From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 10 Jan 2018 15:20:56 +0000 (+0000)
Subject: JAL-1793 update spike branch to latest
X-Git-Tag: Release_2_11_0~62^2~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=14b1b2a878190d5fffda298c4b9a901c72c74ad3;p=jalview.git

JAL-1793 update spike branch to latest
---

diff --git a/examples/exampleFeatures.txt b/examples/exampleFeatures.txt
index 9e65534..99af214 100755
--- a/examples/exampleFeatures.txt
+++ b/examples/exampleFeatures.txt
@@ -26,6 +26,11 @@ BETA-TURN-IIL	8b5b50
 ST-MOTIF	ac25a1
 kdHydrophobicity	ccffcc|333300|-3.9|4.5|above|-2.0
 
+STARTFILTERS
+GAMMA-TURN-INVERSE	Label Contains PDB
+kdHydrophobicity	(Score LT 1.5) OR (Score GE 2.8)
+ENDFILTERS
+
 STARTGROUP	uniprot
 <html><a href="http://pfam.xfam.org/family/PF00111">Pfam family</a></html>	FER_CAPAA	-1	0	0	Pfam
 Iron-sulfur (2Fe-2S)	FER_CAPAA	-1	39	39	METAL
diff --git a/help/html/releases.html b/help/html/releases.html
index e1402e9..a36e31a 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -77,7 +77,13 @@ li:before {
           <em></em>
       </td>
       <td><div align="left">
-          <ul><li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li><ul>
+          <ul>
+            <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
+            <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
+            <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
+            <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
+            <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
+          <ul>
       </td>
     </tr>
     <tr>
diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 00888d5..1277a86 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -368,6 +368,8 @@ label.optimise_order = Optimise Order
 label.seq_sort_by_score = Sequence sort by Score
 label.load_colours = Load Colours
 label.save_colours = Save Colours
+label.load_colours_tooltip = Load feature colours and filters from file
+label.save_colours_tooltip = Save feature colours and filters to file
 label.fetch_das_features = Fetch DAS Features
 label.selected_database_to_fetch_from = Selected {0} database {1} to fetch from {2} 
 label.database_param = Database: {0}
@@ -1355,4 +1357,5 @@ label.by_text_of = By text of
 label.by_range_of = By range of
 label.filters_tooltip = Click to set or amend filters
 label.or = Or
-label.and = And
\ No newline at end of file
+label.and = And
+label.sequence_feature_colours = Sequence Feature Colours
diff --git a/schemas/JalviewUserColours.xsd b/schemas/JalviewUserColours.xsd
index bd43e9d..3934d66 100755
--- a/schemas/JalviewUserColours.xsd
+++ b/schemas/JalviewUserColours.xsd
@@ -16,8 +16,7 @@
   
   You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 -->
-<!-- edited with XMLSpy v2005 rel. 3 U (http://www.altova.com) by lj (jl) -->
-<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" targetNamespace="www.jalview.org/colours">
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:jalview="www.jalview.org/colours" targetNamespace="www.jalview.org/colours">
 	<xs:complexType name="JalviewUserColours">
 		<xs:sequence>
 			<xs:element name="Version" maxOccurs="1" minOccurs="0" type="xs:string">
@@ -29,13 +28,29 @@
 			</xs:element>
 			<xs:element name="colour" maxOccurs="unbounded" minOccurs="0">
 				<xs:complexType>
-					<xs:attribute name="Name" type="xs:string"/>
+				    <xs:sequence>
+					    <xs:element name="attributeName" type="xs:string" minOccurs="0" maxOccurs="2">
+						    	<xs:annotation>
+						    		<xs:documentation>name of feature attribute to colour by, or attribute and sub-attribute</xs:documentation>
+						    	</xs:annotation>
+					    </xs:element> 
+					</xs:sequence>
+					<xs:attribute name="Name" type="xs:string">
+					    	<xs:annotation>
+					    		<xs:documentation>Single letter residue code for an alignment colour scheme, or feature type for a feature colour scheme</xs:documentation>
+					    	</xs:annotation>
+					</xs:attribute>
 					<xs:attribute name="RGB" type="xs:string" use="required"/>
 					<xs:attribute name="minRGB" type="xs:string" use="optional"/>
-					<xs:attribute name="threshType" type="xs:string" use="optional">
-					<xs:annotation>
-					<xs:documentation>loosely specified enumeration: NONE,ABOVE, or BELOW</xs:documentation>
-					</xs:annotation>
+					<xs:attribute name="noValueColour" use="optional" type="jalview:NoValueColour" default="Min" />
+					<xs:attribute name="threshType" use="optional">
+						<xs:simpleType> 
+							<xs:restriction base="xs:string">
+						      <xs:enumeration value="NONE" />
+						      <xs:enumeration value="ABOVE" />
+						      <xs:enumeration value="BELOW" />
+						    </xs:restriction>	
+					    </xs:simpleType> 
 					</xs:attribute>
 					<xs:attribute name="threshold" type="xs:float" use="optional"/>
 					<xs:attribute name="max" type="xs:float" use="optional"/>
@@ -44,7 +59,68 @@
 					<xs:attribute name="autoScale" type="xs:boolean" use="optional"/>
 				</xs:complexType>
 			</xs:element>
+			<xs:element name="filter" maxOccurs="unbounded" minOccurs="0" >
+			    <xs:complexType>
+			    		<xs:sequence> 
+	    			  		<xs:element name="matcherSet" type="jalview:FeatureMatcherSet" />
+	    			  	</xs:sequence> 
+					<xs:attribute name="featureType" type="xs:string" use="required"/>
+			    </xs:complexType>
+			</xs:element>
 		</xs:sequence>
 		<xs:attribute name="schemeName" type="xs:string" use="optional"/>
 	</xs:complexType>
+
+	<xs:complexType name="FeatureMatcherSet"> 
+	    	<xs:annotation>
+	    		<xs:documentation>A feature match condition, which may be simple or compound</xs:documentation>
+	    	</xs:annotation>
+	  <xs:choice> 
+	    <xs:element name="matchCondition" type="jalview:FeatureMatcher" /> 
+	    <xs:element name="compoundMatcher">
+		    <xs:complexType>
+			  <xs:sequence> 
+			      <xs:element name="matcherSet" minOccurs="2" maxOccurs="2" type="jalview:FeatureMatcherSet" /> 
+			  </xs:sequence> 
+		      <xs:attribute name="and" type="xs:boolean" use="required">
+				  <xs:annotation>
+				  	<xs:documentation>If true, matchers are AND-ed, if false they are OR-ed</xs:documentation>
+				  </xs:annotation>
+		      </xs:attribute>
+		    </xs:complexType>
+	    </xs:element>
+	  </xs:choice> 
+	</xs:complexType> 
+	
+	<xs:complexType name="FeatureMatcher"> 
+	  <xs:sequence> 
+	    <xs:element name="attributeName" type="xs:string" minOccurs="0" maxOccurs="2">
+		    	<xs:annotation>
+		    		<xs:documentation>name of feature attribute to filter on, or attribute and sub-attribute</xs:documentation>
+		    	</xs:annotation>
+	    </xs:element> 
+	    <xs:element name="condition" type="xs:string" /> 
+	    <xs:element name="value" type="xs:string" /> 
+	  </xs:sequence>
+	  <xs:attribute name="by">
+		<xs:simpleType> 
+			<xs:restriction base="xs:string">
+		      <xs:enumeration value="byLabel" />
+		      <xs:enumeration value="byScore" />
+		      <xs:enumeration value="byAttribute" />
+		    </xs:restriction>	
+	    </xs:simpleType> 
+	  </xs:attribute> 
+	</xs:complexType> 
+	
+	<xs:simpleType name="NoValueColour">
+	    	<xs:annotation>
+	    		<xs:documentation>Graduated feature colour if no score (or attribute) value</xs:documentation>
+	    	</xs:annotation>
+		<xs:restriction base="xs:string">
+	      <xs:enumeration value="None" />
+	      <xs:enumeration value="Min" />
+	      <xs:enumeration value="Max" />
+	    </xs:restriction>	
+	</xs:simpleType>
 </xs:schema>
diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index f0bd638..48824e7 100755
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -500,6 +500,18 @@
 						<xs:sequence>
 							<xs:element name="setting" minOccurs="0" maxOccurs="unbounded">
 								<xs:complexType>
+									<xs:sequence>
+									    <xs:element name="attributeName" type="xs:string" minOccurs="0" maxOccurs="2">
+										    	<xs:annotation>
+										    		<xs:documentation>name of feature attribute to colour by, or attribute and sub-attribute</xs:documentation>
+										    	</xs:annotation>
+									    </xs:element> 
+			    			  		   		<xs:element name="matcherSet" minOccurs="0" type="jalview:FeatureMatcherSet">
+										    	<xs:annotation>
+										    		<xs:documentation>optional filter(s) applied to the feature type</xs:documentation>
+										    	</xs:annotation>
+										</xs:element>
+								  	</xs:sequence>
 									<xs:attribute name="type" type="xs:string" use="required" />
 									<xs:attribute name="colour" type="xs:int" use="required" />
 									<xs:attribute name="display" type="xs:boolean"
@@ -515,6 +527,7 @@
 											</xs:documentation>
 										</xs:annotation>
 									</xs:attribute>
+									<xs:attribute name="noValueColour" use="optional" type="jalview:NoValueColour" default="Min" />
 									<xs:attribute name="threshold" type="xs:float"
 										use="optional">
 										<xs:annotation>
@@ -559,6 +572,11 @@
 			<xs:element name="otherData" minOccurs="0" maxOccurs="unbounded">
 				<xs:complexType>
 					<xs:attribute name="key" type="xs:string" use="required" />
+					<xs:attribute name="key2" type="xs:string" use="optional">
+						<xs:annotation>
+							<xs:documentation>key2 may be used for a sub-attribute of key</xs:documentation>
+						</xs:annotation>
+					</xs:attribute>
 					<xs:attribute name="value" type="xs:string" use="required" />
 				</xs:complexType>
 			</xs:element>
diff --git a/src/jalview/api/FeatureColourI.java b/src/jalview/api/FeatureColourI.java
index 0780271..4dbb1bb 100644
--- a/src/jalview/api/FeatureColourI.java
+++ b/src/jalview/api/FeatureColourI.java
@@ -72,7 +72,8 @@ public interface FeatureColourI
   boolean isSimpleColour();
 
   /**
-   * Answers true if the feature is coloured by label (description)
+   * Answers true if the feature is coloured by label (description) or by text
+   * value of an attribute
    * 
    * @return
    */
diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java
index ead84fa..cf3c8da 100644
--- a/src/jalview/api/FeatureRenderer.java
+++ b/src/jalview/api/FeatureRenderer.java
@@ -226,7 +226,7 @@ public interface FeatureRenderer
   FeatureMatcherSetI getFeatureFilter(String featureType);
 
   /**
-   * Answers a shallow copy of the feature filters map
+   * Answers the feature filters map
    * 
    * @return
    */
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index ef87671..fe6b8d9 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1445,9 +1445,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     FeaturesFile formatter = new FeaturesFile();
     if (format.equalsIgnoreCase("Jalview"))
     {
-      features = formatter.printJalviewFormat(viewport.getAlignment()
-              .getSequencesArray(), getDisplayedFeatureCols(),
-              getDisplayedFeatureGroups(), true);
+      features = formatter.printJalviewFormat(
+              viewport.getAlignment().getSequencesArray(),
+              getDisplayedFeatureCols(), null, getDisplayedFeatureGroups(),
+              true);
     }
     else
     {
diff --git a/src/jalview/appletgui/AnnotationColumnChooser.java b/src/jalview/appletgui/AnnotationColumnChooser.java
index 7674de716..206b132 100644
--- a/src/jalview/appletgui/AnnotationColumnChooser.java
+++ b/src/jalview/appletgui/AnnotationColumnChooser.java
@@ -46,7 +46,6 @@ import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.TextEvent;
 import java.awt.event.TextListener;
-import java.util.ArrayList;
 import java.util.Vector;
 
 //import javax.swing.JPanel;
@@ -293,16 +292,6 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       {
         HiddenColumns oldHidden = av.getAnnotationColumnSelectionState()
                 .getOldHiddenColumns();
-        if (oldHidden != null)
-        {
-          ArrayList<int[]> regions = oldHidden.getHiddenColumnsCopy();
-          for (int[] positions : regions)
-          {
-            av.hideColumns(positions[0], positions[1]);
-          }
-        }
-        // TODO not clear why we need to hide all the columns (above) if we are
-        // going to copy the hidden columns over wholesale anyway
         av.getAlignment().setHiddenColumns(oldHidden);
       }
       av.sendSelection();
diff --git a/src/jalview/binding/Colour.java b/src/jalview/binding/Colour.java
index 25cf9bf..f51e9af 100644
--- a/src/jalview/binding/Colour.java
+++ b/src/jalview/binding/Colour.java
@@ -27,7 +27,8 @@ public class Colour implements java.io.Serializable
   // --------------------------/
 
   /**
-   * Field _name.
+   * Single letter residue code for an alignment colour scheme, or feature type
+   * for a feature colour scheme
    */
   private java.lang.String _name;
 
@@ -42,9 +43,15 @@ public class Colour implements java.io.Serializable
   private java.lang.String _minRGB;
 
   /**
-   * loosely specified enumeration: NONE,ABOVE, or BELOW
+   * Field _noValueColour.
    */
-  private java.lang.String _threshType;
+  private jalview.binding.types.NoValueColour _noValueColour = jalview.binding.types.NoValueColour
+          .valueOf("Min");
+
+  /**
+   * Field _threshType.
+   */
+  private jalview.binding.types.ColourThreshTypeType _threshType;
 
   /**
    * Field _threshold.
@@ -96,6 +103,11 @@ public class Colour implements java.io.Serializable
    */
   private boolean _has_autoScale;
 
+  /**
+   * name of feature attribute to colour by, or attribute and sub-attribute
+   */
+  private java.util.Vector _attributeNameList;
+
   // ----------------/
   // - Constructors -/
   // ----------------/
@@ -103,6 +115,8 @@ public class Colour implements java.io.Serializable
   public Colour()
   {
     super();
+    setNoValueColour(jalview.binding.types.NoValueColour.valueOf("Min"));
+    this._attributeNameList = new java.util.Vector();
   }
 
   // -----------/
@@ -110,41 +124,140 @@ public class Colour implements java.io.Serializable
   // -----------/
 
   /**
-     */
+   * 
+   * 
+   * @param vAttributeName
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAttributeName(final java.lang.String vAttributeName)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check for the maximum size
+    if (this._attributeNameList.size() >= 2)
+    {
+      throw new IndexOutOfBoundsException(
+              "addAttributeName has a maximum of 2");
+    }
+
+    this._attributeNameList.addElement(vAttributeName);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAttributeName
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAttributeName(final int index,
+          final java.lang.String vAttributeName)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check for the maximum size
+    if (this._attributeNameList.size() >= 2)
+    {
+      throw new IndexOutOfBoundsException(
+              "addAttributeName has a maximum of 2");
+    }
+
+    this._attributeNameList.add(index, vAttributeName);
+  }
+
+  /**
+   */
   public void deleteAutoScale()
   {
     this._has_autoScale = false;
   }
 
   /**
-     */
+   */
   public void deleteColourByLabel()
   {
     this._has_colourByLabel = false;
   }
 
   /**
-     */
+   */
   public void deleteMax()
   {
     this._has_max = false;
   }
 
   /**
-     */
+   */
   public void deleteMin()
   {
     this._has_min = false;
   }
 
   /**
-     */
+   */
   public void deleteThreshold()
   {
     this._has_threshold = false;
   }
 
