = 0f;
+    String attributeValue = getAttributeValue(variant,
+            ALLELE_FREQUENCY_KEY, alleleIndex);
+    if (attributeValue != null)
+    {
+      try
+      {
+        score = Float.parseFloat(attributeValue);
+      } catch (NumberFormatException e)
+      {
+        // leave as 0
+      }
+    }
+
+    return score;
+  }
+
+  /**
+   * A convenience method to get an attribute value for an alternate allele
+   * 
+   * @param variant
+   * @param attributeName
+   * @param alleleIndex
+   * @return
+   */
+  protected String getAttributeValue(VariantContext variant,
+          String attributeName, int alleleIndex)
+  {
+    Object att = variant.getAttribute(attributeName);
+
+    if (att instanceof String)
+    {
+      return (String) att;
+    }
+    else if (att instanceof ArrayList)
+    {
+      return ((List<String>) att).get(alleleIndex);
+    }
+
+    return null;
+  }
+
+  /**
+   * Adds one variant feature for each allele in the VCF variant record, and
+   * returns the number of features added.
+   * 
+   * @param seq
+   * @param variant
+   * @param featureStart
+   * @param featureEnd
+   * @param forwardStrand
+   * @return
+   */
+  protected int addAlleleFeatures(SequenceI seq, VariantContext variant,
+          int featureStart, int featureEnd, boolean forwardStrand)
+  {
+    int added = 0;
+
+    /*
+     * Javadoc says getAlternateAlleles() imposes no order on the list returned
+     * so we proceed defensively to get them in strict order
+     */
+    int altAlleleCount = variant.getAlternateAlleles().size();
+    for (int i = 0; i < altAlleleCount; i++)
+    {
+      added += addAlleleFeature(seq, variant, i, featureStart, featureEnd,
+              forwardStrand);
+    }
+    return added;
+  }
+
+  /**
+   * Inspects one allele and attempts to add a variant feature for it to the
+   * sequence. We extract as much as possible of the additional data associated
+   * with this allele to store in the feature's key-value map. Answers the
+   * number of features added (0 or 1).
+   * 
+   * @param seq
+   * @param variant
+   * @param altAlleleIndex
+   *          (0, 1..)
+   * @param featureStart
+   * @param featureEnd
+   * @param forwardStrand
+   * @return
+   */
+  protected int addAlleleFeature(SequenceI seq, VariantContext variant,
+          int altAlleleIndex, int featureStart, int featureEnd,
+          boolean forwardStrand)
+  {
+    String reference = variant.getReference().getBaseString();
+    Allele alt = variant.getAlternateAllele(altAlleleIndex);
+    String allele = alt.getBaseString();
+
+    /*
+     * build the ref,alt allele description e.g. "G,A", using the base
+     * complement if the sequence is on the reverse strand
+     */
+    // TODO check how structural variants are shown on reverse strand
+    StringBuilder sb = new StringBuilder();
+    sb.append(forwardStrand ? reference : Dna.reverseComplement(reference));
+    sb.append(COMMA);
+    sb.append(forwardStrand ? allele : Dna.reverseComplement(allele));
+    String alleles = sb.toString(); // e.g. G,A
+
+    String type = SequenceOntologyI.SEQUENCE_VARIANT;
+    float score = getAlleleFrequency(variant, altAlleleIndex);
+
+    SequenceFeature sf = new SequenceFeature(type, alleles, featureStart,
+            featureEnd, score, FEATURE_GROUP_VCF);
+    sf.setSource(sourceId);
+
+    sf.setValue(Gff3Helper.ALLELES, alleles);
+
+    addAlleleProperties(variant, seq, sf, altAlleleIndex);
+
+    seq.addSequenceFeature(sf);
+
+    return 1;
+  }
+
+  /**
+   * Add any allele-specific VCF key-value data to the sequence feature
+   * 
+   * @param variant
+   * @param seq
+   * @param sf
+   * @param altAlelleIndex
+   *          (0, 1..)
+   */
+  protected void addAlleleProperties(VariantContext variant, SequenceI seq,
+          SequenceFeature sf, final int altAlelleIndex)
+  {
+    Map<String, Object> atts = variant.getAttributes();
+
+    for (Entry<String, Object> att : atts.entrySet())
+    {
+      String key = att.getKey();
+
+      /*
+       * extract Consequence data (if present) that we are able to
+       * associated with the allele for this variant feature
+       */
+      if (CSQ.equals(key))
+      {
+        addConsequences(variant, seq, sf, altAlelleIndex);
+        continue;
+      }
+
+      /*
+       * we extract values for other data which are allele-specific; 
+       * these may be per alternate allele (INFO[key].Number = 'A') 
+       * or per allele including reference (INFO[key].Number = 'R') 
+       */
+      VCFInfoHeaderLine infoHeader = header.getInfoHeaderLine(key);
+      if (infoHeader == null)
+      {
+        /*
+         * can't be sure what data belongs to this allele, so
+         * play safe and don't take any
+         */
+        continue;
+      }
+
+      VCFHeaderLineCount number = infoHeader.getCountType();
+      int index = altAlelleIndex;
+      if (number == VCFHeaderLineCount.R)
+      {
+        /*
+         * one value per allele including reference, so bump index
+         * e.g. the 3rd value is for the  2nd alternate allele
+         */
+        index++;
+      }
+      else if (number != VCFHeaderLineCount.A)
+      {
+        /*
+         * don't save other values as not allele-related
+         */
+        continue;
+      }
+
+      /*
+       * take the index'th value
+       */
+      String value = getAttributeValue(variant, key, index);
+      if (value != null)
+      {
+        sf.setValue(key, value);
+      }
+    }
+  }
+
+  /**
+   * Inspects CSQ data blocks (consequences) and adds attributes on the sequence
+   * feature for the current allele (and transcript if applicable)
+   * <p>
+   * Allele matching: if field ALLELE_NUM is present, it must match
+   * altAlleleIndex. If not present, then field Allele value must match the VCF
+   * Allele.
+   * <p>
+   * Transcript matching: if sequence name can be identified to at least one of
+   * the consequences' Feature values, then select only consequences that match
+   * the value (i.e. consequences for the current transcript sequence). If not,
+   * take all consequences (this is the case when adding features to the gene
+   * sequence).
+   * 
+   * @param variant
+   * @param seq
+   * @param sf
+   * @param altAlelleIndex
+   *          (0, 1..)
+   */
+  protected void addConsequences(VariantContext variant, SequenceI seq,
+          SequenceFeature sf, int altAlelleIndex)
+  {
+    Object value = variant.getAttribute(CSQ);
+
+    if (value == null || !(value instanceof ArrayList<?>))
+    {
+      return;
+    }
+
+    List<String> consequences = (List<String>) value;
+
+    /*
+     * if CSQ data includes 'Feature', and any value matches the sequence name,
+     * then restrict consequence data to only the matching value (transcript)
+     * i.e. just pick out consequences for the transcript the variant feature is on
+     */
+    String seqName = seq.getName()== null ? "" : seq.getName().toLowerCase();
+    String matchFeature = null;
+    if (csqFeatureFieldIndex > -1)
+    {
+      for (String consequence : consequences)
+      {
+        String[] csqFields = consequence.split(PIPE_REGEX);
+        if (csqFields.length > csqFeatureFieldIndex)
+        {
+          String featureIdentifier = csqFields[csqFeatureFieldIndex];
+          if (featureIdentifier.length() > 4
+                  && seqName.indexOf(featureIdentifier.toLowerCase()) > -1)
+          {
+            matchFeature = featureIdentifier;
+          }
+        }
+      }
+    }
+
+    StringBuilder sb = new StringBuilder(128);
+    boolean found = false;
+
+    for (String consequence : consequences)
+    {
+      String[] csqFields = consequence.split(PIPE_REGEX);
+
+      if (includeConsequence(csqFields, matchFeature, variant,
+              altAlelleIndex))
+      {
+        if (found)
+        {
+          sb.append(COMMA);
+        }
+        found = true;
+        sb.append(consequence);
+      }
+    }
+
+    if (found)
+    {
+      sf.setValue(CSQ, sb.toString());
+    }
+  }
+
+  /**
+   * Answers true if we want to associate this block of consequence data with
+   * the specified alternate allele of the VCF variant.
+   * <p>
+   * If consequence data includes the ALLELE_NUM field, then this has to match
+   * altAlleleIndex. Otherwise the Allele field of the consequence data has to
+   * match the allele value.
+   * <p>
+   * Optionally (if matchFeature is not null), restrict to only include
+   * consequences whose Feature value matches. This allows us to attach
+   * consequences to their respective transcripts.
+   * 
+   * @param csqFields
+   * @param matchFeature
+   * @param variant
+   * @param altAlelleIndex
+   *          (0, 1..)
+   * @return
+   */
+  protected boolean includeConsequence(String[] csqFields,
+          String matchFeature, VariantContext variant, int altAlelleIndex)
+  {
+    /*
+     * check consequence is for the current transcript
+     */
+    if (matchFeature != null)
+    {
+      if (csqFields.length <= csqFeatureFieldIndex)
+      {
+        return false;
+      }
+      String featureIdentifier = csqFields[csqFeatureFieldIndex];
+      if (!featureIdentifier.equals(matchFeature))
+      {
+        return false; // consequence is for a different transcript
+      }
+    }
+
+    /*
+     * if ALLELE_NUM is present, it must match altAlleleIndex
+     * NB first alternate allele is 1 for ALLELE_NUM, 0 for altAlleleIndex
+     */
+    if (csqAlleleNumberFieldIndex > -1)
+    {
+      if (csqFields.length <= csqAlleleNumberFieldIndex)
+      {
+        return false;
+      }
+      String alleleNum = csqFields[csqAlleleNumberFieldIndex];
+      return String.valueOf(altAlelleIndex + 1).equals(alleleNum);
+    }
+
+    /*
+     * else consequence allele must match variant allele
+     */
+    if (csqAlleleFieldIndex > -1 && csqFields.length > csqAlleleFieldIndex)
+    {
+      String csqAllele = csqFields[csqAlleleFieldIndex];
+      String vcfAllele = variant.getAlternateAllele(altAlelleIndex)
+              .getBaseString();
+      return csqAllele.equals(vcfAllele);
+    }
+
+    return false;
+  }
+
+  /**
+   * A convenience method to complement a dna base and return the string value
+   * of its complement
+   * 
+   * @param reference
+   * @return
+   */
+  protected String complement(byte[] reference)
+  {
+    return String.valueOf(Dna.getComplement((char) reference[0]));
+  }
+
+  /**
+   * Determines the location of the query range (chromosome positions) in a
+   * different reference assembly.
+   * <p>
+   * If the range is just a subregion of one for which we already have a mapping
+   * (for example, an exon sub-region of a gene), then the mapping is just
+   * computed arithmetically.
+   * <p>
+   * Otherwise, calls the Ensembl REST service that maps from one assembly
+   * reference's coordinates to another's
+   * 
+   * @param queryRange
+   *          start-end chromosomal range in 'fromRef' coordinates
+   * @param chromosome
+   * @param species
+   * @param fromRef
+   *          assembly reference for the query coordinates
+   * @param toRef
+   *          assembly reference we wish to translate to
+   * @return the start-end range in 'toRef' coordinates
+   */
+  protected int[] mapReferenceRange(int[] queryRange, String chromosome,
+          String species, String fromRef, String toRef)
+  {
+    /*
+     * first try shorcut of computing the mapping as a subregion of one
+     * we already have (e.g. for an exon, if we have the gene mapping)
+     */
+    int[] mappedRange = findSubsumedRangeMapping(queryRange, chromosome,
+            species, fromRef, toRef);
+    if (mappedRange != null)
+    {
+      return mappedRange;
+    }
+
+    /*
+     * call (e.g.) http://rest.ensembl.org/map/human/GRCh38/17:45051610..45109016:1/GRCh37
+     */
+    EnsemblMap mapper = new EnsemblMap();
+    int[] mapping = mapper.getAssemblyMapping(species, chromosome, fromRef,
+            toRef, queryRange);
+
+    if (mapping == null)
+    {
+      // mapping service failure
+      return null;
+    }
+
+    /*
+     * save mapping for possible future re-use
+     */
+    String key = makeRangesKey(chromosome, species, fromRef, toRef);
+    if (!assemblyMappings.containsKey(key))
+    {
+      assemblyMappings.put(key, new HashMap<int[], int[]>());
+    }
+
+    assemblyMappings.get(key).put(queryRange, mapping);
+
+    return mapping;
+  }
+
+  /**
+   * If we already have a 1:1 contiguous mapping which subsumes the given query
+   * range, this method just calculates and returns the subset of that mapping,
+   * else it returns null. In practical terms, if a gene has a contiguous
+   * mapping between (for example) GRCh37 and GRCh38, then we assume that its
+   * subsidiary exons occupy unchanged relative positions, and just compute
+   * these as offsets, rather than do another lookup of the mapping.
+   * <p>
+   * If in future these assumptions prove invalid (e.g. for bacterial dna?!),
+   * simply remove this method or let it always return null.
+   * <p>
+   * Warning: many rapid calls to the /map service map result in a 429 overload
+   * error response
+   * 
+   * @param queryRange
+   * @param chromosome
+   * @param species
+   * @param fromRef
+   * @param toRef
+   * @return
+   */
+  protected int[] findSubsumedRangeMapping(int[] queryRange, String chromosome,
+          String species, String fromRef, String toRef)
+  {
+    String key = makeRangesKey(chromosome, species, fromRef, toRef);
+    if (assemblyMappings.containsKey(key))
+    {
+      Map<int[], int[]> mappedRanges = assemblyMappings.get(key);
+      for (Entry<int[], int[]> mappedRange : mappedRanges.entrySet())
+      {
+        int[] fromRange = mappedRange.getKey();
+        int[] toRange = mappedRange.getValue();
+        if (fromRange[1] - fromRange[0] == toRange[1] - toRange[0])
+        {
+          /*
+           * mapping is 1:1 in length, so we trust it to have no discontinuities
+           */
+          if (MappingUtils.rangeContains(fromRange, queryRange))
+          {
+            /*
+             * fromRange subsumes our query range
+             */
+            int offset = queryRange[0] - fromRange[0];
+            int mappedRangeFrom = toRange[0] + offset;
+            int mappedRangeTo = mappedRangeFrom + (queryRange[1] - queryRange[0]);
+            return new int[] { mappedRangeFrom, mappedRangeTo };
+          }
+        }
+      }
+    }
+    return null;
+  }
+
+  /**
+   * Transfers the sequence feature to the target sequence, locating its start
+   * and end range based on the mapping. Features which do not overlap the
+   * target sequence are ignored.
+   * 
+   * @param sf
+   * @param targetSequence
+   * @param mapping
+   *          mapping from the feature's coordinates to the target sequence
+   */
+  protected void transferFeature(SequenceFeature sf,
+          SequenceI targetSequence, MapList mapping)
+  {
+    int[] mappedRange = mapping.locateInTo(sf.getBegin(), sf.getEnd());
+  
+    if (mappedRange != null)
+    {
+      String group = sf.getFeatureGroup();
+      int newBegin = Math.min(mappedRange[0], mappedRange[1]);
+      int newEnd = Math.max(mappedRange[0], mappedRange[1]);
+      SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd,
+              group, sf.getScore());
+      targetSequence.addSequenceFeature(copy);
+    }
+  }
+
+  /**
+   * Formats a ranges map lookup key
+   * 
+   * @param chromosome
+   * @param species
+   * @param fromRef
+   * @param toRef
+   * @return
+   */
+  protected static String makeRangesKey(String chromosome, String species,
+          String fromRef, String toRef)
+  {
+    return species + EXCL + chromosome + EXCL + fromRef + EXCL
+            + toRef;
+  }
+}
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 86d0c85..1cf482d 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -147,6 +147,8 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem runGroovy = new JMenuItem();
 