   /**
+   * Method enumerateAttributeName.
+   * 
+   * @return an Enumeration over all java.lang.String elements
+   */
+  public java.util.Enumeration enumerateAttributeName()
+  {
+    return this._attributeNameList.elements();
+  }
+
+  /**
+   * Method getAttributeName.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the java.lang.String at the given index
+   */
+  public java.lang.String getAttributeName(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._attributeNameList.size())
+    {
+      throw new IndexOutOfBoundsException("getAttributeName: Index value '"
+              + index + "' not in range [0.."
+              + (this._attributeNameList.size() - 1) + "]");
+    }
+
+    return (java.lang.String) _attributeNameList.get(index);
+  }
+
+  /**
+   * Method getAttributeName.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public java.lang.String[] getAttributeName()
+  {
+    java.lang.String[] array = new java.lang.String[0];
+    return (java.lang.String[]) this._attributeNameList.toArray(array);
+  }
+
+  /**
+   * Method getAttributeNameCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getAttributeNameCount()
+  {
+    return this._attributeNameList.size();
+  }
+
+  /**
    * Returns the value of field 'autoScale'.
    * 
    * @return the value of field 'AutoScale'.
@@ -195,7 +308,9 @@ public class Colour implements java.io.Serializable
   }
 
   /**
-   * Returns the value of field 'name'.
+   * Returns the value of field 'name'. The field 'name' has the following
+   * description: Single letter residue code for an alignment colour scheme, or
+   * feature type for a feature colour scheme
    * 
    * @return the value of field 'Name'.
    */
@@ -205,6 +320,16 @@ public class Colour implements java.io.Serializable
   }
 
   /**
+   * Returns the value of field 'noValueColour'.
+   * 
+   * @return the value of field 'NoValueColour'.
+   */
+  public jalview.binding.types.NoValueColour getNoValueColour()
+  {
+    return this._noValueColour;
+  }
+
+  /**
    * Returns the value of field 'RGB'.
    * 
    * @return the value of field 'RGB'.
@@ -215,12 +340,11 @@ public class Colour implements java.io.Serializable
   }
 
   /**
-   * Returns the value of field 'threshType'. The field 'threshType' has the
-   * following description: loosely specified enumeration: NONE,ABOVE, or BELOW
+   * Returns the value of field 'threshType'.
    * 
    * @return the value of field 'ThreshType'.
    */
-  public java.lang.String getThreshType()
+  public jalview.binding.types.ColourThreshTypeType getThreshType()
   {
     return this._threshType;
   }
@@ -360,6 +484,76 @@ public class Colour implements java.io.Serializable
   }
 
   /**
+   */
+  public void removeAllAttributeName()
+  {
+    this._attributeNameList.clear();
+  }
+
+  /**
+   * Method removeAttributeName.
+   * 
+   * @param vAttributeName
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeAttributeName(final java.lang.String vAttributeName)
+  {
+    boolean removed = _attributeNameList.remove(vAttributeName);
+    return removed;
+  }
+
+  /**
+   * Method removeAttributeNameAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public java.lang.String removeAttributeNameAt(final int index)
+  {
+    java.lang.Object obj = this._attributeNameList.remove(index);
+    return (java.lang.String) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAttributeName
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setAttributeName(final int index,
+          final java.lang.String vAttributeName)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._attributeNameList.size())
+    {
+      throw new IndexOutOfBoundsException("setAttributeName: Index value '"
+              + index + "' not in range [0.."
+              + (this._attributeNameList.size() - 1) + "]");
+    }
+
+    this._attributeNameList.set(index, vAttributeName);
+  }
+
+  /**
+   * 
+   * 
+   * @param vAttributeNameArray
+   */
+  public void setAttributeName(final java.lang.String[] vAttributeNameArray)
+  {
+    // -- copy array
+    _attributeNameList.clear();
+
+    for (int i = 0; i < vAttributeNameArray.length; i++)
+    {
+      this._attributeNameList.add(vAttributeNameArray[i]);
+    }
+  }
+
+  /**
    * Sets the value of field 'autoScale'.
    * 
    * @param autoScale
@@ -419,7 +613,9 @@ public class Colour implements java.io.Serializable
   }
 
   /**
-   * Sets the value of field 'name'.
+   * Sets the value of field 'name'. The field 'name' has the following
+   * description: Single letter residue code for an alignment colour scheme, or
+   * feature type for a feature colour scheme
    * 
    * @param name
    *          the value of field 'name'.
@@ -430,6 +626,18 @@ public class Colour implements java.io.Serializable
   }
 
   /**
+   * Sets the value of field 'noValueColour'.
+   * 
+   * @param noValueColour
+   *          the value of field 'noValueColour'.
+   */
+  public void setNoValueColour(
+          final jalview.binding.types.NoValueColour noValueColour)
+  {
+    this._noValueColour = noValueColour;
+  }
+
+  /**
    * Sets the value of field 'RGB'.
    * 
    * @param RGB
@@ -441,13 +649,13 @@ public class Colour implements java.io.Serializable
   }
 
   /**
-   * Sets the value of field 'threshType'. The field 'threshType' has the
-   * following description: loosely specified enumeration: NONE,ABOVE, or BELOW
+   * Sets the value of field 'threshType'.
    * 
    * @param threshType
    *          the value of field 'threshType'.
    */
-  public void setThreshType(final java.lang.String threshType)
+  public void setThreshType(
+          final jalview.binding.types.ColourThreshTypeType threshType)
   {
     this._threshType = threshType;
   }
diff --git a/src/jalview/binding/CompoundMatcher.java b/src/jalview/binding/CompoundMatcher.java
new file mode 100644
index 0000000..a2d1048
--- /dev/null
+++ b/src/jalview/binding/CompoundMatcher.java
@@ -0,0 +1,368 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class CompoundMatcher.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class CompoundMatcher implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * If true, matchers are AND-ed, if false they are OR-ed
+   */
+  private boolean _and;
+
+  /**
+   * keeps track of state for field: _and
+   */
+  private boolean _has_and;
+
+  /**
+   * Field _matcherSetList.
+   */
+  private java.util.Vector _matcherSetList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public CompoundMatcher()
+  {
+    super();
+    this._matcherSetList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vMatcherSet
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addMatcherSet(final jalview.binding.MatcherSet vMatcherSet)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check for the maximum size
+    if (this._matcherSetList.size() >= 2)
+    {
+      throw new IndexOutOfBoundsException(
+              "addMatcherSet has a maximum of 2");
+    }
+
+    this._matcherSetList.addElement(vMatcherSet);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vMatcherSet
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addMatcherSet(final int index,
+          final jalview.binding.MatcherSet vMatcherSet)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check for the maximum size
+    if (this._matcherSetList.size() >= 2)
+    {
+      throw new IndexOutOfBoundsException(
+              "addMatcherSet has a maximum of 2");
+    }
+
+    this._matcherSetList.add(index, vMatcherSet);
+  }
+
+  /**
+   */
+  public void deleteAnd()
+  {
+    this._has_and = false;
+  }
+
+  /**
+   * Method enumerateMatcherSet.
+   * 
+   * @return an Enumeration over all jalview.binding.MatcherSet elements
+   */
+  public java.util.Enumeration enumerateMatcherSet()
+  {
+    return this._matcherSetList.elements();
+  }
+
+  /**
+   * Returns the value of field 'and'. The field 'and' has the following
+   * description: If true, matchers are AND-ed, if false they are OR-ed
+   * 
+   * @return the value of field 'And'.
+   */
+  public boolean getAnd()
+  {
+    return this._and;
+  }
+
+  /**
+   * Method getMatcherSet.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.MatcherSet at the given index
+   */
+  public jalview.binding.MatcherSet getMatcherSet(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._matcherSetList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "getMatcherSet: Index value '" + index + "' not in range [0.."
+                      + (this._matcherSetList.size() - 1) + "]");
+    }
+
+    return (jalview.binding.MatcherSet) _matcherSetList.get(index);
+  }
+
+  /**
+   * Method getMatcherSet.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.MatcherSet[] getMatcherSet()
+  {
+    jalview.binding.MatcherSet[] array = new jalview.binding.MatcherSet[0];
+    return (jalview.binding.MatcherSet[]) this._matcherSetList
+            .toArray(array);
+  }
+
+  /**
+   * Method getMatcherSetCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getMatcherSetCount()
+  {
+    return this._matcherSetList.size();
+  }
+
+  /**
+   * Method hasAnd.
+   * 
+   * @return true if at least one And has been added
+   */
+  public boolean hasAnd()
+  {
+    return this._has_and;
+  }
+
+  /**
+   * Returns the value of field 'and'. The field 'and' has the following
+   * description: If true, matchers are AND-ed, if false they are OR-ed
+   * 
+   * @return the value of field 'And'.
+   */
+  public boolean isAnd()
+  {
+    return this._and;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   */
+  public void removeAllMatcherSet()
+  {
+    this._matcherSetList.clear();
+  }
+
+  /**
+   * Method removeMatcherSet.
+   * 
+   * @param vMatcherSet
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeMatcherSet(
+          final jalview.binding.MatcherSet vMatcherSet)
+  {
+    boolean removed = _matcherSetList.remove(vMatcherSet);
+    return removed;
+  }
+
+  /**
+   * Method removeMatcherSetAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.MatcherSet removeMatcherSetAt(final int index)
+  {
+    java.lang.Object obj = this._matcherSetList.remove(index);
+    return (jalview.binding.MatcherSet) obj;
+  }
+
+  /**
+   * Sets the value of field 'and'. The field 'and' has the following
+   * description: If true, matchers are AND-ed, if false they are OR-ed
+   * 
+   * @param and
+   *          the value of field 'and'.
+   */
+  public void setAnd(final boolean and)
+  {
+    this._and = and;
+    this._has_and = true;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vMatcherSet
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setMatcherSet(final int index,
+          final jalview.binding.MatcherSet vMatcherSet)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._matcherSetList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "setMatcherSet: Index value '" + index + "' not in range [0.."
+                      + (this._matcherSetList.size() - 1) + "]");
+    }
+
+    this._matcherSetList.set(index, vMatcherSet);
+  }
+
+  /**
+   * 
+   * 
+   * @param vMatcherSetArray
+   */
+  public void setMatcherSet(
+          final jalview.binding.MatcherSet[] vMatcherSetArray)
+  {
+    // -- copy array
+    _matcherSetList.clear();
+
+    for (int i = 0; i < vMatcherSetArray.length; i++)
+    {
+      this._matcherSetList.add(vMatcherSetArray[i]);
+    }
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.CompoundMatcher
+   */
+  public static jalview.binding.CompoundMatcher unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.CompoundMatcher) Unmarshaller
+            .unmarshal(jalview.binding.CompoundMatcher.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
+
+}
diff --git a/src/jalview/binding/FeatureMatcher.java b/src/jalview/binding/FeatureMatcher.java
new file mode 100644
index 0000000..e4e52fb
--- /dev/null
+++ b/src/jalview/binding/FeatureMatcher.java
@@ -0,0 +1,381 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class FeatureMatcher.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class FeatureMatcher implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _by.
+   */
+  private jalview.binding.types.FeatureMatcherByType _by;
+
+  /**
+   * name of feature attribute to filter on, or attribute and sub-attribute
+   */
+  private java.util.Vector _attributeNameList;
+
+  /**
+   * Field _condition.
+   */
+  private java.lang.String _condition;
+
+  /**
+   * Field _value.
+   */
+  private java.lang.String _value;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public FeatureMatcher()
+  {
+    super();
+    this._attributeNameList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vAttributeName
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAttributeName(final java.lang.String vAttributeName)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check for the maximum size
+    if (this._attributeNameList.size() >= 2)
+    {
+      throw new IndexOutOfBoundsException(
+              "addAttributeName has a maximum of 2");
+    }
+
+    this._attributeNameList.addElement(vAttributeName);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAttributeName
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAttributeName(final int index,
+          final java.lang.String vAttributeName)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check for the maximum size
+    if (this._attributeNameList.size() >= 2)
+    {
+      throw new IndexOutOfBoundsException(
+              "addAttributeName has a maximum of 2");
+    }
+
+    this._attributeNameList.add(index, vAttributeName);
+  }
+
+  /**
+   * Method enumerateAttributeName.
+   * 
+   * @return an Enumeration over all java.lang.String elements
+   */
+  public java.util.Enumeration enumerateAttributeName()
+  {
+    return this._attributeNameList.elements();
+  }
+
+  /**
+   * Method getAttributeName.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the java.lang.String at the given index
+   */
+  public java.lang.String getAttributeName(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._attributeNameList.size())
+    {
+      throw new IndexOutOfBoundsException("getAttributeName: Index value '"
+              + index + "' not in range [0.."
+              + (this._attributeNameList.size() - 1) + "]");
+    }
+
+    return (java.lang.String) _attributeNameList.get(index);
+  }
+
+  /**
+   * Method getAttributeName.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public java.lang.String[] getAttributeName()
+  {
+    java.lang.String[] array = new java.lang.String[0];
+    return (java.lang.String[]) this._attributeNameList.toArray(array);
+  }
+
+  /**
+   * Method getAttributeNameCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getAttributeNameCount()
+  {
+    return this._attributeNameList.size();
+  }
+
+  /**
+   * Returns the value of field 'by'.
+   * 
+   * @return the value of field 'By'.
+   */
+  public jalview.binding.types.FeatureMatcherByType getBy()
+  {
+    return this._by;
+  }
+
+  /**
+   * Returns the value of field 'condition'.
+   * 
+   * @return the value of field 'Condition'.
+   */
+  public java.lang.String getCondition()
+  {
+    return this._condition;
+  }
+
+  /**
+   * Returns the value of field 'value'.
+   * 
+   * @return the value of field 'Value'.
+   */
+  public java.lang.String getValue()
+  {
+    return this._value;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   */
+  public void removeAllAttributeName()
+  {
+    this._attributeNameList.clear();
+  }
+
+  /**
+   * Method removeAttributeName.
+   * 
+   * @param vAttributeName
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeAttributeName(final java.lang.String vAttributeName)
+  {
+    boolean removed = _attributeNameList.remove(vAttributeName);
+    return removed;
+  }
+
+  /**
+   * Method removeAttributeNameAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public java.lang.String removeAttributeNameAt(final int index)
+  {
+    java.lang.Object obj = this._attributeNameList.remove(index);
+    return (java.lang.String) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAttributeName
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setAttributeName(final int index,
+          final java.lang.String vAttributeName)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._attributeNameList.size())
+    {
+      throw new IndexOutOfBoundsException("setAttributeName: Index value '"
+              + index + "' not in range [0.."
+              + (this._attributeNameList.size() - 1) + "]");
+    }
+
+    this._attributeNameList.set(index, vAttributeName);
+  }
+
+  /**
+   * 
+   * 
+   * @param vAttributeNameArray
+   */
+  public void setAttributeName(final java.lang.String[] vAttributeNameArray)
+  {
+    // -- copy array
+    _attributeNameList.clear();
+
+    for (int i = 0; i < vAttributeNameArray.length; i++)
+    {
+      this._attributeNameList.add(vAttributeNameArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'by'.
+   * 
+   * @param by
+   *          the value of field 'by'.
+   */
+  public void setBy(final jalview.binding.types.FeatureMatcherByType by)
+  {
+    this._by = by;
+  }
+
+  /**
+   * Sets the value of field 'condition'.
+   * 
+   * @param condition
+   *          the value of field 'condition'.
+   */
+  public void setCondition(final java.lang.String condition)
+  {
+    this._condition = condition;
+  }
+
+  /**
+   * Sets the value of field 'value'.
+   * 
+   * @param value
+   *          the value of field 'value'.
+   */
+  public void setValue(final java.lang.String value)
+  {
+    this._value = value;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.FeatureMatcher
+   */
+  public static jalview.binding.FeatureMatcher unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.FeatureMatcher) Unmarshaller
+            .unmarshal(jalview.binding.FeatureMatcher.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
+
+}
diff --git a/src/jalview/binding/FeatureMatcherSet.java b/src/jalview/binding/FeatureMatcherSet.java
new file mode 100644
index 0000000..7ba5f0e
--- /dev/null
+++ b/src/jalview/binding/FeatureMatcherSet.java
@@ -0,0 +1,200 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * A feature match condition, which may be simple or compound
+ * 
+ * @version $Revision$ $Date$
+ */
+public class FeatureMatcherSet implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Internal choice value storage
+   */
+  private java.lang.Object _choiceValue;
+
+  /**
+   * Field _matchCondition.
+   */
+  private jalview.binding.MatchCondition _matchCondition;
+
+  /**
+   * Field _compoundMatcher.
+   */
+  private jalview.binding.CompoundMatcher _compoundMatcher;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public FeatureMatcherSet()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'choiceValue'. The field 'choiceValue' has the
+   * following description: Internal choice value storage
+   * 
+   * @return the value of field 'ChoiceValue'.
+   */
+  public java.lang.Object getChoiceValue()
+  {
+    return this._choiceValue;
+  }
+
+  /**
+   * Returns the value of field 'compoundMatcher'.
+   * 
+   * @return the value of field 'CompoundMatcher'.
+   */
+  public jalview.binding.CompoundMatcher getCompoundMatcher()
+  {
+    return this._compoundMatcher;
+  }
+
+  /**
+   * Returns the value of field 'matchCondition'.
+   * 
+   * @return the value of field 'MatchCondition'.
+   */
+  public jalview.binding.MatchCondition getMatchCondition()
+  {
+    return this._matchCondition;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'compoundMatcher'.
+   * 
+   * @param compoundMatcher
+   *          the value of field 'compoundMatcher'.
+   */
+  public void setCompoundMatcher(
+          final jalview.binding.CompoundMatcher compoundMatcher)
+  {
+    this._compoundMatcher = compoundMatcher;
+    this._choiceValue = compoundMatcher;
+  }
+
+  /**
+   * Sets the value of field 'matchCondition'.
+   * 
+   * @param matchCondition
+   *          the value of field 'matchCondition'.
+   */
+  public void setMatchCondition(
+          final jalview.binding.MatchCondition matchCondition)
+  {
+    this._matchCondition = matchCondition;
+    this._choiceValue = matchCondition;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.FeatureMatcherSet
+   */
+  public static jalview.binding.FeatureMatcherSet unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.FeatureMatcherSet) Unmarshaller
+            .unmarshal(jalview.binding.FeatureMatcherSet.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
+
+}
diff --git a/src/jalview/binding/Filter.java b/src/jalview/binding/Filter.java
new file mode 100644
index 0000000..687ae91
--- /dev/null
+++ b/src/jalview/binding/Filter.java
@@ -0,0 +1,180 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class Filter.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class Filter implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _featureType.
+   */
+  private java.lang.String _featureType;
+
+  /**
+   * Field _matcherSet.
+   */
+  private jalview.binding.MatcherSet _matcherSet;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Filter()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'featureType'.
+   * 
+   * @return the value of field 'FeatureType'.
+   */
+  public java.lang.String getFeatureType()
+  {
+    return this._featureType;
+  }
+
+  /**
+   * Returns the value of field 'matcherSet'.
+   * 
+   * @return the value of field 'MatcherSet'.
+   */
+  public jalview.binding.MatcherSet getMatcherSet()
+  {
+    return this._matcherSet;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'featureType'.
+   * 
+   * @param featureType
+   *          the value of field 'featureType'.
+   */
+  public void setFeatureType(final java.lang.String featureType)
+  {
+    this._featureType = featureType;
+  }
+
+  /**
+   * Sets the value of field 'matcherSet'.
+   * 
+   * @param matcherSet
+   *          the value of field 'matcherSet'.
+   */
+  public void setMatcherSet(final jalview.binding.MatcherSet matcherSet)
+  {
+    this._matcherSet = matcherSet;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.Filter
+   */
+  public static jalview.binding.Filter unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Filter) Unmarshaller
+            .unmarshal(jalview.binding.Filter.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
+
+}
diff --git a/src/jalview/binding/JalviewUserColours.java b/src/jalview/binding/JalviewUserColours.java
index 6709487..67ee5a2 100644
--- a/src/jalview/binding/JalviewUserColours.java
+++ b/src/jalview/binding/JalviewUserColours.java
@@ -42,6 +42,11 @@ public class JalviewUserColours implements java.io.Serializable
    */
   private java.util.Vector _colourList;
 
+  /**
+   * Field _filterList.
+   */
+  private java.util.Vector _filterList;
+
   // ----------------/
   // - Constructors -/
   // ----------------/
@@ -50,6 +55,7 @@ public class JalviewUserColours implements java.io.Serializable
   {
     super();
     this._colourList = new java.util.Vector();
+    this._filterList = new java.util.Vector();
   }
 
   // -----------/
@@ -84,6 +90,33 @@ public class JalviewUserColours implements java.io.Serializable
   }
 
   /**
+   * 
+   * 
+   * @param vFilter
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addFilter(final Filter vFilter)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._filterList.addElement(vFilter);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vFilter
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addFilter(final int index, final Filter vFilter)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._filterList.add(index, vFilter);
+  }
+
+  /**
    * Method enumerateColour.
    * 
    * @return an Enumeration over all Colour elements
@@ -94,6 +127,16 @@ public class JalviewUserColours implements java.io.Serializable
   }
 
   /**
+   * Method enumerateFilter.
+   * 
+   * @return an Enumeration over all Filter elements
+   */
+  public java.util.Enumeration enumerateFilter()
+  {
+    return this._filterList.elements();
+  }
+
+  /**
    * Method getColour.
    * 
    * @param index
@@ -141,6 +184,53 @@ public class JalviewUserColours implements java.io.Serializable
   }
 
   /**
+   * Method getFilter.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the Filter at the given index
+   */
+  public Filter getFilter(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._filterList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "getFilter: Index value '" + index + "' not in range [0.."
+                      + (this._filterList.size() - 1) + "]");
+    }
+
+    return (Filter) _filterList.get(index);
+  }
+
+  /**
+   * Method getFilter.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public Filter[] getFilter()
+  {
+    Filter[] array = new Filter[0];
+    return (Filter[]) this._filterList.toArray(array);
+  }
+
+  /**
+   * Method getFilterCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getFilterCount()
+  {
+    return this._filterList.size();
+  }
+
+  /**
    * Returns the value of field 'schemeName'.
    * 
    * @return the value of field 'SchemeName'.
@@ -217,13 +307,20 @@ public class JalviewUserColours implements java.io.Serializable
   }
 
   /**
-     */
+   */
   public void removeAllColour()
   {
     this._colourList.clear();
   }
 
   /**
+   */
+  public void removeAllFilter()
+  {
+    this._filterList.clear();
+  }
+
+  /**
    * Method removeColour.
    * 
    * @param vColour
@@ -248,6 +345,30 @@ public class JalviewUserColours implements java.io.Serializable
   }
 
   /**
+   * Method removeFilter.
+   * 
+   * @param vFilter
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeFilter(final Filter vFilter)
+  {
+    boolean removed = _filterList.remove(vFilter);
+    return removed;
+  }
+
+  /**
+   * Method removeFilterAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public Filter removeFilterAt(final int index)
+  {
+    java.lang.Object obj = this._filterList.remove(index);
+    return (Filter) obj;
+  }
+
+  /**
    * 
    * 
    * @param index
@@ -286,6 +407,44 @@ public class JalviewUserColours implements java.io.Serializable
   }
 
   /**
+   * 
+   * 
+   * @param index
+   * @param vFilter
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setFilter(final int index, final Filter vFilter)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._filterList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "setFilter: Index value '" + index + "' not in range [0.."
+                      + (this._filterList.size() - 1) + "]");
+    }
+
+    this._filterList.set(index, vFilter);
+  }
+
+  /**
+   * 
+   * 
+   * @param vFilterArray
+   */
+  public void setFilter(final Filter[] vFilterArray)
+  {
+    // -- copy array
+    _filterList.clear();
+
+    for (int i = 0; i < vFilterArray.length; i++)
+    {
+      this._filterList.add(vFilterArray[i]);
+    }
+  }
+
+  /**
    * Sets the value of field 'schemeName'.
    * 
    * @param schemeName
diff --git a/src/jalview/binding/MatchCondition.java b/src/jalview/binding/MatchCondition.java
new file mode 100644
index 0000000..44a3d3e
--- /dev/null
+++ b/src/jalview/binding/MatchCondition.java
@@ -0,0 +1,125 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class MatchCondition.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class MatchCondition extends FeatureMatcher
+        implements java.io.Serializable
+{
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public MatchCondition()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.FeatureMatcher
+   */
+  public static jalview.binding.FeatureMatcher unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.FeatureMatcher) Unmarshaller
+            .unmarshal(jalview.binding.MatchCondition.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
+
+}
diff --git a/src/jalview/binding/MatcherSet.java b/src/jalview/binding/MatcherSet.java
new file mode 100644
index 0000000..756d93a
--- /dev/null
+++ b/src/jalview/binding/MatcherSet.java
@@ -0,0 +1,125 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class MatcherSet.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class MatcherSet extends FeatureMatcherSet
+        implements java.io.Serializable
+{
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public MatcherSet()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.binding.FeatureMatcherSet
+   */
+  public static jalview.binding.FeatureMatcherSet unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.FeatureMatcherSet) Unmarshaller
+            .unmarshal(jalview.binding.MatcherSet.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
+
+}
diff --git a/src/jalview/binding/types/ColourThreshTypeType.java b/src/jalview/binding/types/ColourThreshTypeType.java
new file mode 100644
index 0000000..024f2c0
--- /dev/null
+++ b/src/jalview/binding/types/ColourThreshTypeType.java
@@ -0,0 +1,168 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding.types;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.util.Hashtable;
+
+/**
+ * Class ColourThreshTypeType.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class ColourThreshTypeType implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * The NONE type
+     */
+    public static final int NONE_TYPE = 0;
+
+    /**
+     * The instance of the NONE type
+     */
+    public static final ColourThreshTypeType NONE = new ColourThreshTypeType(NONE_TYPE, "NONE");
+
+    /**
+     * The ABOVE type
+     */
+    public static final int ABOVE_TYPE = 1;
+
+    /**
+     * The instance of the ABOVE type
+     */
+    public static final ColourThreshTypeType ABOVE = new ColourThreshTypeType(ABOVE_TYPE, "ABOVE");
+
+    /**
+     * The BELOW type
+     */
+    public static final int BELOW_TYPE = 2;
+
+    /**
+     * The instance of the BELOW type
+     */
+    public static final ColourThreshTypeType BELOW = new ColourThreshTypeType(BELOW_TYPE, "BELOW");
+
+    /**
+     * Field _memberTable.
+     */
+    private static java.util.Hashtable _memberTable = init();
+
+    /**
+     * Field type.
+     */
+    private int type = -1;
+
+    /**
+     * Field stringValue.
+     */
+    private java.lang.String stringValue = null;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    private ColourThreshTypeType(final int type, final java.lang.String value) {
+        super();
+        this.type = type;
+        this.stringValue = value;
+    }
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method enumerate.Returns an enumeration of all possible
+     * instances of ColourThreshTypeType
+     * 
+     * @return an Enumeration over all possible instances of
+     * ColourThreshTypeType
+     */
+    public static java.util.Enumeration enumerate(
+    ) {
+        return _memberTable.elements();
+    }
+
+    /**
+     * Method getType.Returns the type of this ColourThreshTypeType
+     * 
+     * @return the type of this ColourThreshTypeType
+     */
+    public int getType(
+    ) {
+        return this.type;
+    }
+
+    /**
+     * Method init.
+     * 
+     * @return the initialized Hashtable for the member table
+     */
+    private static java.util.Hashtable init(
+    ) {
+        Hashtable members = new Hashtable();
+        members.put("NONE", NONE);
+        members.put("ABOVE", ABOVE);
+        members.put("BELOW", BELOW);
+        return members;
+    }
+
+    /**
+     * Method readResolve. will be called during deserialization to
+     * replace the deserialized object with the correct constant
+     * instance.
+     * 
+     * @return this deserialized object
+     */
+    private java.lang.Object readResolve(
+    ) {
+        return valueOf(this.stringValue);
+    }
+
+    /**
+     * Method toString.Returns the String representation of this
+     * ColourThreshTypeType
+     * 
+     * @return the String representation of this ColourThreshTypeTyp
+     */
+    public java.lang.String toString(
+    ) {
+        return this.stringValue;
+    }
+
+    /**
+     * Method valueOf.Returns a new ColourThreshTypeType based on
+     * the given String value.
+     * 
+     * @param string
+     * @return the ColourThreshTypeType value of parameter 'string'
+     */
+    public static jalview.binding.types.ColourThreshTypeType valueOf(
+            final java.lang.String string) {
+        java.lang.Object obj = null;
+        if (string != null) {
+            obj = _memberTable.get(string);
+        }
+        if (obj == null) {
+            String err = "" + string + " is not a valid ColourThreshTypeType";
+            throw new IllegalArgumentException(err);
+        }
+        return (ColourThreshTypeType) obj;
+    }
+
+}
diff --git a/src/jalview/binding/types/FeatureMatcherByType.java b/src/jalview/binding/types/FeatureMatcherByType.java
new file mode 100644
index 0000000..2185bba
--- /dev/null
+++ b/src/jalview/binding/types/FeatureMatcherByType.java
@@ -0,0 +1,168 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding.types;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.util.Hashtable;
+
+/**
+ * Class FeatureMatcherByType.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class FeatureMatcherByType implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * The byLabel type
+     */
+    public static final int BYLABEL_TYPE = 0;
+
+    /**
+     * The instance of the byLabel type
+     */
+    public static final FeatureMatcherByType BYLABEL = new FeatureMatcherByType(BYLABEL_TYPE, "byLabel");
+
+    /**
+     * The byScore type
+     */
+    public static final int BYSCORE_TYPE = 1;
+
+    /**
+     * The instance of the byScore type
+     */
+    public static final FeatureMatcherByType BYSCORE = new FeatureMatcherByType(BYSCORE_TYPE, "byScore");
+
+    /**
+     * The byAttribute type
+     */
+    public static final int BYATTRIBUTE_TYPE = 2;
+
+    /**
+     * The instance of the byAttribute type
+     */
+    public static final FeatureMatcherByType BYATTRIBUTE = new FeatureMatcherByType(BYATTRIBUTE_TYPE, "byAttribute");
+
+    /**
+     * Field _memberTable.
+     */
+    private static java.util.Hashtable _memberTable = init();
+
+    /**
+     * Field type.
+     */
+    private int type = -1;
+
+    /**
+     * Field stringValue.
+     */
+    private java.lang.String stringValue = null;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    private FeatureMatcherByType(final int type, final java.lang.String value) {
+        super();
+        this.type = type;
+        this.stringValue = value;
+    }
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method enumerate.Returns an enumeration of all possible
+     * instances of FeatureMatcherByType
+     * 
+     * @return an Enumeration over all possible instances of
+     * FeatureMatcherByType
+     */
+    public static java.util.Enumeration enumerate(
+    ) {
+        return _memberTable.elements();
+    }
+
+    /**
+     * Method getType.Returns the type of this FeatureMatcherByType
+     * 
+     * @return the type of this FeatureMatcherByType
+     */
+    public int getType(
+    ) {
+        return this.type;
+    }
+
+    /**
+     * Method init.
+     * 
+     * @return the initialized Hashtable for the member table
+     */
+    private static java.util.Hashtable init(
+    ) {
+        Hashtable members = new Hashtable();
+        members.put("byLabel", BYLABEL);
+        members.put("byScore", BYSCORE);
+        members.put("byAttribute", BYATTRIBUTE);
+        return members;
+    }
+
+    /**
+     * Method readResolve. will be called during deserialization to
+     * replace the deserialized object with the correct constant
+     * instance.
+     * 
+     * @return this deserialized object
+     */
+    private java.lang.Object readResolve(
+    ) {
+        return valueOf(this.stringValue);
+    }
+
+    /**
+     * Method toString.Returns the String representation of this
+     * FeatureMatcherByType
+     * 
+     * @return the String representation of this FeatureMatcherByTyp
+     */
+    public java.lang.String toString(
+    ) {
+        return this.stringValue;
+    }
+
+    /**
+     * Method valueOf.Returns a new FeatureMatcherByType based on
+     * the given String value.
+     * 
+     * @param string
+     * @return the FeatureMatcherByType value of parameter 'string'
+     */
+    public static jalview.binding.types.FeatureMatcherByType valueOf(
+            final java.lang.String string) {
+        java.lang.Object obj = null;
+        if (string != null) {
+            obj = _memberTable.get(string);
+        }
+        if (obj == null) {
+            String err = "" + string + " is not a valid FeatureMatcherByType";
+            throw new IllegalArgumentException(err);
+        }
+        return (FeatureMatcherByType) obj;
+    }
+
+}
diff --git a/src/jalview/binding/types/NoValueColour.java b/src/jalview/binding/types/NoValueColour.java
new file mode 100644
index 0000000..c1540f6
--- /dev/null
+++ b/src/jalview/binding/types/NoValueColour.java
@@ -0,0 +1,169 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding.types;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import java.util.Hashtable;
+
+/**
+ * Graduated feature colour if no score (or attribute) value
+ * 
+ * @version $Revision$ $Date$
+ */
+public class NoValueColour implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * The None type
+   */
+  public static final int NONE_TYPE = 0;
+
+  /**
+   * The instance of the None type
+   */
+  public static final NoValueColour NONE = new NoValueColour(NONE_TYPE,
+          "None");
+
+  /**
+   * The Min type
+   */
+  public static final int MIN_TYPE = 1;
+
+  /**
+   * The instance of the Min type
+   */
+  public static final NoValueColour MIN = new NoValueColour(MIN_TYPE,
+          "Min");
+
+  /**
+   * The Max type
+   */
+  public static final int MAX_TYPE = 2;
+
+  /**
+   * The instance of the Max type
+   */
+  public static final NoValueColour MAX = new NoValueColour(MAX_TYPE,
+          "Max");
+
+  /**
+   * Field _memberTable.
+   */
+  private static java.util.Hashtable _memberTable = init();
+
+  /**
+   * Field type.
+   */
+  private int type = -1;
+
+  /**
+   * Field stringValue.
+   */
+  private java.lang.String stringValue = null;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  private NoValueColour(final int type, final java.lang.String value)
+  {
+    super();
+    this.type = type;
+    this.stringValue = value;
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method enumerate.Returns an enumeration of all possible instances of
+   * NoValueColour
+   * 
+   * @return an Enumeration over all possible instances of NoValueColour
+   */
+  public static java.util.Enumeration enumerate()
+  {
+    return _memberTable.elements();
+  }
+
+  /**
+   * Method getType.Returns the type of this NoValueColour
+   * 
+   * @return the type of this NoValueColour
+   */
+  public int getType()
+  {
+    return this.type;
+  }
+
+  /**
+   * Method init.
+   * 
+   * @return the initialized Hashtable for the member table
+   */
+  private static java.util.Hashtable init()
+  {
+    Hashtable members = new Hashtable();
+    members.put("None", NONE);
+    members.put("Min", MIN);
+    members.put("Max", MAX);
+    return members;
+  }
+
+  /**
+   * Method readResolve. will be called during deserialization to replace the
+   * deserialized object with the correct constant instance.
+   * 
+   * @return this deserialized object
+   */
+  private java.lang.Object readResolve()
+  {
+    return valueOf(this.stringValue);
+  }
+
+  /**
+   * Method toString.Returns the String representation of this NoValueColour
+   * 
+   * @return the String representation of this NoValueColour
+   */
+  public java.lang.String toString()
+  {
+    return this.stringValue;
+  }
+
+  /**
+   * Method valueOf.Returns a new NoValueColour based on the given String value.
+   * 
+   * @param string
+   * @return the NoValueColour value of parameter 'string'
+   */
+  public static jalview.binding.types.NoValueColour valueOf(
+          final java.lang.String string)
+  {
+    java.lang.Object obj = null;
+    if (string != null)
+    {
+      obj = _memberTable.get(string);
+    }
+    if (obj == null)
+    {
+      String err = "" + string + " is not a valid NoValueColour";
+      throw new IllegalArgumentException(err);
+    }
+    return (NoValueColour) obj;
+  }
+
+}
diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 5662d0c..d992e4e 100644
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -352,25 +352,25 @@ public class AlignViewController implements AlignViewControllerI
   public boolean parseFeaturesFile(String file, DataSourceType protocol,
           boolean relaxedIdMatching)
   {
-    boolean featuresFile = false;
+    boolean featuresAdded = false;
+    FeatureRenderer fr = alignPanel.getFeatureRenderer();
     try
     {
-      featuresFile = new FeaturesFile(false, file, protocol).parse(
-              viewport.getAlignment().getDataset(),
-              alignPanel.getFeatureRenderer().getFeatureColours(), false,
-              relaxedIdMatching);
+      featuresAdded = new FeaturesFile(false, file, protocol).parse(
+              viewport.getAlignment().getDataset(), fr.getFeatureColours(),
+              fr.getFeatureFilters(), false, relaxedIdMatching);
     } catch (Exception ex)
     {
       ex.printStackTrace();
     }
 