+  protected JMenuItem loadVcf;
+
   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
@@ -1308,6 +1310,16 @@ public class GAlignFrame extends JInternalFrame
         associatedData_actionPerformed(e);
       }
     });
+    loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
+    loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
+    loadVcf.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        loadVcf_actionPerformed();
+      }
+    });
     autoCalculate.setText(
             MessageManager.getString("label.autocalculate_consensus"));
     autoCalculate.setState(
@@ -1710,6 +1722,7 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.add(exportAnnotations);
     fileMenu.add(loadTreeMenuItem);
     fileMenu.add(associatedData);
+    fileMenu.add(loadVcf);
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
 
@@ -1855,6 +1868,10 @@ public class GAlignFrame extends JInternalFrame
     // selectMenu.add(listenToViewSelections);
   }
 
+  protected void loadVcf_actionPerformed()
+  {
+  }
+
   /**
    * Constructs the entries on the Colour menu (but does not add them to the
    * menu).
diff --git a/src/jalview/jbgui/GCutAndPasteHtmlTransfer.java b/src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
index abc0b3d..a6e0ace 100644
--- a/src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
+++ b/src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
@@ -39,6 +39,8 @@ import javax.swing.JMenuBar;
 import javax.swing.JMenuItem;
 import javax.swing.JPanel;
 import javax.swing.JScrollPane;
+import javax.swing.text.EditorKit;
+import javax.swing.text.html.HTMLEditorKit;
 
 /**
  * DOCUMENT ME!
@@ -85,6 +87,7 @@ public class GCutAndPasteHtmlTransfer extends JInternalFrame
   {
     try
     {
+      textarea.setEditorKit(new HTMLEditorKit());
       setJMenuBar(editMenubar);
       jbInit();
     } catch (Exception e)
@@ -272,4 +275,20 @@ public class GCutAndPasteHtmlTransfer extends JInternalFrame
   {
 
   }
+
+  /**
+   * Adds the given stylesheet rule to the Html editor. However note that CSS
+   * support is limited.
+   * 
+   * @param rule
+   * @see javax.swing.text.html.CSS
+   */
+  public void addStylesheetRule(String rule)
+  {
+    EditorKit editorKit = textarea.getEditorKit();
+    if (editorKit != null)
+    {
+      ((HTMLEditorKit) editorKit).getStyleSheet().addRule(rule);
+    }
+  }
 }
diff --git a/src/jalview/schemes/FeatureColour.java b/src/jalview/schemes/FeatureColour.java
index 54d1c6c..2dac7db 100644
--- a/src/jalview/schemes/FeatureColour.java
+++ b/src/jalview/schemes/FeatureColour.java
@@ -24,9 +24,11 @@ import jalview.api.FeatureColourI;
 import jalview.datamodel.SequenceFeature;
 import jalview.util.ColorUtils;
 import jalview.util.Format;
+import jalview.util.matcher.KeyedMatcherSetI;
 
 import java.awt.Color;
 import java.util.StringTokenizer;
+import java.util.function.Function;
 
 /**
  * A class that wraps either a simple colour or a graduated colour
@@ -73,6 +75,11 @@ public class FeatureColour implements FeatureColourI
 
   final private float deltaBlue;
 
+  /*
+   * optional filter(s) by attribute values
+   */
+  private KeyedMatcherSetI attributeFilters;
+
   /**
    * Parses a Jalview features file format colour descriptor
    * [label|][mincolour|maxcolour
@@ -359,6 +366,7 @@ public class FeatureColour implements FeatureColourI
     base = fc.base;
     range = fc.range;
     isHighToLow = fc.isHighToLow;
+    attributeFilters = fc.attributeFilters;
     setAboveThreshold(fc.isAboveThreshold());
     setBelowThreshold(fc.isBelowThreshold());
     setThreshold(fc.getThreshold());
@@ -540,6 +548,11 @@ public class FeatureColour implements FeatureColourI
   @Override
   public Color getColor(SequenceFeature feature)
   {
+    if (!matchesFilters(feature))
+    {
+      return null;
+    }
+
     if (isColourByLabel())
     {
       return ColorUtils.createColourFromName(feature.getDescription());
@@ -589,6 +602,28 @@ public class FeatureColour implements FeatureColourI
   }
 
   /**
+   * Answers true if either there are no attribute value filters defined, or the
+   * feature matches all of the filter conditions. Answers false if the feature
+   * fails the filter conditions.
+   * 
+   * @param feature
+   * 
+   * @return
+   */
+  boolean matchesFilters(SequenceFeature feature)
+  {
+    if (attributeFilters == null)
+    {
+      return true;
+    }
+
+    Function<String, String> valueProvider = key -> feature.otherDetails == null ? null
+                    : (feature.otherDetails.containsKey(key) ? feature.otherDetails
+                            .get(key).toString() : null);
+    return attributeFilters.matches(valueProvider);
+  }
+
+  /**
    * Returns the maximum score of the graduated colour range
    * 
    * @return
@@ -674,4 +709,21 @@ public class FeatureColour implements FeatureColourI
     return String.format("%s\t%s", featureType, colourString);
   }
 
+  /**
+   * Adds an attribute filter
+   * 
+   * @param attName
+   * @param filter
+   */
+  @Override
+  public void setAttributeFilters(KeyedMatcherSetI matcher)
+  {
+    attributeFilters = matcher;
+  }
+
+  @Override
+  public KeyedMatcherSetI getAttributeFilters()
+  {
+    return attributeFilters;
+  }
 }
diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index 4658724..3ce0bb3 100644
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -1120,4 +1120,63 @@ public class MapList
             || (fromRatio == 3 && toRatio == 1);
   }
 
+  /**
+   * Returns a map which is the composite of this one and the input map. That
+   * is, the output map has the fromRanges of this map, and its toRanges are the
+   * toRanges of this map as transformed by the input map.
+   * <p>
+   * Returns null if the mappings cannot be traversed (not all toRanges of this
+   * map correspond to fromRanges of the input), or if this.toRatio does not
+   * match map.fromRatio.
+   * 
+   * <pre>
+   * Example 1:
+   *    this:   from [1-100] to [501-600]
+   *    input:  from [10-40] to [60-90]
+   *    output: from [10-40] to [560-590]
+   * Example 2 ('reverse strand exons'):
+   *    this:   from [1-100] to [2000-1951], [1000-951] // transcript to loci
+   *    input:  from [1-50]  to [41-90] // CDS to transcript
+   *    output: from [10-40] to [1960-1951], [1000-971] // CDS to gene loci
+   * </pre>
+   * 
+   * @param map
+   * @return
+   */
+  public MapList traverse(MapList map)
+  {
+    if (map == null)
+    {
+      return null;
+    }
+
+    /*
+     * compound the ratios by this rule:
+     * A:B with M:N gives A*M:B*N
+     * reduced by greatest common divisor
+     * so 1:3 with 3:3 is 3:9 or 1:3
+     * 1:3 with 3:1 is 3:3 or 1:1
+     * 1:3 with 1:3 is 1:9
+     * 2:5 with 3:7 is 6:35
+     */
+    int outFromRatio = getFromRatio() * map.getFromRatio();
+    int outToRatio = getToRatio() * map.getToRatio();
+    int gcd = MathUtils.gcd(outFromRatio, outToRatio);
+    outFromRatio /= gcd;
+    outToRatio /= gcd;
+
+    List<int[]> toRanges = new ArrayList<>();
+    for (int[] range : getToRanges())
+    {
+      int[] transferred = map.locateInTo(range[0], range[1]);
+      if (transferred == null)
+      {
+        return null;
+      }
+      toRanges.add(transferred);
+    }
+
+    return new MapList(getFromRanges(), toRanges, outFromRatio, outToRatio);
+  }
+
 }
diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index 9c5c109..f5dd883 100644
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -941,6 +941,34 @@ public final class MappingUtils
   }
 
   /**
+   * Answers true if range's start-end positions include those of queryRange,
+   * where either range might be in reverse direction, else false
+   * 
+   * @param range
+   *          a start-end range
+   * @param queryRange
+   *          a candidate subrange of range (start2-end2)
+   * @return
+   */
+  public static boolean rangeContains(int[] range, int[] queryRange)
+  {
+    if (range == null || queryRange == null || range.length != 2
+            || queryRange.length != 2)
+    {
+      /*
+       * invalid arguments
+       */
+      return false;
+    }
+
+    int min = Math.min(range[0], range[1]);
+    int max = Math.max(range[0], range[1]);
+  
+    return (min <= queryRange[0] && max >= queryRange[0]
+            && min <= queryRange[1] && max >= queryRange[1]);
+  }
+
+  /**
    * Removes the specified number of positions from the given ranges. Provided
    * to allow a stop codon to be stripped from a CDS sequence so that it matches
    * the peptide translation length.
diff --git a/src/jalview/util/MathUtils.java b/src/jalview/util/MathUtils.java
new file mode 100644
index 0000000..72d46a2
--- /dev/null
+++ b/src/jalview/util/MathUtils.java
@@ -0,0 +1,22 @@
+package jalview.util;
+
+public class MathUtils
+{
+
+  /**
+   * Returns the greatest common divisor of two integers
+   * 
+   * @param a
+   * @param b
+   * @return
+   */
+  public static int gcd(int a, int b)
+  {
+    if (b == 0)
+    {
+      return Math.abs(a);
+    }
+    return gcd(b, a % b);
+  }
+
+}
diff --git a/src/jalview/util/StringUtils.java b/src/jalview/util/StringUtils.java
index b3456aa..2e8ace8 100644
--- a/src/jalview/util/StringUtils.java
+++ b/src/jalview/util/StringUtils.java
@@ -403,4 +403,45 @@ public class StringUtils
     }
     return s.substring(0, 1).toUpperCase() + s.substring(1).toLowerCase();
   }
+
+  /**
+   * A helper method that strips off any leading or trailing html and body tags.
+   * If no html tag is found, then also html-encodes angle bracket characters.
+   * 
+   * @param text
+   * @return
+   */
+  public static String stripHtmlTags(String text)
+  {
+    if (text == null)
+    {
+      return null;
+    }
+    String tmp2up = text.toUpperCase();
+    int startTag = tmp2up.indexOf("<HTML>");
+    if (startTag > -1)
+    {
+      text = text.substring(startTag + 6);
+      tmp2up = tmp2up.substring(startTag + 6);
+    }
+    // is omission of "<BODY>" intentional here??
+    int endTag = tmp2up.indexOf("</BODY>");
+    if (endTag > -1)
+    {
+      text = text.substring(0, endTag);
+      tmp2up = tmp2up.substring(0, endTag);
+    }
+    endTag = tmp2up.indexOf("</HTML>");
+    if (endTag > -1)
+    {
+      text = text.substring(0, endTag);
+    }
+  
+    if (startTag == -1 && (text.contains("<") || text.contains(">")))
+    {
+      text = text.replaceAll("<", "&lt;");
+      text = text.replaceAll(">", "&gt;");
+    }
+    return text;
+  }
 }
diff --git a/src/jalview/util/matcher/Condition.java b/src/jalview/util/matcher/Condition.java
new file mode 100644
index 0000000..455f805
--- /dev/null
+++ b/src/jalview/util/matcher/Condition.java
@@ -0,0 +1,57 @@
+package jalview.util.matcher;
+
+import jalview.util.MessageManager;
+
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * An enumeration for binary conditions that a user might choose from when
+ * setting filter or match conditions for values
+ */
+public enum Condition
+{
+  Contains(false), NotContains(false), Matches(false), NotMatches(false),
+  EQ(true), NE(true), LT(true), LE(true), GT(true), GE(true);
+
+  private static Map<Condition, String> displayNames = new HashMap<>();
+  
+  private boolean numeric;
+
+  Condition(boolean isNumeric)
+  {
+    numeric = isNumeric;
+  }
+
+  /**
+   * Answers true if the condition does a numerical comparison, else false
+   * (string comparison)
+   * 
+   * @return
+   */
+  public boolean isNumeric()
+  {
+    return numeric;
+  }
+
+  /**
+   * Answers a display name for the match condition, suitable for showing in
+   * drop-down menus. The value may be internationalized using the resource key
+   * "label.matchCondition_" with the enum name appended.
+   * 
+   * @return
+   */
+  @Override
+  public String toString()
+  {
+    String name = displayNames.get(this);
+    if (name != null)
+    {
+      return name;
+    }
+    name = MessageManager
+            .getStringOrReturn("label.matchCondition_", name());
+    displayNames.put(this, name);
+    return name;
+  }
+}
diff --git a/src/jalview/util/matcher/KeyedMatcher.java b/src/jalview/util/matcher/KeyedMatcher.java
new file mode 100644
index 0000000..474dc31
--- /dev/null
+++ b/src/jalview/util/matcher/KeyedMatcher.java
@@ -0,0 +1,86 @@
+package jalview.util.matcher;
+
+import java.util.function.Function;
+
+/**
+ * An immutable class that models one or more match conditions, each of which is
+ * applied to the value obtained by lookup given the match key.
+ * <p>
+ * For example, the value provider could be a SequenceFeature's attributes map,
+ * and the conditions might be
+ * <ul>
+ * <li>CSQ contains "pathological"</li>
+ * <li>AND</li>
+ * <li>AF <= 1.0e-5</li>
+ * </ul>
+ * 
+ * @author gmcarstairs
+ *
+ */
+public class KeyedMatcher implements KeyedMatcherI
+{
+  final private String key;
+
+  final private MatcherI matcher;
+
+  /**
+   * Constructor given a key, a test condition and a match pattern
+   * 
+   * @param theKey
+   * @param cond
+   * @param pattern
+   */
+  public KeyedMatcher(String theKey, Condition cond, String pattern)
+  {
+    key = theKey;
+    matcher = new Matcher(cond, pattern);
+  }
+
+  /**
+   * Constructor given a key, a test condition and a numerical value to compare
+   * to. Note that if a non-numerical condition is specified, the float will be
+   * converted to a string.
+   * 
+   * @param theKey
+   * @param cond
+   * @param value
+   */
+  public KeyedMatcher(String theKey, Condition cond, float value)
+  {
+    key = theKey;
+    matcher = new Matcher(cond, value);
+  }
+
+  @Override
+  public boolean matches(Function<String, String> valueProvider)
+  {
+    String value = valueProvider.apply(key);
+    return matcher.matches(value);
+  }
+
+  @Override
+  public String getKey()
+  {
+    return key;
+  }
+
+  @Override
+  public MatcherI getMatcher()
+  {
+    return matcher;
+  }
+
+  /**
+   * Answers a string description of this matcher, suitable for debugging or
+   * logging. The format may change in future.
+   */
+  @Override
+  public String toString()
+  {
+    StringBuilder sb = new StringBuilder();
+    sb.append(key).append(" ").append(matcher.getCondition().name())
+            .append(" ").append(matcher.getPattern());
+
+    return sb.toString();
+  }
+}
diff --git a/src/jalview/util/matcher/KeyedMatcherI.java b/src/jalview/util/matcher/KeyedMatcherI.java
new file mode 100644
index 0000000..e9fe014
--- /dev/null
+++ b/src/jalview/util/matcher/KeyedMatcherI.java
@@ -0,0 +1,36 @@
+package jalview.util.matcher;
+
+import java.util.function.Function;
+
+/**
+ * An interface for an object that can apply one or more match conditions, given
+ * a key-value provider. The match conditions are stored against key values, and
+ * applied to the value obtained by a key-value lookup.
+ * 
+ * @author gmcarstairs
+ */
+public interface KeyedMatcherI
+{
+  /**
+   * Answers true if the value provided for this matcher's key passes this
+   * matcher's match condition
+   * 
+   * @param valueProvider
+   * @return
+   */
+  boolean matches(Function<String, String> valueProvider);
+
+  /**
+   * Answers the value key this matcher operates on
+   * 
+   * @return
+   */
+  String getKey();
+
+  /**
+   * Answers the match condition that is applied
+   * 
+   * @return
+   */
+  MatcherI getMatcher();
+}
diff --git a/src/jalview/util/matcher/KeyedMatcherSet.java b/src/jalview/util/matcher/KeyedMatcherSet.java
new file mode 100644
index 0000000..3c21d50
--- /dev/null
+++ b/src/jalview/util/matcher/KeyedMatcherSet.java
@@ -0,0 +1,116 @@
+package jalview.util.matcher;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import java.util.function.Function;
+
+public class KeyedMatcherSet implements KeyedMatcherSetI
+{
+  List<KeyedMatcherI> matchConditions;
+
+  boolean andConditions;
+
+  /**
+   * Constructor
+   */
+  public KeyedMatcherSet()
+  {
+    matchConditions = new ArrayList<>();
+  }
+
+  @Override
+  public boolean matches(Function<String, String> valueProvider)
+  {
+    /*
+     * no conditions matches anything
+     */
+    if (matchConditions.isEmpty())
+    {
+      return true;
+    }
+
+    /*
+     * AND until failure
+     */
+    if (andConditions)
+    {
+      for (KeyedMatcherI m : matchConditions)
+      {
+        if (!m.matches(valueProvider))
+        {
+          return false;
+        }
+      }
+      return true;
+    }
+
+    /*
+     * OR until match
+     */
+    for (KeyedMatcherI m : matchConditions)
+    {
+      if (m.matches(valueProvider))
+      {
+        return true;
+      }
+    }
+    return false;
+  }
+
+  @Override
+  public KeyedMatcherSetI and(KeyedMatcherI m)
+  {
+    if (!andConditions && matchConditions.size() > 1)
+    {
+      throw new IllegalStateException("Can't add an AND to OR conditions");
+    }
+    matchConditions.add(m);
+    andConditions = true;
+
+    return this;
+  }
+
+  @Override
+  public KeyedMatcherSetI or(KeyedMatcherI m)
+  {
+    if (andConditions && matchConditions.size() > 1)
+    {
+      throw new IllegalStateException("Can't add an OR to AND conditions");
+    }
+    matchConditions.add(m);
+    andConditions = false;
+
+    return this;
+  }
+
+  @Override
+  public boolean isAnded()
+  {
+    return andConditions;
+  }
+
+  @Override
+  public Iterator<KeyedMatcherI> getMatchers()
+  {
+    return matchConditions.iterator();
+  }
+
+  @Override
+  public String toString()
+  {
+    StringBuilder sb = new StringBuilder();
+    boolean first = true;
+    for (KeyedMatcherI matcher : matchConditions)
+    {
+      if (!first)
+      {
+        sb.append(andConditions ? " AND " : " OR ");
+      }
+      first = false;
+      sb.append("(").append(matcher.toString()).append(")");
+    }
+    return sb.toString();
+  }
+
+}
diff --git a/src/jalview/util/matcher/KeyedMatcherSetI.java b/src/jalview/util/matcher/KeyedMatcherSetI.java
new file mode 100644
index 0000000..09532a4
--- /dev/null
+++ b/src/jalview/util/matcher/KeyedMatcherSetI.java
@@ -0,0 +1,58 @@
+package jalview.util.matcher;
+
+import java.util.Iterator;
+import java.util.function.Function;
+
+/**
+ * An interface to describe a set of one or more key-value match conditions,
+ * where all conditions are combined with either AND or OR
+ * 
+ * @author gmcarstairs
+ *
+ */
+public interface KeyedMatcherSetI
+{
+  /**
+   * Answers true if the value provided for this matcher's key passes this
+   * matcher's match condition
+   * 
+   * @param valueProvider
+   * @return
+   */
+  boolean matches(Function<String, String> valueProvider);
+
+  /**
+   * Answers a new object that matches the logical AND of this and m
+   * 
+   * @param m
+   * @return
+   * @throws IllegalStateException
+   *           if an attempt is made to AND to existing OR-ed conditions
+   */
+  KeyedMatcherSetI and(KeyedMatcherI m);
+
+  /**
+   * Answers true if any second condition is AND-ed with this one, false if it
+   * is OR-ed
+   * 
+   * @return
+   */
+  boolean isAnded();
+
+  /**
+   * Answers a new object that matches the logical OR of this and m
+   * 
+   * @param m
+   * @return
+   * @throws IllegalStateException
+   *           if an attempt is made to OR to existing AND-ed conditions
+   */
+  KeyedMatcherSetI or(KeyedMatcherI m);
+
+  /**
+   * Answers an iterator over the combined match conditions
+   * 
+   * @return
+   */
+  Iterator<KeyedMatcherI> getMatchers();
+}
diff --git a/src/jalview/util/matcher/Matcher.java b/src/jalview/util/matcher/Matcher.java
new file mode 100644
index 0000000..638933d
--- /dev/null
+++ b/src/jalview/util/matcher/Matcher.java
@@ -0,0 +1,218 @@
+package jalview.util.matcher;
+
+import java.util.Objects;
+import java.util.regex.Pattern;
+
+/**
+ * A bean to describe one attribute-based filter
+ */
+public class Matcher implements MatcherI
+{
+  /*
+   * the comparison condition
+   */
+  Condition condition;
+
+  /*
+   * the string value (upper-cased), or the regex, to compare to
+   * also holds the string form of float value if a numeric condition
+   */
+  String pattern;
+
+  /*
+   * the compiled regex if using a pattern match condition
+   * (reserved for possible future enhancement)
+   */
+  Pattern regexPattern;
+
+  /*
+   * the value to compare to for a numerical condition
+   */
+  float value;
+
+  /**
+   * Constructor
+   * 
+   * @param cond
+   * @param compareTo
+   * @return
+   * @throws NumberFormatException
+   *           if a numerical condition is specified with a non-numeric
+   *           comparision value
+   * @throws NullPointerException
+   *           if a null comparison string is specified
+   */
+  public Matcher(Condition cond, String compareTo)
+  {
+    condition = cond;
+    if (cond.isNumeric())
+    {
+      value = Float.valueOf(compareTo);
+      pattern = String.valueOf(value);
+    }
+    else
+    {
+      // pattern matches will be non-case-sensitive
+      pattern = compareTo.toUpperCase();
+    }
+
+    // if we add regex conditions (e.g. matchesPattern), then
+    // pattern should hold the raw regex, and
+    // regexPattern = Pattern.compile(compareTo);
+  }
+
+  /**
+   * Constructor for a numerical match condition. Note that if a string
+   * comparison condition is specified, this will be converted to a comparison
+   * with the float value as string
+   * 
+   * @param cond
+   * @param compareTo
+   */
+  public Matcher(Condition cond, float compareTo)
+  {
+    Objects.requireNonNull(cond);
+    condition = cond;
+    value = compareTo;
+    pattern = String.valueOf(compareTo).toUpperCase();
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @SuppressWarnings("incomplete-switch")
+  @Override
+  public boolean matches(String val)
+  {
+    if (condition.isNumeric())
+    {
+      try
+      {
+        /*
+         * treat a null value (no such attribute) as
+         * failing any numerical filter condition
+         */
+        return val == null ? false : matches(Float.valueOf(val));
+      } catch (NumberFormatException e)
+      {
+        return false;
+      }
+    }
+    
+    /*
+     * a null value matches a negative condition, fails a positive test
+     */
+    if (val == null)
+    {
+      return condition == Condition.NotContains
+              || condition == Condition.NotMatches;
+    }
+    
+    String upper = val.toUpperCase().trim();
+    boolean matched = false;
+    switch(condition) {
+    case Matches:
+      matched = upper.equals(pattern);
+      break;
+    case NotMatches:
+      matched = !upper.equals(pattern);
+      break;
+    case Contains:
+      matched = upper.indexOf(pattern) > -1;
+      break;
+    case NotContains:
+      matched = upper.indexOf(pattern) == -1;
+      break;
+    }
+    return matched;
+  }
+
+  /**
+   * Applies a numerical comparison match condition
+   * 
+   * @param f
+   * @return
+   */
+  @SuppressWarnings("incomplete-switch")
+  boolean matches(float f)
+  {
+    if (!condition.isNumeric())
+    {
+      return matches(String.valueOf(f));
+    }
+    
+    boolean matched = false;
+    switch (condition) {
+    case LT:
+      matched = f < value;
+      break;
+    case LE:
+      matched = f <= value;
+      break;
+    case EQ:
+      matched = f == value;
+      break;
+    case NE:
+      matched = f != value;
+      break;
+    case GT:
+      matched = f > value;
+      break;
+    case GE:
+      matched = f >= value;
+      break;
+    }
+
+    return matched;
+  }
+
+  /**
+   * A simple hash function that guarantees that when two objects are equal,
+   * they have the same hashcode
+   */
+  @Override
+  public int hashCode()
+  {
+    return pattern.hashCode() + condition.hashCode() + (int) value;
+  }
+
+  /**
+   * equals is overridden so that we can safely remove Matcher objects from
+   * collections (e.g. delete an attribut match condition for a feature colour)
+   */
+  @Override
+  public boolean equals(Object obj)
+  {
+    if (obj == null || !(obj instanceof Matcher))
+    {
+      return false;
+    }
+    Matcher m = (Matcher) obj;
+    return condition == m.condition && value == m.value
+            && pattern.equals(m.pattern);
+  }
+
+  @Override
+  public Condition getCondition()
+  {
+    return condition;
+  }
+
+  @Override
+  public String getPattern()
+  {
+    return pattern;
+  }
+
+  @Override
+  public float getFloatValue()
+  {
+    return value;
+  }
+
+  @Override
+  public String toString()
+  {
+    return condition.name() + " " + pattern;
+  }
+}
diff --git a/src/jalview/util/matcher/MatcherI.java b/src/jalview/util/matcher/MatcherI.java
new file mode 100644
index 0000000..ca6d44c
--- /dev/null
+++ b/src/jalview/util/matcher/MatcherI.java
@@ -0,0 +1,18 @@
+package jalview.util.matcher;
+
+public interface MatcherI
+{
+  /**
+   * Answers true if the given value is matched, else false
+   * 
+   * @param s
+   * @return
+   */
+  boolean matches(String s);
+
+  Condition getCondition();
+
+  String getPattern();
+
+  float getFloatValue();
+}
diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 06b51e6..1bff8bf 100644
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -34,6 +34,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.GeneLociI;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResultsI;
@@ -63,6 +64,8 @@ import org.testng.annotations.Test;
 
 public class AlignmentUtilsTests
 {
+  private static Sequence ts = new Sequence("short",
+          "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
 
   @BeforeClass(alwaysRun = true)
   public void setUpJvOptionPane()
@@ -71,9 +74,6 @@ public class AlignmentUtilsTests
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-  public static Sequence ts = new Sequence("short",
-          "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
-
   @Test(groups = { "Functional" })
   public void testExpandContext()
   {
@@ -1044,14 +1044,18 @@ public class AlignmentUtilsTests
     dna.addCodonFrame(acf);
 
     /*
-     * In this case, mappings originally came from matching Uniprot accessions - so need an xref on dna involving those regions. These are normally constructed from CDS annotation
+     * In this case, mappings originally came from matching Uniprot accessions 
+     * - so need an xref on dna involving those regions. 
+     * These are normally constructed from CDS annotation
      */
     DBRefEntry dna1xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep1",
             new Mapping(mapfordna1));
-    dna1.getDatasetSequence().addDBRef(dna1xref);
+    dna1.addDBRef(dna1xref);
+    assertEquals(2, dna1.getDBRefs().length); // to self and to pep1
     DBRefEntry dna2xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep2",
             new Mapping(mapfordna2));
-    dna2.getDatasetSequence().addDBRef(dna2xref);
+    dna2.addDBRef(dna2xref);
+    assertEquals(2, dna2.getDBRefs().length); // to self and to pep2
 
     /*
      * execute method under test:
@@ -1106,6 +1110,38 @@ public class AlignmentUtilsTests
     assertEquals(cdsMapping.getInverse(), dbref.getMap().getMap());
 
     /*
+     * verify cDNA has added a dbref with mapping to CDS
+     */
+    assertEquals(3, dna1.getDBRefs().length);
+    DBRefEntry dbRefEntry = dna1.getDBRefs()[2];
+    assertSame(cds1Dss, dbRefEntry.getMap().getTo());
+    MapList dnaToCdsMapping = new MapList(new int[] { 4, 6, 10, 12 },
+            new int[] { 1, 6 }, 1, 1);
+    assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap());
+    assertEquals(3, dna2.getDBRefs().length);
+    dbRefEntry = dna2.getDBRefs()[2];
+    assertSame(cds2Dss, dbRefEntry.getMap().getTo());
+    dnaToCdsMapping = new MapList(new int[] { 1, 3, 7, 9, 13, 15 },
+            new int[] { 1, 9 }, 1, 1);
+    assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap());
+
+    /*
+     * verify CDS has added a dbref with mapping to cDNA
+     */
+    assertEquals(2, cds1Dss.getDBRefs().length);
+    dbRefEntry = cds1Dss.getDBRefs()[1];
+    assertSame(dna1.getDatasetSequence(), dbRefEntry.getMap().getTo());
+    MapList cdsToDnaMapping = new MapList(new int[] { 1, 6 }, new int[] {
+        4, 6, 10, 12 }, 1, 1);
+    assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap());
+    assertEquals(2, cds2Dss.getDBRefs().length);
+    dbRefEntry = cds2Dss.getDBRefs()[1];
+    assertSame(dna2.getDatasetSequence(), dbRefEntry.getMap().getTo());
+    cdsToDnaMapping = new MapList(new int[] { 1, 9 }, new int[] { 1, 3, 7,
+        9, 13, 15 }, 1, 1);
+    assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap());
+
+    /*
      * Verify mappings from CDS to peptide, cDNA to CDS, and cDNA to peptide
      * the mappings are on the shared alignment dataset
      * 6 mappings, 2*(DNA->CDS), 2*(DNA->Pep), 2*(CDS->Pep) 
@@ -2533,6 +2569,70 @@ public class AlignmentUtilsTests
     assertEquals(s_as3, uas3.getSequenceAsString());
   }
 