-    if (featuresFile)
+    if (featuresAdded)
     {
       avcg.refreshFeatureUI(true);
-      if (alignPanel.getFeatureRenderer() != null)
+      if (fr != null)
       {
         // update the min/max ranges where necessary
-        alignPanel.getFeatureRenderer().findAllFeatures(true);
+        fr.findAllFeatures(true);
       }
       if (avcg.getFeatureSettingsUI() != null)
       {
@@ -379,7 +379,7 @@ public class AlignViewController implements AlignViewControllerI
       alignPanel.paintAlignment(true, true);
     }
 
-    return featuresFile;
+    return featuresAdded;
 
   }
 
diff --git a/src/jalview/datamodel/features/FeatureMatcher.java b/src/jalview/datamodel/features/FeatureMatcher.java
index b86468d..f844141 100644
--- a/src/jalview/datamodel/features/FeatureMatcher.java
+++ b/src/jalview/datamodel/features/FeatureMatcher.java
@@ -23,6 +23,14 @@ import jalview.util.matcher.MatcherI;
  */
 public class FeatureMatcher implements FeatureMatcherI
 {
+  private static final String SCORE = "Score";
+
+  private static final String LABEL = "Label";
+
+  private static final String SPACE = " ";
+
+  private static final String QUOTE = "'";
+
   /*
    * a dummy matcher that comes in useful for the 'add a filter' gui row
    */
@@ -49,12 +57,188 @@ public class FeatureMatcher implements FeatureMatcherI
   final private MatcherI matcher;
 
   /**
+   * A helper method that converts a 'compound' attribute name from its display
+   * form, e.g. CSQ:PolyPhen to array form, e.g. { "CSQ", "PolyPhen" }
+   * 
+   * @param attribute
+   * @return
+   */
+  public static String[] fromAttributeDisplayName(String attribute)
+  {
+    return attribute == null ? null : attribute.split(COLON);
+  }
+
+  /**
+   * A helper method that converts a 'compound' attribute name to its display
+   * form, e.g. CSQ:PolyPhen from its array form, e.g. { "CSQ", "PolyPhen" }
+   * 
+   * @param attName
+   * @return
+   */
+  public static String toAttributeDisplayName(String[] attName)
+  {
+    return attName == null ? "" : String.join(COLON, attName);
+  }
+
+  /**
+   * A factory constructor that converts a stringified object (as output by
+   * toStableString) to an object instance. Returns null if parsing fails.
+   * <p>
+   * Leniency in parsing (for manually created feature files):
+   * <ul>
+   * <li>keywords Score and Label, and the condition, are not
+   * case-sensitive</li>
+   * <li>quotes around value and pattern are optional if string does not include
+   * a space</li>
+   * </ul>
+   * 
+   * @param descriptor
+   * @return
+   */
+  public static FeatureMatcher fromString(final String descriptor)
+  {
+    String invalidFormat = "Invalid matcher format: " + descriptor;
+
+    /*
+     * expect 
+     * value condition pattern
+     * where value is Label or Space or attributeName or attName1:attName2
+     * and pattern is a float value as string, or a text string
+     * attribute names or patterns may be quoted (must be if include space)
+     */
+    String attName = null;
+    boolean byScore = false;
+    boolean byLabel = false;
+    Condition cond = null;
+    String pattern = null;
+
+    /*
+     * parse first field (Label / Score / attribute)
+     * optionally in quotes (required if attName includes space)
+     */
+    String leftToParse = descriptor;
+    String firstField = null;
+
+    if (descriptor.startsWith(QUOTE))
+    {
+      // 'Label' / 'Score' / 'attName'
+      int nextQuotePos = descriptor.indexOf(QUOTE, 1);
+      if (nextQuotePos == -1)
+      {
+        System.err.println(invalidFormat);
+        return null;
+      }
+      firstField = descriptor.substring(1, nextQuotePos);
+      leftToParse = descriptor.substring(nextQuotePos + 1).trim();
+    }
+    else
+    {
+      // Label / Score / attName (unquoted)
+      int nextSpacePos = descriptor.indexOf(SPACE);
+      if (nextSpacePos == -1)
+      {
+        System.err.println(invalidFormat);
+        return null;
+      }
+      firstField = descriptor.substring(0, nextSpacePos);
+      leftToParse = descriptor.substring(nextSpacePos + 1).trim();
+    }
+    String lower = firstField.toLowerCase();
+    if (lower.startsWith(LABEL.toLowerCase()))
+    {
+      byLabel = true;
+    }
+    else if (lower.startsWith(SCORE.toLowerCase()))
+    {
+      byScore = true;
+    }
+    else
+    {
+      attName = firstField;
+    }
+
+    /*
+     * next field is the comparison condition
+     * most conditions require a following pattern (optionally quoted)
+     * although some conditions e.g. Present do not
+     */
+    int nextSpacePos = leftToParse.indexOf(SPACE);
+    if (nextSpacePos == -1)
+    {
+      /*
+       * no value following condition - only valid for some conditions
+       */
+      cond = Condition.fromString(leftToParse);
+      if (cond == null || cond.needsAPattern())
+      {
+        System.err.println(invalidFormat);
+        return null;
+      }
+    }
+    else
+    {
+      /*
+       * condition and pattern
+       */
+      cond = Condition.fromString(leftToParse.substring(0, nextSpacePos));
+      leftToParse = leftToParse.substring(nextSpacePos + 1).trim();
+      if (leftToParse.startsWith(QUOTE))
+      {
+        // pattern in quotes
+        if (leftToParse.endsWith(QUOTE))
+        {
+          pattern = leftToParse.substring(1, leftToParse.length() - 1);
+        }
+        else
+        {
+          // unbalanced quote
+          System.err.println(invalidFormat);
+          return null;
+        }
+      }
+      else
+      {
+        // unquoted pattern
+        pattern = leftToParse;
+      }
+    }
+
+    /*
+     * we have parsed out value, condition and pattern
+     * so can now make the FeatureMatcher
+     */
+    try
+    {
+      if (byLabel)
+      {
+        return FeatureMatcher.byLabel(cond, pattern);
+      }
+      else if (byScore)
+      {
+        return FeatureMatcher.byScore(cond, pattern);
+      }
+      else
+      {
+        String[] attNames = FeatureMatcher
+                .fromAttributeDisplayName(attName);
+        return FeatureMatcher.byAttribute(cond, pattern, attNames);
+      }
+    } catch (NumberFormatException e)
+    {
+      // numeric condition with non-numeric pattern
+      return null;
+    }
+  }
+
+  /**
    * A factory constructor method for a matcher that applies its match condition
    * to the feature label (description)
    * 
    * @param cond
    * @param pattern
    * @return
+   * @throws NumberFormatException
+   *           if an invalid numeric pattern is supplied
    */
   public static FeatureMatcher byLabel(Condition cond, String pattern)
   {
@@ -69,6 +253,8 @@ public class FeatureMatcher implements FeatureMatcherI
    * @param cond
    * @param pattern
    * @return
+   * @throws NumberFormatException
+   *           if an invalid numeric pattern is supplied
    */
   public static FeatureMatcher byScore(Condition cond, String pattern)
   {
@@ -84,6 +270,8 @@ public class FeatureMatcher implements FeatureMatcherI
    * @param pattern
    * @param attName
    * @return
+   * @throws NumberFormatException
+   *           if an invalid numeric pattern is supplied
    */
   public static FeatureMatcher byAttribute(Condition cond, String pattern,
           String... attName)
@@ -143,14 +331,14 @@ public class FeatureMatcher implements FeatureMatcherI
     }
 
     Condition condition = matcher.getCondition();
-    sb.append(" ").append(condition.toString().toLowerCase());
+    sb.append(SPACE).append(condition.toString().toLowerCase());
     if (condition.isNumeric())
     {
-      sb.append(" ").append(matcher.getPattern());
+      sb.append(SPACE).append(matcher.getPattern());
     }
     else if (condition.needsAPattern())
     {
-      sb.append(" '").append(matcher.getPattern()).append("'");
+      sb.append(" '").append(matcher.getPattern()).append(QUOTE);
     }
 
     return sb.toString();
@@ -167,4 +355,63 @@ public class FeatureMatcher implements FeatureMatcherI
   {
     return byScore;
   }
+
+  @Override
+  public boolean isByAttribute()
+  {
+    return getAttribute() != null;
+  }
+
+  /**
+   * {@inheritDoc} The output of this method should be parseable by method
+   * <code>fromString<code> to restore the original object.
+   */
+  @Override
+  public String toStableString()
+  {
+    StringBuilder sb = new StringBuilder();
+    if (byLabel)
+    {
+      sb.append(LABEL); // no i18n here unlike toString() !
+    }
+    else if (byScore)
+    {
+      sb.append(SCORE);
+    }
+    else
+    {
+      /*
+       * enclose attribute name in quotes if it includes space
+       */
+      String displayName = toAttributeDisplayName(key);
+      if (displayName.contains(SPACE))
+      {
+        sb.append(QUOTE).append(displayName).append(QUOTE);
+      }
+      else
+      {
+        sb.append(displayName);
+      }
+    }
+  
+    Condition condition = matcher.getCondition();
+    sb.append(SPACE).append(condition.getStableName());
+    String pattern = matcher.getPattern();
+    if (condition.needsAPattern())
+    {
+      /*
+       * enclose pattern in quotes if it includes space
+       */
+      if (pattern.contains(SPACE))
+      {
+        sb.append(SPACE).append(QUOTE).append(pattern).append(QUOTE);
+      }
+      else
+      {
+        sb.append(SPACE).append(pattern);
+      }
+    }
+  
+    return sb.toString();
+  }
 }
diff --git a/src/jalview/datamodel/features/FeatureMatcherI.java b/src/jalview/datamodel/features/FeatureMatcherI.java
index 07b060c..f1f8585 100644
--- a/src/jalview/datamodel/features/FeatureMatcherI.java
+++ b/src/jalview/datamodel/features/FeatureMatcherI.java
@@ -43,9 +43,23 @@ public interface FeatureMatcherI
   boolean isByScore();
 
   /**
+   * Answers true if match is against a feature attribute (text or range)
+   * 
+   * @return
+   */
+  boolean isByAttribute();
+
+  /**
    * Answers the match condition that is applied
    * 
    * @return
    */
   MatcherI getMatcher();
+
+  /**
+   * Answers a string representation of this object suitable for use when
+   * persisting data, in a format that can be reliably read back. Any changes to
+   * the format should be backwards compatible.
+   */
+  String toStableString();
 }
diff --git a/src/jalview/datamodel/features/FeatureMatcherSet.java b/src/jalview/datamodel/features/FeatureMatcherSet.java
index eb55387..b51f2f0 100644
--- a/src/jalview/datamodel/features/FeatureMatcherSet.java
+++ b/src/jalview/datamodel/features/FeatureMatcherSet.java
@@ -6,8 +6,24 @@ import jalview.util.MessageManager;
 import java.util.ArrayList;
 import java.util.List;
 
+/**
+ * A class that models one or more match conditions, which may be combined with
+ * AND or OR (but not a mixture)
+ * 
+ * @author gmcarstairs
+ */
 public class FeatureMatcherSet implements FeatureMatcherSetI
 {
+  private static final String OR = "OR";
+
+  private static final String AND = "AND";
+
+  private static final String SPACE = " ";
+
+  private static final String CLOSE_BRACKET = ")";
+
+  private static final String OPEN_BRACKET = "(";
+
   private static final String OR_I18N = MessageManager
           .getString("label.or");
 
@@ -19,6 +35,112 @@ public class FeatureMatcherSet implements FeatureMatcherSetI
   boolean andConditions;
 
   /**
+   * A factory constructor that converts a stringified object (as output by
+   * toStableString) to an object instance.
+   * 
+   * Format:
+   * <ul>
+   * <li>(condition1) AND (condition2) AND (condition3)</li>
+   * <li>or</li>
+   * <li>(condition1) OR (condition2) OR (condition3)</li>
+   * </ul>
+   * where OR and AND are not case-sensitive, and may not be mixed. Brackets are
+   * optional if there is only one condition.
+   * 
+   * @param descriptor
+   * @return
+   * @see FeatureMatcher#fromString(String)
+   */
+  public static FeatureMatcherSet fromString(final String descriptor)
+  {
+    String invalid = "Invalid descriptor: " + descriptor;
+    boolean firstCondition = true;
+    FeatureMatcherSet result = new FeatureMatcherSet();
+
+    String leftToParse = descriptor.trim();
+
+    while (leftToParse.length() > 0)
+    {
+      /*
+       * inspect AND or OR condition, check not mixed
+       */
+      boolean and = true;
+      if (!firstCondition)
+      {
+        int spacePos = leftToParse.indexOf(SPACE);
+        if (spacePos == -1)
+        {
+          // trailing junk after a match condition
+          System.err.println(invalid);
+          return null;
+        }
+        String conjunction = leftToParse.substring(0, spacePos);
+        leftToParse = leftToParse.substring(spacePos + 1).trim();
+        if (conjunction.equalsIgnoreCase(AND))
+        {
+          and = true;
+        }
+        else if (conjunction.equalsIgnoreCase(OR))
+        {
+          and = false;
+        }
+        else
+        {
+          // not an AND or an OR - invalid
+          System.err.println(invalid);
+          return null;
+        }
+      }
+
+      /*
+       * now extract the next condition and AND or OR it
+       */
+      String nextCondition = leftToParse;
+      if (leftToParse.startsWith(OPEN_BRACKET))
+      {
+        int closePos = leftToParse.indexOf(CLOSE_BRACKET);
+        if (closePos == -1)
+        {
+          System.err.println(invalid);
+          return null;
+        }
+        nextCondition = leftToParse.substring(1, closePos);
+        leftToParse = leftToParse.substring(closePos + 1).trim();
+      }
+      else
+      {
+        leftToParse = "";
+      }
+
+      FeatureMatcher fm = FeatureMatcher.fromString(nextCondition);
+      if (fm == null)
+      {
+        System.err.println(invalid);
+        return null;
+      }
+      try
+      {
+        if (and)
+        {
+          result.and(fm);
+        }
+        else
+        {
+          result.or(fm);
+        }
+        firstCondition = false;
+      } catch (IllegalStateException e)
+      {
+        // thrown if OR and AND are mixed
+        System.err.println(invalid);
+        return null;
+      }
+
+    }
+    return result;
+  }
+
+  /**
    * Constructor
    */
   public FeatureMatcherSet()
@@ -66,7 +188,7 @@ public class FeatureMatcherSet implements FeatureMatcherSetI
   }
 
   @Override
-  public FeatureMatcherSetI and(FeatureMatcherI m)
+  public void and(FeatureMatcherI m)
   {
     if (!andConditions && matchConditions.size() > 1)
     {
@@ -74,12 +196,10 @@ public class FeatureMatcherSet implements FeatureMatcherSetI
     }
     matchConditions.add(m);
     andConditions = true;
-
-    return this;
   }
 
   @Override
-  public FeatureMatcherSetI or(FeatureMatcherI m)
+  public void or(FeatureMatcherI m)
   {
     if (andConditions && matchConditions.size() > 1)
     {
@@ -87,8 +207,6 @@ public class FeatureMatcherSet implements FeatureMatcherSetI
     }
     matchConditions.add(m);
     andConditions = false;
-
-    return this;
   }
 
   @Override
@@ -103,20 +221,34 @@ public class FeatureMatcherSet implements FeatureMatcherSetI
     return matchConditions;
   }
 
+  /**
+   * Answers a string representation of this object suitable for display, and
+   * possibly internationalized. The format is not guaranteed stable and may
+   * change in future.
+   */
   @Override
   public String toString()
   {
     StringBuilder sb = new StringBuilder();
     boolean first = true;
+    boolean multiple = matchConditions.size() > 1;
     for (FeatureMatcherI matcher : matchConditions)
     {
       if (!first)
       {
         String joiner = andConditions ? AND_18N : OR_I18N;
-        sb.append(" ").append(joiner.toLowerCase()).append(" ");
+        sb.append(SPACE).append(joiner.toLowerCase()).append(SPACE);
       }
       first = false;
-      sb.append("(").append(matcher.toString()).append(")");
+      if (multiple)
+      {
+        sb.append(OPEN_BRACKET).append(matcher.toString())
+                .append(CLOSE_BRACKET);
+      }
+      else
+      {
+        sb.append(matcher.toString());
+      }
     }
     return sb.toString();
   }
@@ -127,4 +259,36 @@ public class FeatureMatcherSet implements FeatureMatcherSetI
     return matchConditions == null || matchConditions.isEmpty();
   }
 
+  /**
+   * {@inheritDoc} The output of this method should be parseable by method
+   * <code>fromString<code> to restore the original object.
+   */
+  @Override
+  public String toStableString()
+  {
+    StringBuilder sb = new StringBuilder();
+    boolean moreThanOne = matchConditions.size() > 1;
+    boolean first = true;
+
+    for (FeatureMatcherI matcher : matchConditions)
+    {
+      if (!first)
+      {
+        String joiner = andConditions ? AND : OR;
+        sb.append(SPACE).append(joiner).append(SPACE);
+      }
+      first = false;
+      if (moreThanOne)
+      {
+        sb.append(OPEN_BRACKET).append(matcher.toStableString())
+                .append(CLOSE_BRACKET);
+      }
+      else
+      {
+        sb.append(matcher.toStableString());
+      }
+    }
+    return sb.toString();
+  }
+
 }
diff --git a/src/jalview/datamodel/features/FeatureMatcherSetI.java b/src/jalview/datamodel/features/FeatureMatcherSetI.java
index f064770..90c2986 100644
--- a/src/jalview/datamodel/features/FeatureMatcherSetI.java
+++ b/src/jalview/datamodel/features/FeatureMatcherSetI.java
@@ -20,14 +20,13 @@ public interface FeatureMatcherSetI
   boolean matches(SequenceFeature feature);
 
   /**
-   * Answers a new object that matches the logical AND of this and m
+   * Adds (ANDs) match condition m to this object's matcher set
    * 
    * @param m
-   * @return
    * @throws IllegalStateException
    *           if an attempt is made to AND to existing OR-ed conditions
    */
-  FeatureMatcherSetI and(FeatureMatcherI m);
+  void and(FeatureMatcherI m);
 
   /**
    * Answers true if any second condition is AND-ed with this one, false if it
@@ -38,14 +37,13 @@ public interface FeatureMatcherSetI
   boolean isAnded();
 
   /**
-   * Answers a new object that matches the logical OR of this and m
+   * Adds (ORs) the given condition to this object's match conditions
    * 
    * @param m
-   * @return
    * @throws IllegalStateException
    *           if an attempt is made to OR to existing AND-ed conditions
    */
-  FeatureMatcherSetI or(FeatureMatcherI m);
+  void or(FeatureMatcherI m);
 
   /**
    * Answers an iterator over the combined match conditions
@@ -60,4 +58,11 @@ public interface FeatureMatcherSetI
    * @return
    */
   boolean isEmpty();
+
+  /**
+   * Answers a string representation of this object suitable for use when
+   * persisting data, in a format that can be reliably read back. Any changes to
+   * the format should be backwards compatible.
+   */
+  String toStableString();
 }
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 8a44f27..4c9360e 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1392,13 +1392,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void exportFeatures_actionPerformed(ActionEvent e)
   {
-    new AnnotationExporter().exportFeatures(alignPanel);
+    new AnnotationExporter(alignPanel).exportFeatures();
   }
 
   @Override
   public void exportAnnotations_actionPerformed(ActionEvent e)
   {
-    new AnnotationExporter().exportAnnotations(alignPanel);
+    new AnnotationExporter(alignPanel).exportAnnotations();
   }
 
   @Override
diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java
index 020e027..6924b63 100644
--- a/src/jalview/gui/AnnotationColumnChooser.java
+++ b/src/jalview/gui/AnnotationColumnChooser.java
@@ -36,7 +36,6 @@ import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
 import java.awt.event.KeyEvent;
-import java.util.ArrayList;
 
 import javax.swing.ButtonGroup;
 import javax.swing.JCheckBox;
@@ -241,16 +240,6 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
       {
         HiddenColumns oldHidden = av.getAnnotationColumnSelectionState()
                 .getOldHiddenColumns();
-        if (oldHidden != null)
-        {
-          ArrayList<int[]> regions = oldHidden.getHiddenColumnsCopy();
-          for (int[] positions : regions)
-          {
-            av.hideColumns(positions[0], positions[1]);
-          }
-        }
-        // TODO not clear why we need to hide all the columns (above) if we are
-        // going to copy the hidden columns over wholesale anyway
         av.getAlignment().setHiddenColumns(oldHidden);
       }
       av.sendSelection();
diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index a619997..6fefbd0 100644
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -21,8 +21,10 @@
 package jalview.gui;
 
 import jalview.api.FeatureColourI;
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcherSetI;
 import jalview.io.AnnotationFile;
 import jalview.io.FeaturesFile;
 import jalview.io.JalviewFileChooser;
@@ -34,6 +36,8 @@ import java.awt.Color;
 import java.awt.FlowLayout;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.io.FileWriter;
+import java.io.PrintWriter;
 import java.util.List;
 import java.util.Map;
 
@@ -57,18 +61,22 @@ import javax.swing.SwingConstants;
  */
 public class AnnotationExporter extends JPanel
 {
-  JInternalFrame frame;
+  private JInternalFrame frame;
 
-  AlignmentPanel ap;
+  private AlignmentPanel ap;
 
-  boolean features = true;
+  /*
+   * true if exporting features, false if exporting annotations
+   */
+  private boolean exportFeatures = true;
 
   private AlignmentAnnotation[] annotations;
 
   private boolean wholeView;
 
-  public AnnotationExporter()
+  public AnnotationExporter(AlignmentPanel panel)
   {
+    this.ap = panel;
     try
     {
       jbInit();
@@ -84,47 +92,54 @@ public class AnnotationExporter extends JPanel
             frame.getPreferredSize().height);
   }
 
-  public void exportFeatures(AlignmentPanel ap)
+  /**
+   * Configures the diglog for options to export visible features
+   */
+  public void exportFeatures()
   {
-    this.ap = ap;
-    features = true;
+    exportFeatures = true;
     CSVFormat.setVisible(false);
     frame.setTitle(MessageManager.getString("label.export_features"));
   }
 
-  public void exportAnnotations(AlignmentPanel ap)
+  /**
+   * Configures the dialog for options to export all visible annotations
+   */
+  public void exportAnnotations()
   {
-    this.ap = ap;
-    annotations = ap.av.isShowAnnotation() ? null
-            : ap.av.getAlignment().getAlignmentAnnotation();
-    wholeView = true;
-    startExportAnnotation();
+    boolean showAnnotation = ap.av.isShowAnnotation();
+    exportAnnotation(showAnnotation ? null
+            : ap.av.getAlignment().getAlignmentAnnotation(), true);
   }
 
-  public void exportAnnotations(AlignmentPanel alp,
-          AlignmentAnnotation[] toExport)
+  /**
+   * Configures the dialog for options to export the given annotation row
+   * 
+   * @param toExport
+   */
+  public void exportAnnotation(AlignmentAnnotation toExport)
   {
-    ap = alp;
-    annotations = toExport;
-    wholeView = false;
-    startExportAnnotation();
+    exportAnnotation(new AlignmentAnnotation[] { toExport }, false);
   }
 
-  private void startExportAnnotation()
+  private void exportAnnotation(AlignmentAnnotation[] toExport,
+          boolean forWholeView)
   {
-    features = false;
+    wholeView = forWholeView;
+    annotations = toExport;
+    exportFeatures = false;
     GFFFormat.setVisible(false);
     CSVFormat.setVisible(true);
     frame.setTitle(MessageManager.getString("label.export_annotations"));
   }
 
-  public void toFile_actionPerformed(ActionEvent e)
+  private void toFile_actionPerformed()
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+            Cache.getProperty("LAST_DIRECTORY"));
 
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(features
+    chooser.setDialogTitle(exportFeatures
             ? MessageManager.getString("label.save_features_to_file")
             : MessageManager.getString("label.save_annotation_to_file"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
@@ -133,13 +148,12 @@ public class AnnotationExporter extends JPanel
 
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-      String text = getFileContents();
+      String text = getText();
 
       try
       {
-        java.io.PrintWriter out = new java.io.PrintWriter(
-                new java.io.FileWriter(chooser.getSelectedFile()));
-
+        PrintWriter out = new PrintWriter(
+                new FileWriter(chooser.getSelectedFile()));
         out.print(text);
         out.close();
       } catch (Exception ex)
@@ -148,64 +162,89 @@ public class AnnotationExporter extends JPanel
       }
     }
 
-    close_actionPerformed(null);
+    close_actionPerformed();
+  }
+
+  /**
+   * Answers the text to output for either Features (in GFF or Jalview format) or
+   * Annotations (in CSV or Jalview format)
+   * 
+   * @return
+   */
+  private String getText()
+  {
+    return exportFeatures ? getFeaturesText() : getAnnotationsText();
   }
 
-  private String getFileContents()
+  /**
+   * Returns the text contents for output of annotations in either CSV or Jalview
+   * format
+   * 
+   * @return
+   */
+  private String getAnnotationsText()
   {
-    String text = MessageManager
-            .getString("label.no_features_on_alignment");
-    if (features)
+    String text;
+    if (CSVFormat.isSelected())
     {
-      FeaturesFile formatter = new FeaturesFile();
-      SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
-      Map<String, FeatureColourI> featureColours = ap.getFeatureRenderer()
-              .getDisplayedFeatureCols();
-      List<String> featureGroups = ap.getFeatureRenderer()
-              .getDisplayedFeatureGroups();
-      boolean includeNonPositional = ap.av.isShowNPFeats();
-      if (GFFFormat.isSelected())
-      {
-        text = formatter.printGffFormat(sequences, featureColours,
-                featureGroups, includeNonPositional);
-      }
-      else
-      {
-        text = formatter.printJalviewFormat(sequences, featureColours,
-                featureGroups, includeNonPositional);
-      }
+      text = new AnnotationFile().printCSVAnnotations(annotations);
     }
     else
     {
-      if (CSVFormat.isSelected())
+      if (wholeView)
       {
-        text = new AnnotationFile().printCSVAnnotations(annotations);
+        text = new AnnotationFile().printAnnotationsForView(ap.av);
       }
       else
       {
-        if (wholeView)
-        {
-          text = new AnnotationFile().printAnnotationsForView(ap.av);
-        }
-        else
-        {
-          text = new AnnotationFile().printAnnotations(annotations, null,
-                  null);
-        }
+        text = new AnnotationFile().printAnnotations(annotations, null,
+                null);
       }
     }
     return text;
   }
 