+  @Test(groups = { "Functional" })
+  public void testTransferGeneLoci()
+  {
+    SequenceI from = new Sequence("transcript",
+            "aaacccgggTTTAAACCCGGGtttaaacccgggttt");
+    SequenceI to = new Sequence("CDS", "TTTAAACCCGGG");
+    MapList map = new MapList(new int[] { 1, 12 }, new int[] { 10, 21 }, 1,
+            1);
+
+    /*
+     * first with nothing to transfer
+     */
+    AlignmentUtils.transferGeneLoci(from, map, to);
+    assertNull(to.getGeneLoci());
+
+    /*
+     * next with gene loci set on 'from' sequence
+     */
+    int[] exons = new int[] { 100, 105, 155, 164, 210, 229 };
+    MapList geneMap = new MapList(new int[] { 1, 36 }, exons, 1, 1);
+    from.setGeneLoci("human", "GRCh38", "7", geneMap);
+    AlignmentUtils.transferGeneLoci(from, map, to);
+
+    GeneLociI toLoci = to.getGeneLoci();
+    assertNotNull(toLoci);
+    // DBRefEntry constructor upper-cases 'source'
+    assertEquals("HUMAN", toLoci.getSpeciesId());
+    assertEquals("GRCh38", toLoci.getAssemblyId());
+    assertEquals("7", toLoci.getChromosomeId());
+
+    /*
+     * transcript 'exons' are 1-6, 7-16, 17-36
+     * CDS 1:12 is transcript 10-21
+     * transcript 'CDS' is 10-16, 17-21
+     * which is 'gene' 158-164, 210-214
+     */
+    MapList toMap = toLoci.getMap();
+    assertEquals(1, toMap.getFromRanges().size());
+    assertEquals(2, toMap.getFromRanges().get(0).length);
+    assertEquals(1, toMap.getFromRanges().get(0)[0]);
+    assertEquals(12, toMap.getFromRanges().get(0)[1]);
+    assertEquals(1, toMap.getToRanges().size());
+    assertEquals(4, toMap.getToRanges().get(0).length);
+    assertEquals(158, toMap.getToRanges().get(0)[0]);
+    assertEquals(164, toMap.getToRanges().get(0)[1]);
+    assertEquals(210, toMap.getToRanges().get(0)[2]);
+    assertEquals(214, toMap.getToRanges().get(0)[3]);
+    // or summarised as (but toString might change in future):
+    assertEquals("[ [1, 12] ] 1:1 to [ [158, 164, 210, 214] ]",
+            toMap.toString());
+
+    /*
+     * an existing value is not overridden 
+     */
+    geneMap = new MapList(new int[] { 1, 36 }, new int[] { 36, 1 }, 1, 1);
+    from.setGeneLoci("inhuman", "GRCh37", "6", geneMap);
+    AlignmentUtils.transferGeneLoci(from, map, to);
+    assertEquals("GRCh38", toLoci.getAssemblyId());
+    assertEquals("7", toLoci.getChromosomeId());
+    toMap = toLoci.getMap();
+    assertEquals("[ [1, 12] ] 1:1 to [ [158, 164, 210, 214] ]",
+            toMap.toString());
+  }
+
   /**
    * Tests for the method that maps nucleotide to protein based on CDS features
    */
@@ -2599,5 +2699,4 @@ public class AlignmentUtilsTests
     assertEquals("[[3, 3], [8, 12]]",
             Arrays.deepToString(ml.getFromRanges().toArray()));
   }
-
 }
diff --git a/test/jalview/datamodel/SequenceFeatureTest.java b/test/jalview/datamodel/SequenceFeatureTest.java
index fbeb365..c955979 100644
--- a/test/jalview/datamodel/SequenceFeatureTest.java
+++ b/test/jalview/datamodel/SequenceFeatureTest.java
@@ -273,4 +273,47 @@ public class SequenceFeatureTest
             "group");
     assertTrue(sf.isContactFeature());
   }
+
+  @Test(groups = { "Functional" })
+  public void testGetDetailsReport()
+  {
+    // single locus, no group, no score
+    SequenceFeature sf = new SequenceFeature("variant", "G,C", 22, 22, null);
+    String expected = "<br><table><tr><td>Type</td><td>variant</td><td></td></tr>"
+            + "<tr><td>Start/end</td><td>22</td><td></td></tr>"
+            + "<tr><td>Description</td><td>G,C</td><td></td></tr></table>";
+    assertEquals(expected, sf.getDetailsReport());
+
+    // contact feature
+    sf = new SequenceFeature("Disulphide Bond", "a description", 28, 31,
+            null);
+    expected = "<br><table><tr><td>Type</td><td>Disulphide Bond</td><td></td></tr>"
+            + "<tr><td>Start/end</td><td>28:31</td><td></td></tr>"
+            + "<tr><td>Description</td><td>a description</td><td></td></tr></table>";
+    assertEquals(expected, sf.getDetailsReport());
+
+    sf = new SequenceFeature("variant", "G,C", 22, 33,
+            12.5f, "group");
+    sf.setValue("Parent", "ENSG001");
+    sf.setValue("Child", "ENSP002");
+    expected = "<br><table><tr><td>Type</td><td>variant</td><td></td></tr>"
+            + "<tr><td>Start/end</td><td>22-33</td><td></td></tr>"
+            + "<tr><td>Description</td><td>G,C</td><td></td></tr>"
+            + "<tr><td>Score</td><td>12.5</td><td></td></tr>"
+            + "<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());
+
+    /*
+     * feature with embedded html link in description
+     */
+    String desc = "<html>Fer2 Status: True Positive <a href=\"http://pfam.xfam.org/family/PF00111\">Pfam 8_8</a></html>";
+    sf = new SequenceFeature("Pfam", desc, 8, 83, "Uniprot");
+    expected = "<br><table><tr><td>Type</td><td>Pfam</td><td></td></tr>"
+            + "<tr><td>Start/end</td><td>8-83</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());
+  }
 }
diff --git a/test/jalview/ext/htsjdk/VCFReaderTest.java b/test/jalview/ext/htsjdk/VCFReaderTest.java
new file mode 100644
index 0000000..bf617ae
--- /dev/null
+++ b/test/jalview/ext/htsjdk/VCFReaderTest.java
@@ -0,0 +1,200 @@
+package jalview.ext.htsjdk;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertTrue;
+import htsjdk.samtools.util.CloseableIterator;
+import htsjdk.variant.variantcontext.Allele;
+import htsjdk.variant.variantcontext.VariantContext;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.List;
+
+import org.testng.annotations.Test;
+
+public class VCFReaderTest
+{
+  private static final String[] VCF = new String[] {
+      "##fileformat=VCFv4.2",
+      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO",
+      "20\t3\t.\tC\tG\t.\tPASS\tDP=100", // SNP C/G
+      "20\t7\t.\tG\tGA\t.\tPASS\tDP=100", // insertion G/GA
+      "18\t2\t.\tACG\tA\t.\tPASS\tDP=100" }; // deletion ACG/A
+
+  // gnomAD exome variant dataset
+  private static final String VCF_PATH = "/Volumes/gjb/smacgowan/NOBACK/resources/gnomad/gnomad.exomes.r2.0.1.sites.vcf.gz";
+
+  // "https://storage.cloud.google.com/gnomad-public/release/2.0.1/vcf/exomes/gnomad.exomes.r2.0.1.sites.vcf.gz";
+
+  /**
+   * A test to exercise some basic functionality of the htsjdk VCF reader,
+   * reading from a non-index VCF file
+   * 
+   * @throws IOException
+   */
+  @Test(groups = "Functional")
+  public void testReadVcf_plain() throws IOException
+  {
+    File f = writeVcfFile();
+    VCFReader reader = new VCFReader(f.getAbsolutePath());
+    CloseableIterator<VariantContext> variants = reader.iterator();
+
+    /*
+     * SNP C/G variant
+     */
+    VariantContext vc = variants.next();
+    assertTrue(vc.isSNP());
+    Allele ref = vc.getReference();
+    assertEquals(ref.getBaseString(), "C");
+    List<Allele> alleles = vc.getAlleles();
+    assertEquals(alleles.size(), 2);
+    assertTrue(alleles.get(0).isReference());
+    assertEquals(alleles.get(0).getBaseString(), "C");
+    assertFalse(alleles.get(1).isReference());
+    assertEquals(alleles.get(1).getBaseString(), "G");
+
+    /*
+     * Insertion G -> GA
+     */
+    vc = variants.next();
+    assertFalse(vc.isSNP());
+    assertTrue(vc.isSimpleInsertion());
+    ref = vc.getReference();
+    assertEquals(ref.getBaseString(), "G");
+    alleles = vc.getAlleles();
+    assertEquals(alleles.size(), 2);
+    assertTrue(alleles.get(0).isReference());
+    assertEquals(alleles.get(0).getBaseString(), "G");
+    assertFalse(alleles.get(1).isReference());
+    assertEquals(alleles.get(1).getBaseString(), "GA");
+
+    /*
+     * Deletion ACG -> A
+     */
+    vc = variants.next();
+    assertFalse(vc.isSNP());
+    assertTrue(vc.isSimpleDeletion());
+    ref = vc.getReference();
+    assertEquals(ref.getBaseString(), "ACG");
+    alleles = vc.getAlleles();
+    assertEquals(alleles.size(), 2);
+    assertTrue(alleles.get(0).isReference());
+    assertEquals(alleles.get(0).getBaseString(), "ACG");
+    assertFalse(alleles.get(1).isReference());
+    assertEquals(alleles.get(1).getBaseString(), "A");
+
+    assertFalse(variants.hasNext());
+
+    variants.close();
+    reader.close();
+  }
+
+  /**
+   * Creates a temporary file to be read by the htsjdk VCF reader
+   * 
+   * @return
+   * @throws IOException
+   */
+  protected File writeVcfFile() throws IOException
+  {
+    File f = File.createTempFile("Test", "vcf");
+    f.deleteOnExit();
+    PrintWriter pw = new PrintWriter(f);
+    for (String vcfLine : VCF) {
+      pw.println(vcfLine);
+    }
+    pw.close();
+    return f;
+  }
+  
+  /**
+   * A 'test' that demonstrates querying an indexed VCF file for features in a
+   * specified interval
+   * 
+   * @throws IOException
+   */
+  @Test
+  public void testQuery_indexed() throws IOException
+  {
+    /*
+     * if not specified, assumes index file is filename.tbi
+     */
+    VCFReader reader = new VCFReader(VCF_PATH);
+  
+    /*
+     * gene NMT1 (human) is on chromosome 17
+     * GCHR38 (Ensembl): 45051610-45109016
+     * GCHR37 (gnoMAD): 43128978-43186384
+     * CDS begins at offset 9720, first CDS variant at offset 9724
+     */
+    CloseableIterator<VariantContext> features = reader.query("17",
+            43128978 + 9724, 43128978 + 9734); // first 11 CDS positions
+
+    assertEquals(printNext(features), 43138702);
+    assertEquals(printNext(features), 43138704);
+    assertEquals(printNext(features), 43138707);
+    assertEquals(printNext(features), 43138708);
+    assertEquals(printNext(features), 43138710);
+    assertEquals(printNext(features), 43138711);
+    assertFalse(features.hasNext());
+
+    features.close();
+    reader.close();
+  }
+
+  /**
+   * Prints the toString value of the next variant, and returns its start
+   * location
+   * 
+   * @param features
+   * @return
+   */
+  protected int printNext(CloseableIterator<VariantContext> features)
+  {
+    VariantContext next = features.next();
+    System.out.println(next.toString());
+    return next.getStart();
+  }
+
+  // "https://storage.cloud.google.com/gnomad-public/release/2.0.1/vcf/exomes/gnomad.exomes.r2.0.1.sites.vcf.gz";
+  
+  /**
+   * Test the query method that wraps a non-indexed VCF file
+   * 
+   * @throws IOException
+   */
+  @Test(groups = "Functional")
+  public void testQuery_plain() throws IOException
+  {
+    File f = writeVcfFile();
+    VCFReader reader = new VCFReader(f.getAbsolutePath());
+
+    /*
+     * query for overlap of 5-8 - should find variant at 7
+     */
+    CloseableIterator<VariantContext> variants = reader.query("20", 5, 8);
+  
+    /*
+     * INDEL G/GA variant
+     */
+    VariantContext vc = variants.next();
+    assertTrue(vc.isIndel());
+    assertEquals(vc.getStart(), 7);
+    assertEquals(vc.getEnd(), 7);
+    Allele ref = vc.getReference();
+    assertEquals(ref.getBaseString(), "G");
+    List<Allele> alleles = vc.getAlleles();
+    assertEquals(alleles.size(), 2);
+    assertTrue(alleles.get(0).isReference());
+    assertEquals(alleles.get(0).getBaseString(), "G");
+    assertFalse(alleles.get(1).isReference());
+    assertEquals(alleles.get(1).getBaseString(), "GA");
+
+    assertFalse(variants.hasNext());
+
+    variants.close();
+    reader.close();
+  }
+}
diff --git a/test/jalview/gui/PopupMenuTest.java b/test/jalview/gui/PopupMenuTest.java
index 335240b..40e624d 100644
--- a/test/jalview/gui/PopupMenuTest.java
+++ b/test/jalview/gui/PopupMenuTest.java
@@ -26,21 +26,26 @@ import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
-import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
+import jalview.urls.api.UrlProviderFactoryI;
+import jalview.urls.desktop.DesktopUrlProviderFactory;
 import jalview.util.MessageManager;
+import jalview.util.UrlConstants;
 
 import java.awt.Component;
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 
 import javax.swing.JMenu;
@@ -80,6 +85,25 @@ public class PopupMenuTest
   @BeforeMethod(alwaysRun = true)
   public void setUp() throws IOException
   {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    String inMenuString = ("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
+            + SEQUENCE_ID
+            + "$"
+            + "|"
+            + "UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION + "$")
+            + "|"
+            + ("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
+                    + DB_ACCESSION + "$")
+            + "|"
+            +
+            // Gene3D entry tests for case (in)sensitivity
+            ("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$"
+                    + DB_ACCESSION + "$&mode=protein");
+
+    UrlProviderFactoryI factory = new DesktopUrlProviderFactory(
+            UrlConstants.DEFAULT_LABEL, inMenuString, "");
+    Preferences.sequenceUrlLinks = factory.createUrlProvider();
+
     alignment = new FormatAdapter().readFile(TEST_DATA,
             DataSourceType.PASTE, FileFormat.Fasta);
     AlignFrame af = new AlignFrame(alignment, 700, 500);
@@ -495,17 +519,19 @@ public class PopupMenuTest
 
     // add all the dbrefs to the sequences: Uniprot 1 each, Interpro all 3 to
     // seq0, Gene3D to seq1
-    seqs.get(0).addDBRef(refs.get(0));
+    SequenceI seq = seqs.get(0);
+    seq.addDBRef(refs.get(0));
 
-    seqs.get(0).addDBRef(refs.get(1));
-    seqs.get(0).addDBRef(refs.get(2));
-    seqs.get(0).addDBRef(refs.get(3));
+    seq.addDBRef(refs.get(1));
+    seq.addDBRef(refs.get(2));
+    seq.addDBRef(refs.get(3));
     
     seqs.get(1).addDBRef(refs.get(4));
     seqs.get(1).addDBRef(refs.get(5));
     
     // get the Popup Menu for first sequence
-    testee = new PopupMenu(parentPanel, (Sequence) seqs.get(0), links);
+    List<SequenceFeature> noFeatures = Collections.<SequenceFeature> emptyList();
+    testee = new PopupMenu(parentPanel, seq, noFeatures);
     Component[] seqItems = testee.sequenceMenu.getMenuComponents();
     JMenu linkMenu = (JMenu) seqItems[6];
     Component[] linkItems = linkMenu.getMenuComponents();
@@ -519,15 +545,18 @@ public class PopupMenuTest
     // sequence id for each link should match corresponding DB accession id
     for (int i = 1; i < 4; i++)
     {
-      assertEquals(refs.get(i - 1).getSource(), ((JMenuItem) linkItems[i])
+      String msg = seq.getName() + " link[" + i + "]";
+      assertEquals(msg, refs.get(i - 1).getSource(),
+              ((JMenuItem) linkItems[i])
               .getText().split("\\|")[0]);
-      assertEquals(refs.get(i - 1).getAccessionId(),
+      assertEquals(msg, refs.get(i - 1).getAccessionId(),
               ((JMenuItem) linkItems[i])
               .getText().split("\\|")[1]);
     }
 