-  public void toTextbox_actionPerformed(ActionEvent e)
+  /**
+   * Returns the text contents for output of features in either GFF or Jalview
+   * format
+   * 
+   * @return
+   */
+  private String getFeaturesText()
+  {
+    String text;
+    SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
+    Map<String, FeatureColourI> featureColours = ap.getFeatureRenderer()
+            .getDisplayedFeatureCols();
+    Map<String, FeatureMatcherSetI> featureFilters = ap.getFeatureRenderer()
+            .getFeatureFilters();
+    List<String> featureGroups = ap.getFeatureRenderer()
+            .getDisplayedFeatureGroups();
+    boolean includeNonPositional = ap.av.isShowNPFeats();
+
+    FeaturesFile formatter = new FeaturesFile();
+    if (GFFFormat.isSelected())
+    {
+      text = formatter.printGffFormat(sequences, featureColours,
+              featureGroups, includeNonPositional);
+    }
+    else
+    {
+      text = formatter.printJalviewFormat(sequences, featureColours,
+              featureFilters, featureGroups, includeNonPositional);
+    }
+    return text;
+  }
+
+  private void toTextbox_actionPerformed()
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
 
     try
     {
-      String text = getFileContents();
+      String text = getText();
       cap.setText(text);
-      Desktop.addInternalFrame(cap, (features ? MessageManager
+      Desktop.addInternalFrame(cap, (exportFeatures ? MessageManager
               .formatMessage("label.features_for_params", new String[]
               { ap.alignFrame.getTitle() })
               : MessageManager.formatMessage("label.annotations_for_params",
@@ -214,7 +253,7 @@ public class AnnotationExporter extends JPanel
               600, 500);
     } catch (OutOfMemoryError oom)
     {
-      new OOMWarning((features ? MessageManager.formatMessage(
+      new OOMWarning((exportFeatures ? MessageManager.formatMessage(
               "label.generating_features_for_params", new String[]
               { ap.alignFrame.getTitle() })
               : MessageManager.formatMessage(
@@ -225,10 +264,10 @@ public class AnnotationExporter extends JPanel
       cap.dispose();
     }
 
-    close_actionPerformed(null);
+    close_actionPerformed();
   }
 
-  public void close_actionPerformed(ActionEvent e)
+  private void close_actionPerformed()
   {
     try
     {
@@ -248,7 +287,7 @@ public class AnnotationExporter extends JPanel
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        toFile_actionPerformed(e);
+        toFile_actionPerformed();
       }
     });
     toTextbox.setText(MessageManager.getString("label.to_textbox"));
@@ -257,7 +296,7 @@ public class AnnotationExporter extends JPanel
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        toTextbox_actionPerformed(e);
+        toTextbox_actionPerformed();
       }
     });
     close.setText(MessageManager.getString("action.close"));
@@ -266,7 +305,7 @@ public class AnnotationExporter extends JPanel
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        close_actionPerformed(e);
+        close_actionPerformed();
       }
     });
     jalviewFormat.setOpaque(false);
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index b94a615..de69907 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -266,9 +266,7 @@ public class AnnotationLabels extends JPanel
     }
     else if (evt.getActionCommand().equals(OUTPUT_TEXT))
     {
-      new AnnotationExporter().exportAnnotations(ap,
-              new AlignmentAnnotation[]
-              { aa[selectedRow] });
+      new AnnotationExporter(ap).exportAnnotation(aa[selectedRow]);
     }
     else if (evt.getActionCommand().equals(COPYCONS_SEQ))
     {
diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 4b4f363..1dbc9b8 100644
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -22,20 +22,20 @@ package jalview.gui;
 
 import jalview.api.FeatureColourI;
 import jalview.api.FeatureSettingsControllerI;
-import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcherI;
 import jalview.datamodel.features.FeatureMatcherSet;
 import jalview.datamodel.features.FeatureMatcherSetI;
 import jalview.gui.Help.HelpId;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
+import jalview.schemabinding.version2.Filter;
 import jalview.schemabinding.version2.JalviewUserColours;
+import jalview.schemabinding.version2.MatcherSet;
 import jalview.schemes.FeatureColour;
-import jalview.util.Format;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
-import jalview.util.QuickSort;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
 import jalview.ws.DasSequenceFeatureFetcher;
@@ -66,6 +66,8 @@ import java.io.InputStreamReader;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
 import java.util.Arrays;
+import java.util.Comparator;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.Iterator;
@@ -105,6 +107,9 @@ import javax.swing.table.TableColumn;
 public class FeatureSettings extends JPanel
         implements FeatureSettingsControllerI
 {
+  private static final String SEQUENCE_FEATURE_COLOURS = MessageManager
+          .getString("label.sequence_feature_colours");
+
   /*
    * column indices of fields in Feature Settings table
    */
@@ -191,7 +196,7 @@ public class FeatureSettings extends JPanel
     int originalTransparencyAsPercent = (int) (originalTransparency * 100);
     transparency.setMaximum(100 - originalTransparencyAsPercent);
 
-    originalFilters = fr.getFeatureFilters();
+    originalFilters = new HashMap<>(fr.getFeatureFilters()); // shallow copy
 
     try
     {
@@ -850,10 +855,14 @@ public class FeatureSettings extends JPanel
     }
   }
 
+  /**
+   * Offers a file chooser dialog, and then loads the feature colours and
+   * filters from file in XML format and unmarshals to Jalview feature settings
+   */
   void load()
   {
     JalviewFileChooser chooser = new JalviewFileChooser("fc",
-            "Sequence Feature Colours");
+            SEQUENCE_FEATURE_COLOURS);
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(
             MessageManager.getString("label.load_feature_colours"));
@@ -864,88 +873,78 @@ public class FeatureSettings extends JPanel
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       File file = chooser.getSelectedFile();
+      load(file);
+    }
+  }
 
-      try
-      {
-        InputStreamReader in = new InputStreamReader(
-                new FileInputStream(file), "UTF-8");
+  /**
+   * Loads feature colours and filters from XML stored in the given file
+   * 
+   * @param file
+   */
+  void load(File file)
+  {
+    try
+    {
+      InputStreamReader in = new InputStreamReader(
+              new FileInputStream(file), "UTF-8");
 
-        JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
+      JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
 
-        for (int i = jucs.getColourCount() - 1; i >= 0; i--)
-        {
-          String name;
-          jalview.schemabinding.version2.Colour newcol = jucs.getColour(i);
-          if (newcol.hasMax())
-          {
-            Color mincol = null, maxcol = null;
-            try
-            {
-              mincol = new Color(Integer.parseInt(newcol.getMinRGB(), 16));
-              maxcol = new Color(Integer.parseInt(newcol.getRGB(), 16));
+      /*
+       * load feature colours
+       */
+      for (int i = jucs.getColourCount() - 1; i >= 0; i--)
+      {
+        jalview.schemabinding.version2.Colour newcol = jucs.getColour(i);
+        FeatureColourI colour = Jalview2XML.unmarshalColour(newcol);
+        fr.setColour(newcol.getName(), colour);
+        fr.setOrder(newcol.getName(), i / (float) jucs.getColourCount());
+      }
 
-            } catch (Exception e)
-            {
-              Cache.log.warn("Couldn't parse out graduated feature color.",
-                      e);
-            }
-            FeatureColourI gcol = new FeatureColour(mincol, maxcol,
-                    newcol.getMin(), newcol.getMax());
-            if (newcol.hasAutoScale())
-            {
-              gcol.setAutoScaled(newcol.getAutoScale());
-            }
-            if (newcol.hasColourByLabel())
-            {
-              gcol.setColourByLabel(newcol.getColourByLabel());
-            }
-            if (newcol.hasThreshold())
-            {
-              gcol.setThreshold(newcol.getThreshold());
-            }
-            if (newcol.getThreshType().length() > 0)
-            {
-              String ttyp = newcol.getThreshType();
-              if (ttyp.equalsIgnoreCase("ABOVE"))
-              {
-                gcol.setAboveThreshold(true);
-              }
-              if (ttyp.equalsIgnoreCase("BELOW"))
-              {
-                gcol.setBelowThreshold(true);
-              }
-            }
-            fr.setColour(name = newcol.getName(), gcol);
-          }
-          else
-          {
-            Color color = new Color(
-                    Integer.parseInt(jucs.getColour(i).getRGB(), 16));
-            fr.setColour(name = jucs.getColour(i).getName(),
-                    new FeatureColour(color));
-          }
-          fr.setOrder(name, (i == 0) ? 0 : i / jucs.getColourCount());
-        }
-        if (table != null)
+      /*
+       * load feature filters; loaded filters will replace any that are
+       * currently defined, other defined filters are left unchanged 
+       */
+      for (int i = 0; i < jucs.getFilterCount(); i++)
+      {
+        jalview.schemabinding.version2.Filter filterModel = jucs
+                .getFilter(i);
+        String featureType = filterModel.getFeatureType();
+        FeatureMatcherSetI filter = Jalview2XML.unmarshalFilter(featureType,
+                filterModel.getMatcherSet());
+        if (!filter.isEmpty())
         {
-          resetTable(null);
-          Object[][] data = ((FeatureTableModel) table.getModel())
-                  .getData();
-          ensureOrder(data);
-          updateFeatureRenderer(data, false);
-          table.repaint();
+          fr.setFeatureFilter(featureType, filter);
         }
-      } catch (Exception ex)
+      }
+
+      /*
+       * update feature settings table
+       */
+      if (table != null)
       {
-        System.out.println("Error loading User Colour File\n" + ex);
+        resetTable(null);
+        Object[][] data = ((FeatureTableModel) table.getModel())
+                .getData();
+        ensureOrder(data);
+        updateFeatureRenderer(data, false);
+        table.repaint();
       }
+    } catch (Exception ex)
+    {
+      System.out.println("Error loading User Colour File\n" + ex);
     }
   }
 
+  /**
+   * Offers a file chooser dialog, and then saves the current feature colours
+   * and any filters to the selected file in XML format
+   */
   void save()
   {
     JalviewFileChooser chooser = new JalviewFileChooser("fc",
-            "Sequence Feature Colours");
+            SEQUENCE_FEATURE_COLOURS);
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(
             MessageManager.getString("label.save_feature_colours"));
@@ -955,57 +954,75 @@ public class FeatureSettings extends JPanel
 
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-      String choice = chooser.getSelectedFile().getPath();
-      jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours();
-      ucs.setSchemeName("Sequence Features");
-      try
-      {
-        PrintWriter out = new PrintWriter(new OutputStreamWriter(
-                new FileOutputStream(choice), "UTF-8"));
+      save(chooser.getSelectedFile());
+    }
+  }
+
+  /**
+   * Saves feature colours and filters to the given file
+   * 
+   * @param file
+   */
+  void save(File file)
+  {
+    JalviewUserColours ucs = new JalviewUserColours();
+    ucs.setSchemeName("Sequence Features");
+    try
+    {
+      PrintWriter out = new PrintWriter(new OutputStreamWriter(
+              new FileOutputStream(file), "UTF-8"));
 
-        Set<String> fr_colours = fr.getAllFeatureColours();
-        Iterator<String> e = fr_colours.iterator();
-        float[] sortOrder = new float[fr_colours.size()];
-        String[] sortTypes = new String[fr_colours.size()];
-        int i = 0;
-        while (e.hasNext())
+      /*
+       * sort feature types by colour order, from 0 (highest)
+       * to 1 (lowest)
+       */
+      Set<String> fr_colours = fr.getAllFeatureColours();
+      String[] sortedTypes = fr_colours
+              .toArray(new String[fr_colours.size()]);
+      Arrays.sort(sortedTypes, new Comparator<String>()
+      {
+        @Override
+        public int compare(String type1, String type2)
         {
-          sortTypes[i] = e.next();
-          sortOrder[i] = fr.getOrder(sortTypes[i]);
-          i++;
+          return Float.compare(fr.getOrder(type1), fr.getOrder(type2));
         }
-        QuickSort.sort(sortOrder, sortTypes);
-        sortOrder = null;
-        for (i = 0; i < sortTypes.length; i++)
+      });
+
+      /*
+       * save feature colours
+       */
+      for (String featureType : sortedTypes)
+      {
+        FeatureColourI fcol = fr.getFeatureStyle(featureType);
+        jalview.schemabinding.version2.Colour col = Jalview2XML.marshalColour(
+                featureType, fcol);
+        ucs.addColour(col);
+      }
+
+      /*
+       * save any feature filters
+       */
+      for (String featureType : sortedTypes)
+      {
+        FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
+        if (filter != null && !filter.isEmpty())
         {
-          jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
-          col.setName(sortTypes[i]);
-          FeatureColourI fcol = fr.getFeatureStyle(sortTypes[i]);
-          if (fcol.isSimpleColour())
-          {
-            col.setRGB(Format.getHexString(fcol.getColour()));
-          }
-          else
-          {
-            col.setRGB(Format.getHexString(fcol.getMaxColour()));
-            col.setMin(fcol.getMin());
-            col.setMax(fcol.getMax());
-            col.setMinRGB(
-                    jalview.util.Format.getHexString(fcol.getMinColour()));
-            col.setAutoScale(fcol.isAutoScaled());
-            col.setThreshold(fcol.getThreshold());
-            col.setColourByLabel(fcol.isColourByLabel());
-            col.setThreshType(fcol.isAboveThreshold() ? "ABOVE"
-                    : (fcol.isBelowThreshold() ? "BELOW" : "NONE"));
-          }
-          ucs.addColour(col);
+          Iterator<FeatureMatcherI> iterator = filter.getMatchers().iterator();
+          FeatureMatcherI firstMatcher = iterator.next();
+          MatcherSet ms = Jalview2XML.marshalFilter(firstMatcher, iterator,
+                  filter.isAnded());
+          Filter filterModel = new Filter();
+          filterModel.setFeatureType(featureType);
+          filterModel.setMatcherSet(ms);
+          ucs.addFilter(filterModel);
         }
-        ucs.marshal(out);
-        out.close();
-      } catch (Exception ex)
-      {
-        ex.printStackTrace();
       }
+
+      ucs.marshal(out);
+      out.close();
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
     }
   }
 
@@ -1256,6 +1273,8 @@ public class FeatureSettings extends JPanel
     JButton loadColours = new JButton(
             MessageManager.getString("label.load_colours"));
     loadColours.setFont(JvSwingUtils.getLabelFont());
+    loadColours.setToolTipText(
+            MessageManager.getString("label.load_colours_tooltip"));
     loadColours.addActionListener(new ActionListener()
     {
       @Override
@@ -1268,6 +1287,8 @@ public class FeatureSettings extends JPanel
     JButton saveColours = new JButton(
             MessageManager.getString("label.save_colours"));
     saveColours.setFont(JvSwingUtils.getLabelFont());
+    saveColours.setToolTipText(
+            MessageManager.getString("label.save_colours_tooltip"));
     saveColours.addActionListener(new ActionListener()
     {
       @Override
diff --git a/src/jalview/gui/FeatureTypeSettings.java b/src/jalview/gui/FeatureTypeSettings.java
index c356731..5480f5d 100644
--- a/src/jalview/gui/FeatureTypeSettings.java
+++ b/src/jalview/gui/FeatureTypeSettings.java
@@ -295,8 +295,8 @@ public class FeatureTypeSettings extends JalviewDialog
         if (fc.isColourByAttribute())
         {
           String[] attributeName = fc.getAttributeName();
-          colourByTextCombo
-                  .setSelectedItem(toAttributeDisplayName(attributeName));
+          colourByTextCombo.setSelectedItem(
+                  FeatureMatcher.toAttributeDisplayName(attributeName));
         }
         else
         {
@@ -325,6 +325,7 @@ public class FeatureTypeSettings extends JalviewDialog
        * Graduated colour, by score or attribute value range
        */
       graduatedColour.setSelected(true);
+      updateColourMinMax(); // ensure min, max are set
       colourByRangeCombo.setEnabled(colourByRangeCombo.getItemCount() > 1);
       minColour.setEnabled(true);
       maxColour.setEnabled(true);
@@ -336,8 +337,8 @@ public class FeatureTypeSettings extends JalviewDialog
       if (fc.isColourByAttribute())
       {
         String[] attributeName = fc.getAttributeName();
-        colourByRangeCombo
-                .setSelectedItem(toAttributeDisplayName(attributeName));
+        colourByRangeCombo.setSelectedItem(
+                FeatureMatcher.toAttributeDisplayName(attributeName));
       }
       else
       {
@@ -478,7 +479,7 @@ public class FeatureTypeSettings extends JalviewDialog
     {
       // colour by attribute range
       minMax = FeatureAttributes.getInstance().getMinMax(featureType,
-              fromAttributeDisplayName(attName));
+              FeatureMatcher.fromAttributeDisplayName(attName));
     }
     return minMax;
   }
@@ -907,7 +908,8 @@ public class FeatureTypeSettings extends JalviewDialog
       String byWhat = (String) colourByTextCombo.getSelectedItem();
       if (!LABEL_18N.equals(byWhat))
       {
-        fc.setAttributeName(fromAttributeDisplayName(byWhat));
+        fc.setAttributeName(
+                FeatureMatcher.fromAttributeDisplayName(byWhat));
       }
       return fc;
     }
@@ -964,7 +966,7 @@ public class FeatureTypeSettings extends JalviewDialog
     String byWhat = (String) colourByRangeCombo.getSelectedItem();
     if (!SCORE_18N.equals(byWhat))
     {
-      fc.setAttributeName(fromAttributeDisplayName(byWhat));
+      fc.setAttributeName(FeatureMatcher.fromAttributeDisplayName(byWhat));
     }
 