     // get the Popup Menu for second sequence
-    testee = new PopupMenu(parentPanel, (Sequence) seqs.get(1), links);
+    seq = seqs.get(1);
+    testee = new PopupMenu(parentPanel, seq, noFeatures);
     seqItems = testee.sequenceMenu.getMenuComponents();
     linkMenu = (JMenu) seqItems[6];
     linkItems = linkMenu.getMenuComponents();
@@ -541,9 +570,11 @@ public class PopupMenuTest
     // sequence id for each link should match corresponding DB accession id
     for (int i = 1; i < 3; i++)
     {
-      assertEquals(refs.get(i + 3).getSource(), ((JMenuItem) linkItems[i])
+      String msg = seq.getName() + " link[" + i + "]";
+      assertEquals(msg, refs.get(i + 3).getSource(),
+              ((JMenuItem) linkItems[i])
               .getText().split("\\|")[0].toUpperCase());
-      assertEquals(refs.get(i + 3).getAccessionId(),
+      assertEquals(msg, refs.get(i + 3).getAccessionId(),
               ((JMenuItem) linkItems[i]).getText().split("\\|")[1]);
     }
 
@@ -552,8 +583,7 @@ public class PopupMenuTest
     nomatchlinks.add("NOMATCH | http://www.uniprot.org/uniprot/$"
             + DB_ACCESSION + "$");
 
-    testee = new PopupMenu(parentPanel, (Sequence) seqs.get(0),
-            nomatchlinks);
+    testee = new PopupMenu(parentPanel, seq, noFeatures);
     seqItems = testee.sequenceMenu.getMenuComponents();
     linkMenu = (JMenu) seqItems[6];
     assertFalse(linkMenu.isEnabled());
diff --git a/test/jalview/gui/SeqCanvasTest.java b/test/jalview/gui/SeqCanvasTest.java
index a27bc3f..05b9aea 100644
--- a/test/jalview/gui/SeqCanvasTest.java
+++ b/test/jalview/gui/SeqCanvasTest.java
@@ -13,8 +13,6 @@ import junit.extensions.PA;
 
 import org.testng.annotations.Test;
 
-import sun.swing.SwingUtilities2;
-
 public class SeqCanvasTest
 {
   /**
@@ -48,7 +46,7 @@ public class SeqCanvasTest
     av.setScaleAboveWrapped(true);
     av.setScaleLeftWrapped(true);
     av.setScaleRightWrapped(true);
-    FontMetrics fm = SwingUtilities2.getFontMetrics(testee, av.getFont());
+    FontMetrics fm = testee.getFontMetrics(av.getFont());
     int labelWidth = fm.stringWidth("000") + charWidth;
     assertEquals(labelWidth, 39); // 3 x 9 + charWidth
 
@@ -218,7 +216,7 @@ public class SeqCanvasTest
     av.setScaleAboveWrapped(true);
     av.setScaleLeftWrapped(true);
     av.setScaleRightWrapped(true);
-    FontMetrics fm = SwingUtilities2.getFontMetrics(testee, av.getFont());
+    FontMetrics fm = testee.getFontMetrics(av.getFont());
     int labelWidth = fm.stringWidth("000") + charWidth;
     assertEquals(labelWidth, 39); // 3 x 9 + charWidth
     int annotationHeight = testee.getAnnotationHeight();
diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java
index 0715857..b3db4de 100644
--- a/test/jalview/io/CrossRef2xmlTests.java
+++ b/test/jalview/io/CrossRef2xmlTests.java
@@ -39,6 +39,9 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
+
+import junit.extensions.PA;
 
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
@@ -90,9 +93,9 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
     // . codonframes
     //
     //
-    HashMap<String, String> dbtoviewBit = new HashMap<>();
+    Map<String, String> dbtoviewBit = new HashMap<>();
     List<String> keyseq = new ArrayList<>();
-    HashMap<String, File> savedProjects = new HashMap<>();
+    Map<String, File> savedProjects = new HashMap<>();
 
     for (String[] did : new String[][] { { "UNIPROT", "P00338" } })
     {
@@ -186,15 +189,16 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
 
             if (pass2 == 0)
             { // retrieve and show cross-refs in this thread
-              cra = new CrossRefAction(af, seqs, dna, db);
+              cra = CrossRefAction.getHandlerFor(seqs, dna, db, af);
               cra.run();
-              if (cra.getXrefViews().size() == 0)
+              cra_views = (List<AlignmentViewPanel>) PA.getValue(cra,
+                      "xrefViews");
+              if (cra_views.size() == 0)
               {
                 failedXrefMenuItems.add("No crossrefs retrieved for "
                         + first + " -> " + db);
                 continue;
               }
-              cra_views = cra.getXrefViews();
               assertNucleotide(cra_views.get(0),
                       "Nucleotide panel included proteins for " + first
                               + " -> " + db);
@@ -286,16 +290,18 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
 
                   if (pass3 == 0)
                   {
-
                     SequenceI[] xrseqs = avp.getAlignment()
                             .getSequencesArray();
                     AlignFrame nextaf = Desktop.getAlignFrameFor(avp
                             .getAlignViewport());
 
-                    cra = new CrossRefAction(nextaf, xrseqs, avp
-                            .getAlignViewport().isNucleotide(), xrefdb);
+                    cra = CrossRefAction.getHandlerFor(xrseqs, avp
+                            .getAlignViewport().isNucleotide(), xrefdb,
+                            nextaf);
                     cra.run();
-                    if (cra.getXrefViews().size() == 0)
+                    cra_views2 = (List<AlignmentViewPanel>) PA.getValue(
+                            cra, "xrefViews");
+                    if (cra_views2.size() == 0)
                     {
                       failedXrefMenuItems
                               .add("No crossrefs retrieved for '"
@@ -303,7 +309,6 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                                       + " via '" + nextaf.getTitle() + "'");
                       continue;
                     }
-                    cra_views2 = cra.getXrefViews();
                     assertNucleotide(cra_views2.get(0),
                             "Nucleotide panel included proteins for '"
                                     + nextxref + "' to " + xrefdb
@@ -541,8 +546,8 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
    *          viewpanel needs to be called with a distinct xrefpath to ensure
    *          each one's strings are compared)
    */
-  private void stringify(HashMap<String, String> dbtoviewBit,
-          HashMap<String, File> savedProjects, String xrefpath,
+  private void stringify(Map<String, String> dbtoviewBit,
+          Map<String, File> savedProjects, String xrefpath,
           AlignmentViewPanel avp)
   {
     if (savedProjects != null)
diff --git a/test/jalview/io/vcf/VCFLoaderTest.java b/test/jalview/io/vcf/VCFLoaderTest.java
new file mode 100644
index 0000000..5607b4b
--- /dev/null
+++ b/test/jalview/io/vcf/VCFLoaderTest.java
@@ -0,0 +1,578 @@
+package jalview.io.vcf;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertTrue;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeatures;
+import jalview.gui.AlignFrame;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+import jalview.io.gff.Gff3Helper;
+import jalview.io.gff.SequenceOntologyI;
+import jalview.util.MapList;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.List;
+
+import org.testng.annotations.Test;
+
+public class VCFLoaderTest
+{
+  private static final float DELTA = 0.00001f;
+
+  // columns 9717- of gene P30419 from Ensembl (much modified)
+  private static final String FASTA = ""
+          +
+          /*
+           * forward strand 'gene' and 'transcript' with two exons
+           */
+          ">gene1/1-25 chromosome:GRCh38:17:45051610:45051634:1\n"
+          + "CAAGCTGGCGGACGAGAGTGTGACA\n"
+          + ">transcript1/1-18\n--AGCTGGCG----AGAGTGTGAC-\n"
+
+          /*
+           * reverse strand gene and transcript (reverse complement alleles!)
+           */
+          + ">gene2/1-25 chromosome:GRCh38:17:45051610:45051634:-1\n"
+          + "TGTCACACTCTCGTCCGCCAGCTTG\n"
+          + ">transcript2/1-18\n" + "-GTCACACTCT----CGCCAGCT--\n"
+
+          /*
+           * 'gene' on chromosome 5 with two transcripts
+           */
+          + ">gene3/1-25 chromosome:GRCh38:5:45051610:45051634:1\n"
+          + "CAAGCTGGCGGACGAGAGTGTGACA\n"
+          + ">transcript3/1-18\n--AGCTGGCG----AGAGTGTGAC-\n"
+          + ">transcript4/1-18\n-----TGG-GGACGAGAGTGTGA-A\n";
+
+  private static final String[] VCF = { "##fileformat=VCFv4.2",
+      "##INFO=<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency, for each ALT allele, in the same order as listed\">",
+      "##reference=Homo_sapiens/GRCh38",
+      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO",
+      // A/T,C variants in position 2 of gene sequence (precedes transcript)
+      // should create 2 variant features with respective scores
+      "17\t45051611\t.\tA\tT,C\t1666.64\tRF\tAC=15;AF=5.0e-03,4.0e-03",
+      // SNP G/C in position 4 of gene sequence, position 2 of transcript
+      // insertion G/GA is transferred to nucleotide but not to peptide
+      "17\t45051613\t.\tG\tGA,C\t1666.64\tRF\tAC=15;AF=3.0e-03,2.0e-03" };
+
+  @Test(groups = "Functional")
+  public void testDoLoad() throws IOException
+  {
+    AlignmentI al = buildAlignment();
+    VCFLoader loader = new VCFLoader(al);
+
+    File f = makeVcf();
+
+    loader.doLoad(f.getPath(), null);
+
+    /*
+     * verify variant feature(s) added to gene
+     * NB alleles at a locus may not be processed, and features added,
+     * in the order in which they appear in the VCF record as method
+     * VariantContext.getAlternateAlleles() does not guarantee order
+     * - order of assertions here matches what we find (is not important) 
+     */
+    List<SequenceFeature> geneFeatures = al.getSequenceAt(0)
+            .getSequenceFeatures();
+    SequenceFeatures.sortFeatures(geneFeatures, true);
+    assertEquals(geneFeatures.size(), 4);
+    SequenceFeature sf = geneFeatures.get(0);
+    assertEquals(sf.getFeatureGroup(), "VCF");
+    assertEquals(sf.getBegin(), 2);
+    assertEquals(sf.getEnd(), 2);
+    assertEquals(sf.getScore(), 4.0e-03, DELTA);
+    assertEquals(sf.getValue(Gff3Helper.ALLELES), "A,C");
+    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+    sf = geneFeatures.get(1);
+    assertEquals(sf.getFeatureGroup(), "VCF");
+    assertEquals(sf.getBegin(), 2);
+    assertEquals(sf.getEnd(), 2);
+    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+    assertEquals(sf.getScore(), 5.0e-03, DELTA);
+    assertEquals(sf.getValue(Gff3Helper.ALLELES), "A,T");
+
+    sf = geneFeatures.get(2);
+    assertEquals(sf.getFeatureGroup(), "VCF");
+    assertEquals(sf.getBegin(), 4);
+    assertEquals(sf.getEnd(), 4);
+    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+    assertEquals(sf.getScore(), 2.0e-03, DELTA);
+    assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,C");
+
+    sf = geneFeatures.get(3);
+    assertEquals(sf.getFeatureGroup(), "VCF");
+    assertEquals(sf.getBegin(), 4);
+    assertEquals(sf.getEnd(), 4);
+    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+    assertEquals(sf.getScore(), 3.0e-03, DELTA);
+    assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GA");
+
+    /*
+     * verify variant feature(s) added to transcript
+     */
+    List<SequenceFeature> transcriptFeatures = al.getSequenceAt(1)
+            .getSequenceFeatures();
+    assertEquals(transcriptFeatures.size(), 2);
+    sf = transcriptFeatures.get(0);
+    assertEquals(sf.getFeatureGroup(), "VCF");
+    assertEquals(sf.getBegin(), 2);
+    assertEquals(sf.getEnd(), 2);
+    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+    assertEquals(sf.getScore(), 2.0e-03, DELTA);
+    assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,C");
+    sf = transcriptFeatures.get(1);
+    assertEquals(sf.getFeatureGroup(), "VCF");
+    assertEquals(sf.getBegin(), 2);
+    assertEquals(sf.getEnd(), 2);
+    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+    assertEquals(sf.getScore(), 3.0e-03, DELTA);
+    assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GA");
+
+    /*
+     * verify SNP variant feature(s) computed and added to protein
+     * first codon AGC varies to ACC giving S/T
+     */
+    DBRefEntry[] dbRefs = al.getSequenceAt(1).getDBRefs();
+    SequenceI peptide = null;
+    for (DBRefEntry dbref : dbRefs)
+    {
+      if (dbref.getMap().getMap().getFromRatio() == 3)
+      {
+        peptide = dbref.getMap().getTo();
+      }
+    }
+    List<SequenceFeature> proteinFeatures = peptide.getSequenceFeatures();
+    assertEquals(proteinFeatures.size(), 1);
+    sf = proteinFeatures.get(0);
+    assertEquals(sf.getFeatureGroup(), "VCF");
+    assertEquals(sf.getBegin(), 1);
+    assertEquals(sf.getEnd(), 1);
+    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+    assertEquals(sf.getDescription(), "p.Ser1Thr");
+  }
+
+  private File makeVcf() throws IOException
+  {
+    File f = File.createTempFile("Test", ".vcf");
+    f.deleteOnExit();
+    PrintWriter pw = new PrintWriter(f);
+    for (String vcfLine : VCF)
+    {
+      pw.println(vcfLine);
+    }
+    pw.close();
+    return f;
+  }
+
+  /**
+   * Make a simple alignment with one 'gene' and one 'transcript'
+   * 
+   * @return
+   */
+  private AlignmentI buildAlignment()
+  {
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(FASTA,
+            DataSourceType.PASTE);
+
+    /*
+     * map gene1 sequence to chromosome (normally done when the sequence is fetched
+     * from Ensembl and transcripts computed)
+     */
+    AlignmentI alignment = af.getViewport().getAlignment();
+    SequenceI gene1 = alignment.findName("gene1");
+    int[] to = new int[] { 45051610, 45051634 };
+    int[] from = new int[] { gene1.getStart(), gene1.getEnd() };
+    gene1.setGeneLoci("homo_sapiens", "GRCh38", "17", new MapList(from, to,
+            1, 1));
+
+    /*
+     * map 'transcript1' to chromosome via 'gene1'
+     * transcript1/1-18 is gene1/3-10,15-24
+     * which is chromosome 45051612-45051619,45051624-45051633
+     */
+    to = new int[] { 45051612, 45051619, 45051624, 45051633 };
+    SequenceI transcript1 = alignment.findName("transcript1");
+    from = new int[] { transcript1.getStart(), transcript1.getEnd() };
+    transcript1.setGeneLoci("homo_sapiens", "GRCh38", "17", new MapList(
+            from, to,
+            1, 1));
+
+    /*
+     * map gene2 to chromosome reverse strand
+     */
+    SequenceI gene2 = alignment.findName("gene2");
+    to = new int[] { 45051634, 45051610 };
+    from = new int[] { gene2.getStart(), gene2.getEnd() };
+    gene2.setGeneLoci("homo_sapiens", "GRCh38", "17", new MapList(from, to,
+            1, 1));
+
+    /*
+     * map 'transcript2' to chromosome via 'gene2'
+     * transcript2/1-18 is gene2/2-11,16-23
+     * which is chromosome 45051633-45051624,45051619-45051612
+     */
+    to = new int[] { 45051633, 45051624, 45051619, 45051612 };
+    SequenceI transcript2 = alignment.findName("transcript2");
+    from = new int[] { transcript2.getStart(), transcript2.getEnd() };
+    transcript2.setGeneLoci("homo_sapiens", "GRCh38", "17", new MapList(
+            from, to,
+            1, 1));
+
+    /*
+     * add a protein product as a DBRef on transcript1
+     */
+    SequenceI peptide1 = new Sequence("ENSP001", "SWRECD");
+    MapList mapList = new MapList(new int[] { 1, 18 }, new int[] { 1, 6 },
+            3, 1);
+    Mapping map = new Mapping(peptide1, mapList);
+    DBRefEntry product = new DBRefEntry("", "", "ENSP001", map);
+    transcript1.addDBRef(product);
+
+    /*
+     * add a protein product as a DBRef on transcript2
+     */
+    SequenceI peptide2 = new Sequence("ENSP002", "VTLSPA");
+    mapList = new MapList(new int[] { 1, 18 }, new int[] { 1, 6 }, 3, 1);
+    map = new Mapping(peptide2, mapList);
+    product = new DBRefEntry("", "", "ENSP002", map);
+    transcript2.addDBRef(product);
+
+    /*
+     * map gene3 to chromosome 
+     */
+    SequenceI gene3 = alignment.findName("gene3");
+    to = new int[] { 45051610, 45051634 };
+    from = new int[] { gene3.getStart(), gene3.getEnd() };
+    gene3.setGeneLoci("homo_sapiens", "GRCh38", "5", new MapList(from, to,
+            1, 1));
+
+    /*
+     * map 'transcript3' to chromosome
+     */
+    SequenceI transcript3 = alignment.findName("transcript3");
+    to = new int[] { 45051612, 45051619, 45051624, 45051633 };
+    from = new int[] { transcript3.getStart(), transcript3.getEnd() };
+    transcript3.setGeneLoci("homo_sapiens", "GRCh38", "5", new MapList(
+            from, to,
+            1, 1));
+
+    /*
+     * map 'transcript4' to chromosome
+     */
+    SequenceI transcript4 = alignment.findName("transcript4");
+    to = new int[] { 45051615, 45051617, 45051619, 45051632, 45051634,
+        45051634 };
+    from = new int[] { transcript4.getStart(), transcript4.getEnd() };
+    transcript4.setGeneLoci("homo_sapiens", "GRCh38", "5", new MapList(
+            from, to,
+            1, 1));
+
+    /*
+     * add a protein product as a DBRef on transcript3
+     */
+    SequenceI peptide3 = new Sequence("ENSP003", "SWRECD");
+    mapList = new MapList(new int[] { 1, 18 }, new int[] { 1, 6 }, 3, 1);
+    map = new Mapping(peptide3, mapList);
+    product = new DBRefEntry("", "", "ENSP003", map);
+    transcript3.addDBRef(product);
+
+    return alignment;
+  }
+
+  /**
+   * Test with 'gene' and 'transcript' mapped to the reverse strand of the
+   * chromosome. The VCF variant positions (in forward coordinates) should get
+   * correctly located on sequence positions.
+   * 
+   * @throws IOException
+   */
+  @Test(groups = "Functional")
+  public void testDoLoad_reverseStrand() throws IOException
+  {
+    AlignmentI al = buildAlignment();
+
+    VCFLoader loader = new VCFLoader(al);
+
+    File f = makeVcf();
+
+    loader.doLoad(f.getPath(), null);
+
+    /*
+     * verify variant feature(s) added to gene2
+     * gene/1-25 maps to chromosome 45051634- reverse strand
+     * variants A/T, A/C at 45051611 and G/GA,G/C at 45051613 map to
+     * T/A, T/G and C/TC,C/G at gene positions 24 and 22 respectively
+     */
+    List<SequenceFeature> geneFeatures = al.getSequenceAt(2)
+            .getSequenceFeatures();
+    SequenceFeatures.sortFeatures(geneFeatures, true);
+    assertEquals(geneFeatures.size(), 4);
+    SequenceFeature sf = geneFeatures.get(0);
+    assertEquals(sf.getFeatureGroup(), "VCF");
+    assertEquals(sf.getBegin(), 22);
+    assertEquals(sf.getEnd(), 22);
+    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+    assertEquals(sf.getScore(), 2.0e-03, DELTA);
+    assertEquals("C,G", sf.getValue(Gff3Helper.ALLELES));
+
+    sf = geneFeatures.get(1);
+    assertEquals(sf.getFeatureGroup(), "VCF");
+    assertEquals(sf.getBegin(), 22);
+    assertEquals(sf.getEnd(), 22);
+    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+    assertEquals(sf.getScore(), 3.0e-03, DELTA);
+    assertEquals("C,TC", sf.getValue(Gff3Helper.ALLELES));
+
+    sf = geneFeatures.get(2);
+    assertEquals(sf.getFeatureGroup(), "VCF");
+    assertEquals(sf.getBegin(), 24);
+    assertEquals(sf.getEnd(), 24);
+    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+    assertEquals(sf.getScore(), 4.0e-03, DELTA);
+    assertEquals("T,G", sf.getValue(Gff3Helper.ALLELES));
+
+    sf = geneFeatures.get(3);
+    assertEquals(sf.getFeatureGroup(), "VCF");
+    assertEquals(sf.getBegin(), 24);
+    assertEquals(sf.getEnd(), 24);
+    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+    assertEquals(sf.getScore(), 5.0e-03, DELTA);
+    assertEquals("T,A", sf.getValue(Gff3Helper.ALLELES));
+
+    /*
+     * verify variant feature(s) added to transcript2
+     * variants G/GA,G/C at position 22 of gene overlap and map to
+     * C/TC,C/G at position 17 of transcript
+     */
+    List<SequenceFeature> transcriptFeatures = al.getSequenceAt(3)
+            .getSequenceFeatures();
+    assertEquals(transcriptFeatures.size(), 2);
+    sf = transcriptFeatures.get(0);
+    assertEquals(sf.getFeatureGroup(), "VCF");
+    assertEquals(sf.getBegin(), 17);
+    assertEquals(sf.getEnd(), 17);
+    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+    assertEquals(sf.getScore(), 2.0e-03, DELTA);
+    assertEquals("C,G", sf.getValue(Gff3Helper.ALLELES));
+
+    sf = transcriptFeatures.get(1);
+    assertEquals(sf.getFeatureGroup(), "VCF");
+    assertEquals(sf.getBegin(), 17);
+    assertEquals(sf.getEnd(), 17);