     /*
@@ -989,30 +991,6 @@ public class FeatureTypeSettings extends JalviewDialog
     return fc;
   }
 
-  /**
-   * A helper method that converts a 'compound' attribute name from its display
-   * form, e.g. CSQ:PolyPhen to array form, e.g. { "CSQ", "PolyPhen" }
-   * 
-   * @param attribute
-   * @return
-   */
-  private String[] fromAttributeDisplayName(String attribute)
-  {
-    return attribute == null ? null : attribute.split(COLON);
-  }
-
-  /**
-   * A helper method that converts a 'compound' attribute name to its display
-   * form, e.g. CSQ:PolyPhen from its array form, e.g. { "CSQ", "PolyPhen" }
-   * 
-   * @param attName
-   * @return
-   */
-  private String toAttributeDisplayName(String[] attName)
-  {
-    return attName == null ? "" : String.join(COLON, attName);
-  }
-
   @Override
   protected void raiseClosed()
   {
@@ -1159,7 +1137,7 @@ public class FeatureTypeSettings extends JalviewDialog
       {
         continue;
       }
-      displayAtts.add(toAttributeDisplayName(attName));
+      displayAtts.add(FeatureMatcher.toAttributeDisplayName(attName));
       String desc = fa.getDescription(featureType, attName);
       if (desc != null && desc.length() > MAX_TOOLTIP_LENGTH)
       {
@@ -1383,7 +1361,8 @@ public class FeatureTypeSettings extends JalviewDialog
     }
     else
     {
-      attCombo.setSelectedItem(toAttributeDisplayName(attName));
+      attCombo.setSelectedItem(
+              FeatureMatcher.toAttributeDisplayName(attName));
     }
     attCombo.addItemListener(new ItemListener()
     {
@@ -1486,7 +1465,7 @@ public class FeatureTypeSettings extends JalviewDialog
     }
     else
     {
-      item = toAttributeDisplayName(filter.getAttribute());
+      item = FeatureMatcher.toAttributeDisplayName(filter.getAttribute());
     }
     attCombo.setSelectedItem(item);
     return item;
@@ -1533,7 +1512,7 @@ public class FeatureTypeSettings extends JalviewDialog
           JComboBox<Condition> condCombo, JTextField patternField)
   {
     Datatype type = FeatureAttributes.getInstance().getDatatype(featureType,
-            fromAttributeDisplayName(attName));
+            FeatureMatcher.fromAttributeDisplayName(attName));
     if (LABEL_18N.equals(attName))
     {
       type = Datatype.Character;
@@ -1693,7 +1672,7 @@ public class FeatureTypeSettings extends JalviewDialog
     else
     {
       km = FeatureMatcher.byAttribute(cond, pattern,
-              fromAttributeDisplayName(attName));
+              FeatureMatcher.fromAttributeDisplayName(attName));
     }
 
     filters.set(filterIndex, km);
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 4a15024..fdc2847 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -37,6 +37,10 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.StructureViewerModel;
 import jalview.datamodel.StructureViewerModel.StructureData;
+import jalview.datamodel.features.FeatureMatcher;
+import jalview.datamodel.features.FeatureMatcherI;
+import jalview.datamodel.features.FeatureMatcherSet;
+import jalview.datamodel.features.FeatureMatcherSetI;
 import jalview.ext.varna.RnaModel;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.DataSourceType;
@@ -48,6 +52,8 @@ import jalview.schemabinding.version2.Annotation;
 import jalview.schemabinding.version2.AnnotationColours;
 import jalview.schemabinding.version2.AnnotationElement;
 import jalview.schemabinding.version2.CalcIdParam;
+import jalview.schemabinding.version2.Colour;
+import jalview.schemabinding.version2.CompoundMatcher;
 import jalview.schemabinding.version2.DBRef;
 import jalview.schemabinding.version2.Features;
 import jalview.schemabinding.version2.Group;
@@ -60,6 +66,8 @@ import jalview.schemabinding.version2.MapListFrom;
 import jalview.schemabinding.version2.MapListTo;
 import jalview.schemabinding.version2.Mapping;
 import jalview.schemabinding.version2.MappingChoice;
+import jalview.schemabinding.version2.MatchCondition;
+import jalview.schemabinding.version2.MatcherSet;
 import jalview.schemabinding.version2.OtherData;
 import jalview.schemabinding.version2.PdbentryItem;
 import jalview.schemabinding.version2.Pdbids;
@@ -75,6 +83,9 @@ import jalview.schemabinding.version2.ThresholdLine;
 import jalview.schemabinding.version2.Tree;
 import jalview.schemabinding.version2.UserColours;
 import jalview.schemabinding.version2.Viewport;
+import jalview.schemabinding.version2.types.ColourThreshTypeType;
+import jalview.schemabinding.version2.types.FeatureMatcherByType;
+import jalview.schemabinding.version2.types.NoValueColour;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
@@ -83,10 +94,12 @@ import jalview.schemes.ResidueProperties;
 import jalview.schemes.UserColourScheme;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.Format;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.util.StringUtils;
 import jalview.util.jarInputStreamProvider;
+import jalview.util.matcher.Condition;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
@@ -115,6 +128,7 @@ import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.Enumeration;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -879,15 +893,33 @@ public class Jalview2XML
         }
         if (sf.otherDetails != null)
         {
-          String key;
-          Iterator<String> keys = sf.otherDetails.keySet().iterator();
-          while (keys.hasNext())
+          /*
+           * save feature attributes, which may be simple strings or
+           * map valued (have sub-attributes)
+           */
+          for (Entry<String, Object> entry : sf.otherDetails.entrySet())
           {
-            key = keys.next();
-            OtherData keyValue = new OtherData();
-            keyValue.setKey(key);
-            keyValue.setValue(sf.otherDetails.get(key).toString());
-            features.addOtherData(keyValue);
+            String key = entry.getKey();
+            Object value = entry.getValue();
+            if (value instanceof Map<?, ?>)
+            {
+              for (Entry<String, Object> subAttribute : ((Map<String, Object>) value)
+                      .entrySet())
+              {
+                OtherData otherData = new OtherData();
+                otherData.setKey(key);
+                otherData.setKey2(subAttribute.getKey());
+                otherData.setValue(subAttribute.getValue().toString());
+                features.addOtherData(otherData);
+              }
+            }
+            else
+            {
+              OtherData otherData = new OtherData();
+              otherData.setKey(key);
+              otherData.setValue(value.toString());
+              features.addOtherData(otherData);
+            }
           }
         }
 
@@ -1313,19 +1345,33 @@ public class Jalview2XML
       {
         jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
 
-        String[] renderOrder = ap.getSeqPanel().seqCanvas
-                .getFeatureRenderer().getRenderOrder()
-                .toArray(new String[0]);
+        FeatureRenderer fr = ap.getSeqPanel().seqCanvas
+                .getFeatureRenderer();
+        String[] renderOrder = fr.getRenderOrder().toArray(new String[0]);
 
         Vector<String> settingsAdded = new Vector<>();
         if (renderOrder != null)
         {
           for (String featureType : renderOrder)
           {
-            FeatureColourI fcol = ap.getSeqPanel().seqCanvas
-                    .getFeatureRenderer().getFeatureStyle(featureType);
             Setting setting = new Setting();
             setting.setType(featureType);
+
+            /*
+             * save any filter for the feature type
+             */
+            FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
+            if (filter != null)  {
+              Iterator<FeatureMatcherI> filters = filter.getMatchers().iterator();
+              FeatureMatcherI firstFilter = filters.next();
+              setting.setMatcherSet(Jalview2XML.marshalFilter(
+                      firstFilter, filters, filter.isAnded()));
+            }
+
+            /*
+             * save colour scheme for the feature type
+             */
+            FeatureColourI fcol = fr.getFeatureStyle(featureType);
             if (!fcol.isSimpleColour())
             {
               setting.setColour(fcol.getMaxColour().getRGB());
@@ -1333,8 +1379,25 @@ public class Jalview2XML
               setting.setMin(fcol.getMin());
               setting.setMax(fcol.getMax());
               setting.setColourByLabel(fcol.isColourByLabel());
+              if (fcol.isColourByAttribute())
+              {
+                setting.setAttributeName(fcol.getAttributeName());
+              }
               setting.setAutoScale(fcol.isAutoScaled());
               setting.setThreshold(fcol.getThreshold());
+              Color noColour = fcol.getNoColour();
+              if (noColour == null)
+              {
+                setting.setNoValueColour(NoValueColour.NONE);
+              }
+              else if (noColour.equals(fcol.getMaxColour()))
+              {
+                setting.setNoValueColour(NoValueColour.MAX);
+              }
+              else
+              {
+                setting.setNoValueColour(NoValueColour.MIN);
+              }
               // -1 = No threshold, 0 = Below, 1 = Above
               setting.setThreshstate(fcol.isAboveThreshold() ? 1
                       : (fcol.isBelowThreshold() ? 0 : -1));
@@ -1346,7 +1409,7 @@ public class Jalview2XML
 
             setting.setDisplay(
                     av.getFeaturesDisplayed().isVisible(featureType));
-            float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+            float rorder = fr
                     .getOrder(featureType);
             if (rorder > -1)
             {
@@ -1358,8 +1421,7 @@ public class Jalview2XML
         }
 
         // is groups actually supposed to be a map here ?
-        Iterator<String> en = ap.getSeqPanel().seqCanvas
-                .getFeatureRenderer().getFeatureGroups().iterator();
+        Iterator<String> en = fr.getFeatureGroups().iterator();
         Vector<String> groupsAdded = new Vector<>();
         while (en.hasNext())
         {
@@ -1370,8 +1432,7 @@ public class Jalview2XML
           }
           Group g = new Group();
           g.setName(grp);
-          g.setDisplay(((Boolean) ap.getSeqPanel().seqCanvas
-                  .getFeatureRenderer().checkGroupVisibility(grp, false))
+          g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false))
                           .booleanValue());
           fs.addGroup(g);
           groupsAdded.addElement(grp);
@@ -2962,19 +3023,46 @@ public class Jalview2XML
                     features[f].getEnd(), features[f].getScore(),
                     features[f].getFeatureGroup());
             sf.setStatus(features[f].getStatus());
+
+            /*
+             * load any feature attributes - include map-valued attributes
+             */
+            Map<String, Map<String, String>> mapAttributes = new HashMap<>();
             for (int od = 0; od < features[f].getOtherDataCount(); od++)
             {
               OtherData keyValue = features[f].getOtherData(od);
-              if (keyValue.getKey().startsWith("LINK"))
+              String attributeName = keyValue.getKey();
+              String attributeValue = keyValue.getValue();
+              if (attributeName.startsWith("LINK"))
               {
-                sf.addLink(keyValue.getValue());
+                sf.addLink(attributeValue);
               }
               else
               {
-                sf.setValue(keyValue.getKey(), keyValue.getValue());
+                String subAttribute = keyValue.getKey2();
+                if (subAttribute == null)
+                {
+                  // simple string-valued attribute
+                  sf.setValue(attributeName, attributeValue);
+                }
+                else
+                {
+                  // attribute 'key' has sub-attribute 'key2'
+                  if (!mapAttributes.containsKey(attributeName))
+                  {
+                    mapAttributes.put(attributeName, new HashMap<>());
+                  }
+                  mapAttributes.get(attributeName).put(subAttribute,
+                          attributeValue);
+                }
               }
-
             }
+            for (Entry<String, Map<String, String>> mapAttribute : mapAttributes
+                    .entrySet())
+            {
+              sf.setValue(mapAttribute.getKey(), mapAttribute.getValue());
+            }
+
             // adds feature to datasequence's feature set (since Jalview 2.10)
             al.getSequenceAt(i).addSequenceFeature(sf);
           }
@@ -4550,9 +4638,11 @@ public class Jalview2XML
       af.viewport.setShowGroupConservation(false);
     }
 
-    // recover featre settings
+    // recover feature settings
     if (jms.getFeatureSettings() != null)
     {
+      FeatureRenderer fr = af.alignPanel.getSeqPanel().seqCanvas
+              .getFeatureRenderer();
       FeaturesDisplayed fdi;
       af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
       String[] renderOrder = new String[jms.getFeatureSettings()
@@ -4564,14 +4654,51 @@ public class Jalview2XML
               .getSettingCount(); fs++)
       {
         Setting setting = jms.getFeatureSettings().getSetting(fs);
+        String featureType = setting.getType();
+
+        /*
+         * restore feature filters (if any)
+         */
+        MatcherSet filters = setting.getMatcherSet();
+        if (filters != null)
+        {
+          FeatureMatcherSetI filter = Jalview2XML
+                  .unmarshalFilter(featureType, filters);
+          if (!filter.isEmpty())
+          {
+            fr.setFeatureFilter(featureType, filter);
+          }
+        }
+
+        /*
+         * restore feature colour scheme
+         */
+        Color maxColour = new Color(setting.getColour());
         if (setting.hasMincolour())
         {
-          FeatureColourI gc = setting.hasMin()
-                  ? new FeatureColour(new Color(setting.getMincolour()),
-                          new Color(setting.getColour()), setting.getMin(),
-                          setting.getMax())
-                  : new FeatureColour(new Color(setting.getMincolour()),
-                          new Color(setting.getColour()), 0, 1);
+          /*
+           * minColour is always set unless a simple colour
+           * (including for colour by label though it doesn't use it)
+           */
+          Color minColour = new Color(setting.getMincolour());
+          Color noValueColour = minColour;
+          NoValueColour noColour = setting.getNoValueColour();
+          if (noColour == NoValueColour.NONE)
+          {
+            noValueColour = null;
+          }
+          else if (noColour == NoValueColour.MAX)
+          {
+            noValueColour = maxColour;
+          }
+          float min = setting.hasMin() ? setting.getMin() : 0f;
+          float max = setting.hasMin() ? setting.getMax() : 1f;
+          FeatureColourI gc = new FeatureColour(minColour, maxColour,
+                  noValueColour, min, max);
+          if (setting.getAttributeNameCount() > 0)
+          {
+            gc.setAttributeName(setting.getAttributeName());
+          }
           if (setting.hasThreshold())
           {
             gc.setThreshold(setting.getThreshold());
@@ -4596,26 +4723,26 @@ public class Jalview2XML
             gc.setColourByLabel(setting.getColourByLabel());
           }
           // and put in the feature colour table.
-          featureColours.put(setting.getType(), gc);
+          featureColours.put(featureType, gc);
         }
         else
         {
-          featureColours.put(setting.getType(),
-                  new FeatureColour(new Color(setting.getColour())));
+          featureColours.put(featureType,
+                  new FeatureColour(maxColour));
         }
-        renderOrder[fs] = setting.getType();
+        renderOrder[fs] = featureType;
         if (setting.hasOrder())
         {
-          featureOrder.put(setting.getType(), setting.getOrder());
+          featureOrder.put(featureType, setting.getOrder());
         }
         else
         {
-          featureOrder.put(setting.getType(), new Float(
+          featureOrder.put(featureType, new Float(
                   fs / jms.getFeatureSettings().getSettingCount()));
         }
         if (setting.getDisplay())
         {
-          fdi.setVisible(setting.getType());
+          fdi.setVisible(featureType);
         }
       }
       Map<String, Boolean> fgtable = new Hashtable<>();
@@ -4629,9 +4756,7 @@ public class Jalview2XML
       // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
       FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
               fgtable, featureColours, 1.0f, featureOrder);
-      af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
-              .transferSettings(frs);
-
+      fr.transferSettings(frs);
     }
 