+    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+    assertEquals(sf.getScore(), 3.0e-03, DELTA);
+    assertEquals("C,TC", sf.getValue(Gff3Helper.ALLELES));
+
+    /*
+     * verify variant feature(s) computed and added to protein
+     * last codon GCT varies to GGT giving A/G in the last peptide position
+     */
+    DBRefEntry[] dbRefs = al.getSequenceAt(3).getDBRefs();
+    SequenceI peptide = null;
+    for (DBRefEntry dbref : dbRefs)
+    {
+      if (dbref.getMap().getMap().getFromRatio() == 3)
+      {
+        peptide = dbref.getMap().getTo();
+      }
+    }
+    List<SequenceFeature> proteinFeatures = peptide.getSequenceFeatures();
+    assertEquals(proteinFeatures.size(), 1);
+    sf = proteinFeatures.get(0);
+    assertEquals(sf.getFeatureGroup(), "VCF");
+    assertEquals(sf.getBegin(), 6);
+    assertEquals(sf.getEnd(), 6);
+    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+    assertEquals(sf.getDescription(), "p.Ala6Gly");
+  }
+
+  /**
+   * Tests that if VEP consequence (CSQ) data is present in the VCF data, then
+   * it is added to the variant feature, but restricted where possible to the
+   * consequences for a specific transcript
+   * 
+   * @throws IOException
+   */
+  @Test(groups = "Functional")
+  public void testDoLoad_vepCsq() throws IOException
+  {
+    AlignmentI al = buildAlignment();
+
+    VCFLoader loader = new VCFLoader(al);
+
+    /*
+     * VCF data file with variants at gene3 positions
+     * 1 C/A
+     * 5 C/T
+     * 9 CGT/C (deletion)
+     * 13 C/G, C/T
+     * 17 A/AC (insertion), A/G
+     */
+    loader.doLoad("test/jalview/io/vcf/testVcf.dat", null);
+
+    /*
+     * verify variant feature(s) added to gene3
+     */
+    List<SequenceFeature> geneFeatures = al.findName("gene3")
+            .getSequenceFeatures();
+    SequenceFeatures.sortFeatures(geneFeatures, true);
+    assertEquals(geneFeatures.size(), 7);
+    SequenceFeature sf = geneFeatures.get(0);
+    assertEquals(sf.getBegin(), 1);
+    assertEquals(sf.getEnd(), 1);
+    assertEquals(sf.getScore(), 0.1f, DELTA);
+    assertEquals(sf.getValue("alleles"), "C,A");
+    // gene features include Consequence for all transcripts
+    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+
+    sf = geneFeatures.get(1);
+    assertEquals(sf.getBegin(), 5);
+    assertEquals(sf.getEnd(), 5);
+    assertEquals(sf.getScore(), 0.2f, DELTA);
+    assertEquals(sf.getValue("alleles"), "C,T");
+    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+
+    sf = geneFeatures.get(2);
+    assertEquals(sf.getBegin(), 9);
+    assertEquals(sf.getEnd(), 11); // deletion over 3 positions
+    assertEquals(sf.getScore(), 0.3f, DELTA);
+    assertEquals(sf.getValue("alleles"), "CGG,C");
+    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+
+    sf = geneFeatures.get(3);
+    assertEquals(sf.getBegin(), 13);
+    assertEquals(sf.getEnd(), 13);
+    assertEquals(sf.getScore(), 0.5f, DELTA);
+    assertEquals(sf.getValue("alleles"), "C,T");
+    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+
+    sf = geneFeatures.get(4);
+    assertEquals(sf.getBegin(), 13);
+    assertEquals(sf.getEnd(), 13);
+    assertEquals(sf.getScore(), 0.4f, DELTA);
+    assertEquals(sf.getValue("alleles"), "C,G");
+    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+
+    sf = geneFeatures.get(5);
+    assertEquals(sf.getBegin(), 17);
+    assertEquals(sf.getEnd(), 17);
+    assertEquals(sf.getScore(), 0.7f, DELTA);
+    assertEquals(sf.getValue("alleles"), "A,G");
+    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+
+    sf = geneFeatures.get(6);
+    assertEquals(sf.getBegin(), 17);
+    assertEquals(sf.getEnd(), 17); // insertion
+    assertEquals(sf.getScore(), 0.6f, DELTA);
+    assertEquals(sf.getValue("alleles"), "A,AC");
+    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+
+    /*
+     * verify variant feature(s) added to transcript3
+     * at columns 5 (1), 17 (2), positions 3, 11
+     * note the deletion at columns 9-11 is not transferred since col 11
+     * has no mapping to transcript 3 
+     */
+    List<SequenceFeature> transcriptFeatures = al.findName("transcript3")
+            .getSequenceFeatures();
+    SequenceFeatures.sortFeatures(transcriptFeatures, true);
+    assertEquals(transcriptFeatures.size(), 3);
+    sf = transcriptFeatures.get(0);
+    assertEquals(sf.getBegin(), 3);
+    assertEquals(sf.getEnd(), 3);
+    assertEquals(sf.getScore(), 0.2f, DELTA);
+    assertEquals(sf.getValue("alleles"), "C,T");
+    // transcript features only have Consequence for that transcripts
+    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
+    assertTrue(sf.getValue("CSQ").toString().contains("transcript3"));
+
+    sf = transcriptFeatures.get(1);
+    assertEquals(sf.getBegin(), 11);
+    assertEquals(sf.getEnd(), 11);
+    assertEquals(sf.getScore(), 0.7f, DELTA);
+    assertEquals(sf.getValue("alleles"), "A,G");
+    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
+    assertTrue(sf.getValue("CSQ").toString().contains("transcript3"));
+
+    sf = transcriptFeatures.get(2);
+    assertEquals(sf.getBegin(), 11);
+    assertEquals(sf.getEnd(), 11);
+    assertEquals(sf.getScore(), 0.6f, DELTA);
+    assertEquals(sf.getValue("alleles"), "A,AC");
+    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
+    assertTrue(sf.getValue("CSQ").toString().contains("transcript3"));
+
+    /*
+     * verify variants computed on protein product for transcript3
+     * peptide is SWRECD
+     * codon variants are AGC/AGT position 1 which is synonymous
+     * and GAG/GGG which is E/G in position 4
+     * the insertion variant is not transferred to the peptide
+     */
+    DBRefEntry[] dbRefs = al.findName("transcript3").getDBRefs();
+    SequenceI peptide = null;
+    for (DBRefEntry dbref : dbRefs)
+    {
+      if (dbref.getMap().getMap().getFromRatio() == 3)
+      {
+        peptide = dbref.getMap().getTo();
+      }
+    }
+    List<SequenceFeature> proteinFeatures = peptide.getSequenceFeatures();
+    assertEquals(proteinFeatures.size(), 1);
+    sf = proteinFeatures.get(0);
+    assertEquals(sf.getFeatureGroup(), "VCF");
+    assertEquals(sf.getBegin(), 4);
+    assertEquals(sf.getEnd(), 4);
+    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+    assertEquals(sf.getDescription(), "p.Glu4Gly");
+
+    /*
+     * verify variant feature(s) added to transcript4
+     * at columns 13 (2) and 17 (2), positions 7 and 11
+     */
+    transcriptFeatures = al.findName("transcript4").getSequenceFeatures();
+    SequenceFeatures.sortFeatures(transcriptFeatures, true);
+    assertEquals(transcriptFeatures.size(), 4);
+    sf = transcriptFeatures.get(0);
+    assertEquals(sf.getBegin(), 7);
+    assertEquals(sf.getEnd(), 7);
+    assertEquals(sf.getScore(), 0.5f, DELTA);
+    assertEquals(sf.getValue("alleles"), "C,T");
+    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
+    assertTrue(sf.getValue("CSQ").toString().contains("transcript4"));
+
+    sf = transcriptFeatures.get(1);
+    assertEquals(sf.getBegin(), 7);
+    assertEquals(sf.getEnd(), 7);
+    assertEquals(sf.getScore(), 0.4f, DELTA);
+    assertEquals(sf.getValue("alleles"), "C,G");
+    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
+    assertTrue(sf.getValue("CSQ").toString().contains("transcript4"));
+
+    sf = transcriptFeatures.get(2);
+    assertEquals(sf.getBegin(), 11);
+    assertEquals(sf.getEnd(), 11);
+    assertEquals(sf.getScore(), 0.7f, DELTA);
+    assertEquals(sf.getValue("alleles"), "A,G");
+    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
+    assertTrue(sf.getValue("CSQ").toString().contains("transcript4"));
+
+    sf = transcriptFeatures.get(3);
+    assertEquals(sf.getBegin(), 11);
+    assertEquals(sf.getEnd(), 11);
+    assertEquals(sf.getScore(), 0.6f, DELTA);
+    assertEquals(sf.getValue("alleles"), "A,AC");
+    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
+    assertTrue(sf.getValue("CSQ").toString().contains("transcript4"));
+  }
+}
diff --git a/test/jalview/io/vcf/testVcf.dat b/test/jalview/io/vcf/testVcf.dat
new file mode 100644
index 0000000..77e070c
--- /dev/null
+++ b/test/jalview/io/vcf/testVcf.dat
@@ -0,0 +1,13 @@
+##fileformat=VCFv4.2
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF_Female,Number=R,Type=Float,Description="Allele Frequency among Female genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|PolyPhen">
+##reference=/Homo_sapiens/GRCh38
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+5	45051610	.	C	A	81.96	RF;AC0	AC=1;AF=0.1;AN=0;AF_Female=2;AB_MEDIAN=6.00000e-01;CSQ=A|missense_variant|MODIFIER|WASH7P|gene3|Transcript|transcript3|rna|Benign,A|downstream_gene_variant|MODIFIER|WASH7P|gene3|Transcript|transcript4|mrna|Bad
+5	45051614	.	C	T	1666.64	RF	AC=1;AF=0.2;AN=0;AF_Female=2;AB_MEDIAN=6.00000e-01;CSQ=T|missense_variant|MODIFIER|WASH7P|gene3|Transcript|transcript3|rna|Benign,T|downstream_gene_variant|MODIFIER|WASH7P|gene3|Transcript|transcript4|mrna|Bad
+5	45051618	.	CGG	C	41.94	AC0	AC=1;AF=0.3;AN=0;AF_Female=2;AB_MEDIAN=6.00000e-01;CSQ=C|missense_variant|MODIFIER|WASH7P|gene3|Transcript|transcript3|rna|Benign,C|downstream_gene_variant|MODIFIER|WASH7P|gene3|Transcript|transcript4|mrna|Bad,CSQ=CGT|missense_variant|MODIFIER|WASH7P|gene3|Transcript|transcript3|rna|Benign,CGT|downstream_gene_variant|MODIFIER|WASH7P|gene3|Transcript|transcript4|mrna|Bad
+5	45051622	.	C	G,T	224.23	RF;AC0	AC=1,2;AF=0.4,0.5;AN=0;AF_Female=2;AB_MEDIAN=6.00000e-01;CSQ=G|missense_variant|MODIFIER|WASH7P|gene3|Transcript|transcript3|rna|Benign,G|downstream_gene_variant|MODIFIER|WASH7P|gene3|Transcript|transcript4|mrna|Bad,T|missense_variant|MODIFIER|WASH7P|gene3|Transcript|transcript3|rna|Benign,T|downstream_gene_variant|MODIFIER|WASH7P|gene3|Transcript|transcript4|mrna|Bad
+5	45051626	.	A	AC,G	433.35	RF;AC0	AC=3,4;AF=0.6,0.7;AN=0;AF_Female=2;AB_MEDIAN=6.00000e-01;CSQ=G|missense_variant|MODIFIER|WASH7P|gene3|Transcript|transcript3|rna|Benign,G|downstream_gene_variant|MODIFIER|WASH7P|gene3|Transcript|transcript4|mrna|Bad,AC|missense_variant|MODIFIER|WASH7P|gene3|Transcript|transcript3|rna|Benign,AC|downstream_gene_variant|MODIFIER|WASH7P|gene3|Transcript|transcript4|mrna|Bad
diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java
index a2f38e2..d2db258 100644
--- a/test/jalview/util/MapListTest.java
+++ b/test/jalview/util/MapListTest.java
@@ -814,4 +814,130 @@ public class MapListTest
     assertEquals(1, merged.size());
     assertArrayEquals(new int[] { 9, 0 }, merged.get(0));
   }
+
+  /**
+   * Test the method that compounds ('traverses') two mappings
+   */
+  @Test
+  public void testTraverse()
+  {
+    /*
+     * simple 1:1 plus 1:1 forwards
+     */
+    MapList ml1 = new MapList(new int[] { 3, 4, 8, 12 }, new int[] { 5, 8,
+        11, 13 }, 1, 1);
+    MapList ml2 = new MapList(new int[] { 1, 50 }, new int[] { 40, 45, 70,
+        75, 90, 127 }, 1, 1);
+    MapList compound = ml1.traverse(ml2);
+
+    assertEquals(compound.getFromRatio(), 1);
+    assertEquals(compound.getToRatio(), 1);
+    List<int[]> fromRanges = compound.getFromRanges();
+    assertEquals(fromRanges.size(), 2);
+    assertArrayEquals(new int[] { 3, 4 }, fromRanges.get(0));
+    assertArrayEquals(new int[] { 8, 12 }, fromRanges.get(1));
+    List<int[]> toRanges = compound.getToRanges();
+    assertEquals(toRanges.size(), 2);
+    // 5-8 maps to 44-45,70-71
+    // 11-13 maps to 74-75,90
+    assertArrayEquals(new int[] { 44, 45, 70, 71 }, toRanges.get(0));
+    assertArrayEquals(new int[] { 74, 75, 90, 90 }, toRanges.get(1));
+
+    /*
+     * 1:1 over 1:1 backwards ('reverse strand')
+     */
+    ml1 = new MapList(new int[] { 1, 50 }, new int[] { 70, 119 }, 1, 1);
+    ml2 = new MapList(new int[] { 1, 500 },
+            new int[] { 1000, 901, 600, 201 }, 1, 1);
+    compound = ml1.traverse(ml2);
+
+    assertEquals(compound.getFromRatio(), 1);
+    assertEquals(compound.getToRatio(), 1);
+    fromRanges = compound.getFromRanges();
+    assertEquals(fromRanges.size(), 1);
+    assertArrayEquals(new int[] { 1, 50 }, fromRanges.get(0));
+    toRanges = compound.getToRanges();
+    assertEquals(toRanges.size(), 1);
+    assertArrayEquals(new int[] { 931, 901, 600, 582 }, toRanges.get(0));
+
+    /*
+     * 1:1 plus 1:3 should result in 1:3
+     */
+    ml1 = new MapList(new int[] { 1, 30 }, new int[] { 11, 40 }, 1, 1);
+    ml2 = new MapList(new int[] { 1, 100 }, new int[] { 1, 50, 91, 340 },
+            1, 3);
+    compound = ml1.traverse(ml2);
+
+    assertEquals(compound.getFromRatio(), 1);
+    assertEquals(compound.getToRatio(), 3);
+    fromRanges = compound.getFromRanges();
+    assertEquals(fromRanges.size(), 1);
+    assertArrayEquals(new int[] { 1, 30 }, fromRanges.get(0));
+    // 11-40 maps to 31-50,91-160
+    toRanges = compound.getToRanges();
+    assertEquals(toRanges.size(), 1);
+    assertArrayEquals(new int[] { 31, 50, 91, 160 }, toRanges.get(0));
+
+    /*
+     * 3:1 plus 1:1 should result in 3:1
+     */
+    ml1 = new MapList(new int[] { 1, 30 }, new int[] { 11, 20 }, 3, 1);
+    ml2 = new MapList(new int[] { 1, 100 }, new int[] { 1, 15, 91, 175 },
+            1, 1);
+    compound = ml1.traverse(ml2);
+
+    assertEquals(compound.getFromRatio(), 3);
+    assertEquals(compound.getToRatio(), 1);
+    fromRanges = compound.getFromRanges();
+    assertEquals(fromRanges.size(), 1);
+    assertArrayEquals(new int[] { 1, 30 }, fromRanges.get(0));
+    // 11-20 maps to 11-15, 91-95
+    toRanges = compound.getToRanges();
+    assertEquals(toRanges.size(), 1);
+    assertArrayEquals(new int[] { 11, 15, 91, 95 }, toRanges.get(0));
+
+    /*
+     * 1:3 plus 3:1 should result in 1:1
+     */
+    ml1 = new MapList(new int[] { 21, 40 }, new int[] { 13, 72 }, 1, 3);
+    ml2 = new MapList(new int[] { 1, 300 }, new int[] { 51, 70, 121, 200 },
+            3, 1);
+    compound = ml1.traverse(ml2);
+
+    assertEquals(compound.getFromRatio(), 1);
+    assertEquals(compound.getToRatio(), 1);
+    fromRanges = compound.getFromRanges();
+    assertEquals(fromRanges.size(), 1);
+    assertArrayEquals(new int[] { 21, 40 }, fromRanges.get(0));
+    // 13-72 maps 3:1 to 55-70, 121-124
+    toRanges = compound.getToRanges();
+    assertEquals(toRanges.size(), 1);
+    assertArrayEquals(new int[] { 55, 70, 121, 124 }, toRanges.get(0));
+
+    /*
+     * 3:1 plus 1:3 should result in 1:1
+     */
+    ml1 = new MapList(new int[] { 31, 90 }, new int[] { 13, 32 }, 3, 1);
+    ml2 = new MapList(new int[] { 11, 40 }, new int[] { 41, 50, 71, 150 },
+            1, 3);
+    compound = ml1.traverse(ml2);
+
+    assertEquals(compound.getFromRatio(), 1);
+    assertEquals(compound.getToRatio(), 1);
+    fromRanges = compound.getFromRanges();
+    assertEquals(fromRanges.size(), 1);
+    assertArrayEquals(new int[] { 31, 90 }, fromRanges.get(0));
+    // 13-32 maps to 47-50,71-126
+    toRanges = compound.getToRanges();
+    assertEquals(toRanges.size(), 1);
+    assertArrayEquals(new int[] { 47, 50, 71, 126 }, toRanges.get(0));
+
+    /*
+     * method returns null if not all regions are mapped through
+     */
+    ml1 = new MapList(new int[] { 1, 50 }, new int[] { 101, 150 }, 1, 1);
+    ml2 = new MapList(new int[] { 131, 180 }, new int[] { 201, 250 }, 1, 3);
+    compound = ml1.traverse(ml2);
+    assertNull(compound);
+  }
 }
diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index 5226819..d4cf98a 100644
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -1149,6 +1149,95 @@ public class MappingUtilsTest
     assertEquals("[12, 11, 8, 4]", Arrays.toString(ranges));
   }
 
+  @Test(groups = { "Functional" })
+  public void testRangeContains()
+  {
+    /*
+     * both forward ranges
+     */
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        1, 10 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        2, 10 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        1, 9 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        4, 5 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        0, 9 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        -10, -9 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        1, 11 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        11, 12 }));
+
+    /*
+     * forward range, reverse query
+     */
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        10, 1 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        9, 1 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        10, 2 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        5, 5 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        11, 1 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        10, 0 }));
+
+    /*
+     * reverse range, forward query
+     */
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        1, 10 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        1, 9 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        2, 10 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        6, 6 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        6, 11 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        11, 20 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        -3, -2 }));
+
+    /*
+     * both reverse
+     */
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        10, 1 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        9, 1 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        10, 2 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        3, 3 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        11, 1 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        10, 0 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        12, 11 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        -5, -8 }));
+
+    /*
+     * bad arguments
+     */
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10, 12 },
+            new int[] {
+        1, 10 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 },
+            new int[] { 1 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, null));
+    assertFalse(MappingUtils.rangeContains(null, new int[] { 1, 10 }));
+  }
+
   @Test(groups = "Functional")
   public void testRemoveEndPositions()
   {
diff --git a/test/jalview/util/MathUtilsTest.java b/test/jalview/util/MathUtilsTest.java
new file mode 100644
index 0000000..fc84741
--- /dev/null
+++ b/test/jalview/util/MathUtilsTest.java
@@ -0,0 +1,26 @@
+package jalview.util;
+
+import static org.testng.Assert.assertEquals;
+
+import org.testng.annotations.Test;
+
+public class MathUtilsTest
+{
+  @Test
+  public void testGcd()
+  {
+    assertEquals(MathUtils.gcd(0, 0), 0);
+    assertEquals(MathUtils.gcd(0, 1), 1);
+    assertEquals(MathUtils.gcd(1, 0), 1);
+    assertEquals(MathUtils.gcd(1, 1), 1);
+    assertEquals(MathUtils.gcd(1, -1), 1);
+    assertEquals(MathUtils.gcd(-1, 1), 1);
+    assertEquals(MathUtils.gcd(2, 3), 1);
+    assertEquals(MathUtils.gcd(4, 2), 2);
+    assertEquals(MathUtils.gcd(2, 4), 2);
+    assertEquals(MathUtils.gcd(2, -4), 2);
+    assertEquals(MathUtils.gcd(-2, 4), 2);
+    assertEquals(MathUtils.gcd(-2, -4), 2);
+    assertEquals(MathUtils.gcd(2 * 3 * 5 * 7 * 11, 3 * 7 * 13 * 17), 3 * 7);
+  }
+}
diff --git a/test/jalview/util/StringUtilsTest.java b/test/jalview/util/StringUtilsTest.java
index b6f8a25..084219a 100644
--- a/test/jalview/util/StringUtilsTest.java
+++ b/test/jalview/util/StringUtilsTest.java
@@ -228,4 +228,26 @@ public class StringUtilsTest
     assertEquals("", StringUtils.toSentenceCase(""));
     assertNull(StringUtils.toSentenceCase(null));
   }
+
+  @Test(groups = { "Functional" })
+  public void testStripHtmlTags()
+  {
+    assertNull(StringUtils.stripHtmlTags(null));
+    assertEquals("", StringUtils.stripHtmlTags(""));
+    assertEquals(
+            "<a href=\"something\">label</href>",
+            StringUtils
+                    .stripHtmlTags("<html><a href=\"something\">label</href></html>"));
+
+    // if no "<html>" tag, < and > get html-encoded (not sure why)
+    assertEquals("&lt;a href=\"something\"&gt;label&lt;/href&gt;",
+            StringUtils.stripHtmlTags("<a href=\"something\">label</href>"));
+
+    // </body> gets removed but not <body> (is this intentional?)
+    assertEquals("<body><p>hello",
+            StringUtils.stripHtmlTags("<html><body><p>hello</body></html>"));
+
+    assertEquals("kdHydro &lt; 12.53",
+            StringUtils.stripHtmlTags("kdHydro < 12.53"));
+  }
 }
diff --git a/test/jalview/util/matcher/ConditionTest.java b/test/jalview/util/matcher/ConditionTest.java
new file mode 100644
index 0000000..11a0630
--- /dev/null
+++ b/test/jalview/util/matcher/ConditionTest.java
@@ -0,0 +1,31 @@
+package jalview.util.matcher;
+
+import static org.testng.Assert.assertEquals;
+
+import java.util.Locale;
+
+import org.testng.annotations.Test;
+
+public class ConditionTest
+{
+  @Test
+  public void testToString()
+  {
+    Locale.setDefault(Locale.UK);
+    assertEquals(Condition.Contains.toString(), "Contains");
+    assertEquals(Condition.NotContains.toString(), "Does not contain");
+    assertEquals(Condition.Matches.toString(), "Matches");
+    assertEquals(Condition.NotMatches.toString(), "Does not match");
+    assertEquals(Condition.LT.toString(), "Is less than");
+    assertEquals(Condition.LE.toString(), "Is less than or equal to");
+    assertEquals(Condition.GT.toString(), "Is greater than");
+    assertEquals(Condition.GE.toString(), "Is greater than or equal to");
+    assertEquals(Condition.EQ.toString(), "Is equal to");
+    assertEquals(Condition.NE.toString(), "Is not equal to");
+
+    /*
+     * repeat call to get coverage of cached value
+     */
+    assertEquals(Condition.NE.toString(), "Is not equal to");
+  }
+}
diff --git a/test/jalview/util/matcher/KeyedMatcherSetTest.java b/test/jalview/util/matcher/KeyedMatcherSetTest.java
new file mode 100644
index 0000000..76ae8a5
--- /dev/null
+++ b/test/jalview/util/matcher/KeyedMatcherSetTest.java
@@ -0,0 +1,117 @@
+package jalview.util.matcher;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertTrue;
+
+import java.util.function.Function;
+
+import org.testng.annotations.Test;
+
+public class KeyedMatcherSetTest
+{
+  @Test
+  public void testMatches()
+  {
+    /*
+     * a numeric matcher - MatcherTest covers more conditions
+     */
+    KeyedMatcherI km = new KeyedMatcher("AF", Condition.GE, -2F);
+    assertTrue(km.matches(key -> "-2"));
+    assertTrue(km.matches(key -> "-1"));
+    assertFalse(km.matches(key -> "-3"));
+    assertFalse(km.matches(key -> ""));
+    assertFalse(km.matches(key -> "junk"));
+    assertFalse(km.matches(key -> null));
+
+    /*
+     * a string pattern matcher
+     */
+    km = new KeyedMatcher("AF", Condition.Contains, "Cat");
+    assertTrue(km.matches(key -> "AF".equals(key) ? "raining cats and dogs"
+            : "showers"));
+  }
+
+  @Test
+  public void testAnd()
+  {
+    // condition1: AF value contains "dog" (matches)
+    KeyedMatcherI km1 = new KeyedMatcher("AF", Condition.Contains, "dog");
+    // condition 2: CSQ value does not contain "how" (does not match)
+    KeyedMatcherI km2 = new KeyedMatcher("CSQ", Condition.NotContains,
+            "how");
+
+    Function<String, String> vp = key -> "AF".equals(key) ? "raining cats and dogs"
+            : "showers";
+    assertTrue(km1.matches(vp));
+    assertFalse(km2.matches(vp));
+
+    KeyedMatcherSetI kms = new KeyedMatcherSet();
+    assertTrue(kms.matches(vp)); // if no conditions, then 'all' pass
+    kms.and(km1);
+    assertTrue(kms.matches(vp));
+    kms.and(km2);
+    assertFalse(kms.matches(vp));
+  }
+
+  @Test
+  public void testToString()
+  {
+    KeyedMatcherI km1 = new KeyedMatcher("AF", Condition.LT, 1.2f);
+    assertEquals(km1.toString(), "AF LT 1.2");
+
+    KeyedMatcher km2 = new KeyedMatcher("CLIN_SIG", Condition.NotContains, "path");
+    assertEquals(km2.toString(), "CLIN_SIG NotContains PATH");
+
+    /*
+     * AND them
+     */
+    KeyedMatcherSetI kms = new KeyedMatcherSet();
+    assertEquals(kms.toString(), "");
+    kms.and(km1);
+    assertEquals(kms.toString(), "(AF LT 1.2)");
+    kms.and(km2);
+    assertEquals(kms.toString(),
+            "(AF LT 1.2) AND (CLIN_SIG NotContains PATH)");
+
+    /*
+     * OR them
+     */
+    kms = new KeyedMatcherSet();
+    assertEquals(kms.toString(), "");
+    kms.or(km1);
+    assertEquals(kms.toString(), "(AF LT 1.2)");
+    kms.or(km2);
+    assertEquals(kms.toString(),
+            "(AF LT 1.2) OR (CLIN_SIG NotContains PATH)");
+  }
+
+  /**
+   * @return
+   */
+  protected KeyedMatcher km3()
+  {
+    return new KeyedMatcher("CSQ", Condition.Contains, "benign");
+  }
+
+  @Test
+  public void testOr()
+  {
+    // condition1: AF value contains "dog" (matches)
+    KeyedMatcherI km1 = new KeyedMatcher("AF", Condition.Contains, "dog");
+    // condition 2: CSQ value does not contain "how" (does not match)
+    KeyedMatcherI km2 = new KeyedMatcher("CSQ", Condition.NotContains,
+            "how");
+
+    Function<String, String> vp = key -> "AF".equals(key) ? "raining cats and dogs"
+            : "showers";
+    assertTrue(km1.matches(vp));
+    assertFalse(km2.matches(vp));
+
+    KeyedMatcherSetI kms = new KeyedMatcherSet();
+    kms.or(km2);
+    assertFalse(kms.matches(vp));
+    kms.or(km1);
+    assertTrue(kms.matches(vp));
+  }
+}
diff --git a/test/jalview/util/matcher/KeyedMatcherTest.java b/test/jalview/util/matcher/KeyedMatcherTest.java
new file mode 100644
index 0000000..ebc09c1
--- /dev/null
+++ b/test/jalview/util/matcher/KeyedMatcherTest.java
@@ -0,0 +1,55 @@
+package jalview.util.matcher;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertTrue;
+
+import org.testng.annotations.Test;
+
+public class KeyedMatcherTest
+{
+  @Test
+  public void testMatches()
+  {
+    /*
+     * a numeric matcher - MatcherTest covers more conditions
+     */
+    KeyedMatcherI km = new KeyedMatcher("AF", Condition.GE, -2F);
+    assertTrue(km.matches(key -> "-2"));
+    assertTrue(km.matches(key -> "-1"));
+    assertFalse(km.matches(key -> "-3"));
+    assertFalse(km.matches(key -> ""));
+    assertFalse(km.matches(key -> "junk"));
+    assertFalse(km.matches(key -> null));
+
+    /*
+     * a string pattern matcher
+     */
+    km = new KeyedMatcher("AF", Condition.Contains, "Cat");
+    assertTrue(km.matches(key -> "AF".equals(key) ? "raining cats and dogs"
+            : "showers"));
+  }
+
+  @Test
+  public void testToString()
+  {
+    KeyedMatcherI km = new KeyedMatcher("AF", Condition.LT, 1.2f);
+    assertEquals(km.toString(), "AF LT 1.2");
+  }
+
+  @Test
+  public void testGetKey()
+  {
+    KeyedMatcherI km = new KeyedMatcher("AF", Condition.GE, -2F);
+    assertEquals(km.getKey(), "AF");
+  }
+
+  @Test
+  public void testGetMatcher()
+  {
+    KeyedMatcherI km = new KeyedMatcher("AF", Condition.GE, -2F);
+    assertEquals(km.getMatcher().getCondition(), Condition.GE);
+    assertEquals(km.getMatcher().getFloatValue(), -2F);
+    assertEquals(km.getMatcher().getPattern(), "-2.0");
+  }
+}
diff --git a/test/jalview/util/matcher/MatcherTest.java b/test/jalview/util/matcher/MatcherTest.java
new file mode 100644
index 0000000..d988c3a
--- /dev/null
+++ b/test/jalview/util/matcher/MatcherTest.java
@@ -0,0 +1,250 @@
+package jalview.util.matcher;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotEquals;
+import static org.testng.Assert.assertTrue;
+import static org.testng.Assert.fail;
+
+import org.testng.annotations.Test;
+
+public class MatcherTest
+{
+  @Test
+  public void testConstructor()
+  {
+    MatcherI m = new Matcher(Condition.Contains, "foo");
+    assertEquals(m.getCondition(), Condition.Contains);
+    assertEquals(m.getPattern(), "FOO"); // all comparisons upper-cased
+    assertEquals(m.getFloatValue(), 0f);
+
+    m = new Matcher(Condition.GT, -2.1f);
+    assertEquals(m.getCondition(), Condition.GT);
+    assertEquals(m.getPattern(), "-2.1");
+    assertEquals(m.getFloatValue(), -2.1f);
+
+    m = new Matcher(Condition.NotContains, "-1.2f");
+    assertEquals(m.getCondition(), Condition.NotContains);
+    assertEquals(m.getPattern(), "-1.2F");
+    assertEquals(m.getFloatValue(), 0f);
+
+    m = new Matcher(Condition.GE, "-1.2f");
+    assertEquals(m.getCondition(), Condition.GE);
+    assertEquals(m.getPattern(), "-1.2");
+    assertEquals(m.getFloatValue(), -1.2f);
+
+    try
+    {
+      new Matcher(null, 0f);
+      fail("Expected exception");
+    } catch (NullPointerException e)
+    {
+      // expected
+    }
+
+    try
+    {
+      new Matcher(Condition.LT, "123,456");
+      fail("Expected exception");
+    } catch (NumberFormatException e)
+    {
+      // expected
+    }
+  }
+
+  /**
+   * Tests for float comparison conditions
+   */
+  @Test
+  public void testMatches_float()
+  {
+    /*
+     * EQUALS test
+     */
+    MatcherI m = new Matcher(Condition.EQ, 2f);
+    assertTrue(m.matches("2"));
+    assertTrue(m.matches("2.0"));
+    assertFalse(m.matches("2.01"));
+
+    /*
+     * NOT EQUALS test
+     */
+    m = new Matcher(Condition.NE, 2f);
+    assertFalse(m.matches("2"));
+    assertFalse(m.matches("2.0"));
+    assertTrue(m.matches("2.01"));
+
+    /*
+     * >= test
+     */
+    m = new Matcher(Condition.GE, 2f);
+    assertTrue(m.matches("2"));
+    assertTrue(m.matches("2.1"));
+    assertFalse(m.matches("1.9"));
+
+    /*
+     * > test
+     */
+    m = new Matcher(Condition.GT, 2f);
+    assertFalse(m.matches("2"));
+    assertTrue(m.matches("2.1"));
+    assertFalse(m.matches("1.9"));
+
+    /*
+     * <= test
+     */
+    m = new Matcher(Condition.LE, 2f);
+    assertTrue(m.matches("2"));
+    assertFalse(m.matches("2.1"));
+    assertTrue(m.matches("1.9"));
+
+    /*
+     * < test
+     */
+    m = new Matcher(Condition.LT, 2f);
+    assertFalse(m.matches("2"));
+    assertFalse(m.matches("2.1"));
+    assertTrue(m.matches("1.9"));
+  }
+
+  @Test
+  public void testMatches_floatNullOrInvalid()
+  {
+    for (Condition cond : Condition.values())
+    {
+      if (cond.isNumeric())
+      {
+        MatcherI m = new Matcher(cond, 2f);
+        assertFalse(m.matches(null));
+        assertFalse(m.matches(""));
+        assertFalse(m.matches("two"));
+      }
+    }
+  }
+
+  /**
+   * Tests for string comparison conditions
+   */
+  @Test
+  public void testMatches_pattern()
+  {
+    /*
+     * Contains
+     */
+    MatcherI m = new Matcher(Condition.Contains, "benign");
+    assertTrue(m.matches("benign"));
+    assertTrue(m.matches("MOSTLY BENIGN OBSERVED")); // not case-sensitive
+    assertFalse(m.matches("pathogenic"));
+    assertFalse(m.matches(null));
+
+    /*
+     * does not contain
+     */
+    m = new Matcher(Condition.NotContains, "benign");
+    assertFalse(m.matches("benign"));
+    assertFalse(m.matches("MOSTLY BENIGN OBSERVED")); // not case-sensitive
+    assertTrue(m.matches("pathogenic"));
+    assertTrue(m.matches(null)); // null value passes this condition
+
+    /*
+     * matches
+     */
+    m = new Matcher(Condition.Matches, "benign");
+    assertTrue(m.matches("benign"));
+    assertTrue(m.matches(" Benign ")); // trim before testing
+    assertFalse(m.matches("MOSTLY BENIGN"));
+    assertFalse(m.matches("pathogenic"));
+    assertFalse(m.matches(null));
+
+    /*
+     * does not match
+     */
+    m = new Matcher(Condition.NotMatches, "benign");
+    assertFalse(m.matches("benign"));
+    assertFalse(m.matches(" Benign ")); // trim before testing
+    assertTrue(m.matches("MOSTLY BENIGN"));
+    assertTrue(m.matches("pathogenic"));
+    assertTrue(m.matches(null));
+
+    /*
+     * a float with a string match condition will be treated as string
+     */
+    Matcher m1 = new Matcher(Condition.Contains, "32");
+    assertFalse(m1.matches(-203f));
+    assertTrue(m1.matches(-4321.0f));
+  }
+
+  /**
+   * If a float is passed with a string condition it gets converted to a string
+   */
+  @Test
+  public void testMatches_floatWithStringCondition()
+  {
+    MatcherI m = new Matcher(Condition.Contains, 1.2e-6f);
+    assertTrue(m.matches("1.2e-6"));
+
+    m = new Matcher(Condition.Contains, 0.0000001f);
+    assertTrue(m.matches("1.0e-7"));
+    assertTrue(m.matches("1.0E-7"));
+    assertFalse(m.matches("0.0000001f"));
+  }
+
+  @Test
+  public void testToString()
+  {
+    MatcherI m = new Matcher(Condition.LT, 1.2e-6f);
+    assertEquals(m.toString(), "LT 1.2E-6");
+
+    m = new Matcher(Condition.NotMatches, "ABC");
+    assertEquals(m.toString(), "NotMatches ABC");
+
+    m = new Matcher(Condition.Contains, -1.2f);
+    assertEquals(m.toString(), "Contains -1.2");
+  }
+
+  @Test
+  public void testEquals()
+  {
+    /*
+     * string condition
+     */
+    MatcherI m = new Matcher(Condition.NotMatches, "ABC");
+    assertFalse(m.equals(null));
+    assertFalse(m.equals("foo"));
+    assertTrue(m.equals(m));
+    assertTrue(m.equals(new Matcher(Condition.NotMatches, "ABC")));
+    // not case-sensitive:
+    assertTrue(m.equals(new Matcher(Condition.NotMatches, "abc")));
+    assertFalse(m.equals(new Matcher(Condition.Matches, "ABC")));
+    assertFalse(m.equals(new Matcher(Condition.NotMatches, "def")));
+
+    /*
+     * numeric conditions
+     */
+    m = new Matcher(Condition.LT, -1f);
+    assertFalse(m.equals(null));
+    assertFalse(m.equals("foo"));
+    assertTrue(m.equals(m));
+    assertTrue(m.equals(new Matcher(Condition.LT, -1f)));
+    assertTrue(m.equals(new Matcher(Condition.LT, "-1f")));
+    assertTrue(m.equals(new Matcher(Condition.LT, "-1.00f")));
+    assertFalse(m.equals(new Matcher(Condition.LE, -1f)));
+    assertFalse(m.equals(new Matcher(Condition.GE, -1f)));
+    assertFalse(m.equals(new Matcher(Condition.NE, -1f)));
+    assertFalse(m.equals(new Matcher(Condition.LT, 1f)));
+    assertFalse(m.equals(new Matcher(Condition.LT, -1.1f)));
+  }
+
+  @Test
+  public void testHashCode()
+  {
+    MatcherI m1 = new Matcher(Condition.NotMatches, "ABC");
+    MatcherI m2 = new Matcher(Condition.NotMatches, "ABC");
+    MatcherI m3 = new Matcher(Condition.NotMatches, "AB");
+    MatcherI m4 = new Matcher(Condition.Matches, "ABC");
+    assertEquals(m1.hashCode(), m2.hashCode());
+    assertNotEquals(m1.hashCode(), m3.hashCode());
+    assertNotEquals(m1.hashCode(), m4.hashCode());
+    assertNotEquals(m3.hashCode(), m4.hashCode());
+  }
+}
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diff --git a/utils/proguard_5.3.3.jar b/utils/proguard_5.3.3.jar
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