     if (view.getHiddenColumnsCount() > 0)
@@ -5333,7 +5458,7 @@ public class Jalview2XML
 
     if (this.frefedSequence == null)
     {
-      frefedSequence = new Vector<SeqFref>();
+      frefedSequence = new Vector<>();
     }
 
     viewportsAdded.clear();
@@ -5585,4 +5710,289 @@ public class Jalview2XML
   {
     return counter++;
   }
+
+  /**
+   * Populates an XML model of the feature colour scheme for one feature type
+   * 
+   * @param featureType
+   * @param fcol
+   * @return
+   */
+  protected static jalview.schemabinding.version2.Colour marshalColour(
+          String featureType, FeatureColourI fcol)
+  {
+    jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
+    if (fcol.isSimpleColour())
+    {
+      col.setRGB(Format.getHexString(fcol.getColour()));
+    }
+    else
+    {
+      col.setRGB(Format.getHexString(fcol.getMaxColour()));
+      col.setMin(fcol.getMin());
+      col.setMax(fcol.getMax());
+      col.setMinRGB(jalview.util.Format.getHexString(fcol.getMinColour()));
+      col.setAutoScale(fcol.isAutoScaled());
+      col.setThreshold(fcol.getThreshold());
+      col.setColourByLabel(fcol.isColourByLabel());
+      col.setThreshType(fcol.isAboveThreshold() ? ColourThreshTypeType.ABOVE
+              : (fcol.isBelowThreshold() ? ColourThreshTypeType.BELOW
+                      : ColourThreshTypeType.NONE));
+      if (fcol.isColourByAttribute())
+      {
+        col.setAttributeName(fcol.getAttributeName());
+      }
+      Color noColour = fcol.getNoColour();
+      if (noColour == null)
+      {
+        col.setNoValueColour(NoValueColour.NONE);
+      }
+      else if (noColour == fcol.getMaxColour())
+      {
+        col.setNoValueColour(NoValueColour.MAX);
+      }
+      else
+      {
+        col.setNoValueColour(NoValueColour.MIN);
+      }
+    }
+    col.setName(featureType);
+    return col;
+  }
+
+  /**
+   * Populates an XML model of the feature filter(s) for one feature type
+   * 
+   * @param firstMatcher
+   *          the first (or only) match condition)
+   * @param filter
+   *          remaining match conditions (if any)
+   * @param and
+   *          if true, conditions are and-ed, else or-ed
+   */
+  protected static MatcherSet marshalFilter(FeatureMatcherI firstMatcher,
+          Iterator<FeatureMatcherI> filters, boolean and)
+  {
+    MatcherSet result = new MatcherSet();
+  
+    if (filters.hasNext())
+    {
+      /*
+       * compound matcher
+       */
+      CompoundMatcher compound = new CompoundMatcher();
+      compound.setAnd(and);
+      MatcherSet matcher1 = marshalFilter(firstMatcher,
+              Collections.emptyIterator(), and);
+      compound.addMatcherSet(matcher1);
+      FeatureMatcherI nextMatcher = filters.next();
+      MatcherSet matcher2 = marshalFilter(nextMatcher, filters, and);
+      compound.addMatcherSet(matcher2);
+      result.setCompoundMatcher(compound);
+    }
+    else
+    {
+      /*
+       * single condition matcher
+       */
+      MatchCondition matcherModel = new MatchCondition();
+      matcherModel.setCondition(
+              firstMatcher.getMatcher().getCondition().getStableName());
+      matcherModel.setValue(firstMatcher.getMatcher().getPattern());
+      if (firstMatcher.isByAttribute())
+      {
+        matcherModel.setBy(FeatureMatcherByType.BYATTRIBUTE);
+        matcherModel.setAttributeName(firstMatcher.getAttribute());
+      }
+      else if (firstMatcher.isByLabel())
+      {
+        matcherModel.setBy(FeatureMatcherByType.BYLABEL);
+      }
+      else if (firstMatcher.isByScore())
+      {
+        matcherModel.setBy(FeatureMatcherByType.BYSCORE);
+      }
+      result.setMatchCondition(matcherModel);
+    }
+  
+    return result;
+  }
+
+  /**
+   * Loads one XML model of a feature filter to a Jalview object
+   * 
+   * @param featureType
+   * @param matcherSetModel
+   * @return
+   */
+  protected static FeatureMatcherSetI unmarshalFilter(
+          String featureType, MatcherSet matcherSetModel)
+  {
+    FeatureMatcherSetI result = new FeatureMatcherSet();
+    try
+    {
+      unmarshalFilterConditions(result, matcherSetModel, true);
+    } catch (IllegalStateException e)
+    {
+      // mixing AND and OR conditions perhaps
+      System.err.println(
+              String.format("Error reading filter conditions for '%s': %s",
+                      featureType, e.getMessage()));
+      // return as much as was parsed up to the error
+    }
+  
+    return result;
+  }
+
+  /**
+   * Adds feature match conditions to matcherSet as unmarshalled from XML
+   * (possibly recursively for compound conditions)
+   * 
+   * @param matcherSet
+   * @param matcherSetModel
+   * @param and
+   *          if true, multiple conditions are AND-ed, else they are OR-ed
+   * @throws IllegalStateException
+   *           if AND and OR conditions are mixed
+   */
+  protected static void unmarshalFilterConditions(
+          FeatureMatcherSetI matcherSet, MatcherSet matcherSetModel,
+          boolean and)
+  {
+    MatchCondition mc = matcherSetModel.getMatchCondition();
+    if (mc != null)
+    {
+      /*
+       * single condition
+       */
+      FeatureMatcherByType filterBy = mc.getBy();
+      Condition cond = Condition.fromString(mc.getCondition());
+      String pattern = mc.getValue();
+      FeatureMatcherI matchCondition = null;
+      if (filterBy == FeatureMatcherByType.BYLABEL)
+      {
+        matchCondition = FeatureMatcher.byLabel(cond, pattern);
+      }
+      else if (filterBy == FeatureMatcherByType.BYSCORE)
+      {
+        matchCondition = FeatureMatcher.byScore(cond, pattern);
+  
+      }
+      else if (filterBy == FeatureMatcherByType.BYATTRIBUTE)
+      {
+        String[] attNames = mc.getAttributeName();
+        matchCondition = FeatureMatcher.byAttribute(cond, pattern,
+                attNames);
+      }
+  
+      /*
+       * note this throws IllegalStateException if AND-ing to a 
+       * previously OR-ed compound condition, or vice versa
+       */
+      if (and)
+      {
+        matcherSet.and(matchCondition);
+      }
+      else
+      {
+        matcherSet.or(matchCondition);
+      }
+    }
+    else
+    {
+      /*
+       * compound condition
+       */
+      MatcherSet[] matchers = matcherSetModel.getCompoundMatcher()
+              .getMatcherSet();
+      boolean anded = matcherSetModel.getCompoundMatcher().getAnd();
+      if (matchers.length == 2)
+      {
+        unmarshalFilterConditions(matcherSet, matchers[0], anded);
+        unmarshalFilterConditions(matcherSet, matchers[1], anded);
+      }
+      else
+      {
+        System.err.println("Malformed compound filter condition");
+      }
+    }
+  }
+
+  /**
+   * Loads one XML model of a feature colour to a Jalview object
+   * 
+   * @param colourModel
+   * @return
+   */
+  protected static FeatureColourI unmarshalColour(
+          jalview.schemabinding.version2.Colour colourModel)
+  {
+    FeatureColourI colour = null;
+  
+    if (colourModel.hasMax())
+    {
+      Color mincol = null;
+      Color maxcol = null;
+      Color noValueColour = null;
+  
+      try
+      {
+        mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
+        maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
+      } catch (Exception e)
+      {
+        Cache.log.warn("Couldn't parse out graduated feature color.", e);
+      }
+  
+      NoValueColour noCol = colourModel.getNoValueColour();
+      if (noCol == NoValueColour.MIN)
+      {
+        noValueColour = mincol;
+      }
+      else if (noCol == NoValueColour.MAX)
+      {
+        noValueColour = maxcol;
+      }
+  
+      colour = new FeatureColour(mincol, maxcol, noValueColour,
+              colourModel.getMin(),
+              colourModel.getMax());
+      String[] attributes = colourModel.getAttributeName();
+      if (attributes != null && attributes.length > 0)
+      {
+        colour.setAttributeName(attributes);
+      }
+      if (colourModel.hasAutoScale())
+      {
+        colour.setAutoScaled(colourModel.getAutoScale());
+      }
+      if (colourModel.hasColourByLabel())
+      {
+        colour.setColourByLabel(colourModel.getColourByLabel());
+      }
+      if (colourModel.hasThreshold())
+      {
+        colour.setThreshold(colourModel.getThreshold());
+      }
+      ColourThreshTypeType ttyp = colourModel.getThreshType();
+      if (ttyp != null)
+      {
+        if (ttyp == ColourThreshTypeType.ABOVE)
+        {
+          colour.setAboveThreshold(true);
+        }
+        else if (ttyp == ColourThreshTypeType.BELOW)
+        {
+          colour.setBelowThreshold(true);
+        }
+      }
+    }
+    else
+    {
+      Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
+      colour = new FeatureColour(color);
+    }
+  
+    return colour;
+  }
 }
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 6635dbe..aa8369a 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -527,6 +527,8 @@ public class Preferences extends GPreferences
     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
     userIdWidth.setText(wi == null ? "" : wi.toString());
+    // TODO: refactor to use common enum via FormatAdapter and allow extension
+    // for new flat file formats
     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index d5a13f3..fb6efe5 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -359,8 +359,11 @@ public class SeqPanel extends JPanel
       int original = seqCanvas.cursorX - dx;
       int maxWidth = av.getAlignment().getWidth();
 
+      // TODO: once JAL-2759 is ready, change this loop to something more
+      // efficient
       while (!hidden.isVisible(seqCanvas.cursorX)
-              && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
+              && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0
+              && dx != 0)
       {
         seqCanvas.cursorX += dx;
       }
diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java
index b142613..fb37b77 100644
--- a/src/jalview/gui/StructureViewer.java
+++ b/src/jalview/gui/StructureViewer.java
@@ -154,6 +154,10 @@ public class StructureViewer
       PDBEntry pdb = pdbs[i];
       SequenceI seq = seqs[i];
       String pdbFile = pdb.getFile();
+      if (pdbFile == null || pdbFile.length() == 0)
+      {
+        pdbFile = pdb.getId();
+      }
       if (!pdbsSeen.containsKey(pdbFile))
       {
         pdbsSeen.put(pdbFile, pdb);
diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index d2282b1..99663c8 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -31,6 +31,8 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceDummy;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcherSet;
+import jalview.datamodel.features.FeatureMatcherSetI;
 import jalview.io.gff.GffHelperBase;
 import jalview.io.gff.GffHelperFactory;
 import jalview.io.gff.GffHelperI;
@@ -68,6 +70,16 @@ import java.util.Map.Entry;
  */
 public class FeaturesFile extends AlignFile implements FeaturesSourceI
 {
+  private static final String TAB_REGEX = "\\t";
+
+  private static final String STARTGROUP = "STARTGROUP";
+
+  private static final String ENDGROUP = "ENDGROUP";
+
+  private static final String STARTFILTERS = "STARTFILTERS";
+
+  private static final String ENDFILTERS = "ENDFILTERS";
+
   private static final String ID_NOT_SPECIFIED = "ID_NOT_SPECIFIED";
 
   private static final String NOTE = "Note";
@@ -169,7 +181,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
    * @param align
    *          - alignment/dataset containing sequences that are to be annotated
    * @param colours
-   *          - hashtable to store feature colour definitions
+   *          - map to store feature colour definitions
    * @param removeHTML
    *          - process html strings into plain text
    * @param relaxedIdmatching
@@ -180,11 +192,34 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
           Map<String, FeatureColourI> colours, boolean removeHTML,
           boolean relaxedIdmatching)
   {
-    Map<String, String> gffProps = new HashMap<String, String>();
+    return parse(align, colours, null, removeHTML, relaxedIdmatching);
+  }
+
+  /**
+   * Parse GFF or Jalview format sequence features file
+   * 
+   * @param align
+   *          - alignment/dataset containing sequences that are to be annotated
+   * @param colours
+   *          - map to store feature colour definitions
+   * @param filters
+   *          - map to store feature filter definitions
+   * @param removeHTML
+   *          - process html strings into plain text
+   * @param relaxedIdmatching
+   *          - when true, ID matches to compound sequence IDs are allowed
+   * @return true if features were added
+   */
+  public boolean parse(AlignmentI align,
+          Map<String, FeatureColourI> colours,
+          Map<String, FeatureMatcherSetI> filters, boolean removeHTML,
+          boolean relaxedIdmatching)
+  {
+    Map<String, String> gffProps = new HashMap<>();
     /*
      * keep track of any sequences we try to create from the data
      */
-    List<SequenceI> newseqs = new ArrayList<SequenceI>();
+    List<SequenceI> newseqs = new ArrayList<>();
 
     String line = null;
     try
@@ -204,7 +239,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
           continue;
         }
 
-        gffColumns = line.split("\\t"); // tab as regex
+        gffColumns = line.split(TAB_REGEX);
         if (gffColumns.length == 1)
         {
           if (line.trim().equalsIgnoreCase("GFF"))
@@ -218,18 +253,23 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
           }
         }
 
-        if (gffColumns.length > 1 && gffColumns.length < 4)
+        if (gffColumns.length > 0 && gffColumns.length < 4)
         {
           /*
            * if 2 or 3 tokens, we anticipate either 'startgroup', 'endgroup' or
            * a feature type colour specification
            */
           String ft = gffColumns[0];
-          if (ft.equalsIgnoreCase("startgroup"))
+          if (ft.equalsIgnoreCase(STARTFILTERS))
+          {
+            parseFilters(filters);
+            continue;
+          }
+          if (ft.equalsIgnoreCase(STARTGROUP))
           {
             featureGroup = gffColumns[1];
           }
-          else if (ft.equalsIgnoreCase("endgroup"))
+          else if (ft.equalsIgnoreCase(ENDGROUP))
           {
             // We should check whether this is the current group,
             // but at present there's no way of showing more than 1 group
@@ -290,6 +330,43 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
   }
 
   /**
+   * Reads input lines from STARTFILTERS to ENDFILTERS and adds a feature type
+   * filter to the map for each line parsed. After exit from this method,
+   * nextLine() should return the line after ENDFILTERS (or we are already at
+   * end of file if ENDFILTERS was missing).
+   * 
+   * @param filters
+   * @throws IOException
+   */
+  protected void parseFilters(Map<String, FeatureMatcherSetI> filters)
+          throws IOException
+  {
+    String line;
+    while ((line = nextLine()) != null)
+    {
+      if (line.toUpperCase().startsWith(ENDFILTERS))
+      {
+        return;
+      }
+      String[] tokens = line.split(TAB_REGEX);
+      if (tokens.length != 2)
+      {
+        System.err.println(String.format("Invalid token count %d for %d",
+                tokens.length, line));
+      }
+      else
+      {
+        String featureType = tokens[0];
+        FeatureMatcherSetI fm = FeatureMatcherSet.fromString(tokens[1]);
+        if (fm != null && filters != null)
+        {
+          filters.put(featureType, fm);
+        }
+      }
+    }
+  }
+
+  /**
    * Try to parse a Jalview format feature specification and add it as a
    * sequence feature to any matching sequences in the alignment. Returns true
    * if successful (a feature was added), or false if not.
@@ -487,15 +564,16 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
   }
 
   /**
-   * Returns contents of a Jalview format features file, for visible features,
-   * as filtered by type and group. Features with a null group are displayed if
-   * their feature type is visible. Non-positional features may optionally be
-   * included (with no check on type or group).
+   * Returns contents of a Jalview format features file, for visible features, as
+   * filtered by type and group. Features with a null group are displayed if their
+   * feature type is visible. Non-positional features may optionally be included
+   * (with no check on type or group).
    * 
    * @param sequences
    *          source of features
    * @param visible
    *          map of colour for each visible feature type
+   * @param featureFilters
    * @param visibleFeatureGroups
    * @param includeNonPositional
    *          if true, include non-positional features (regardless of group or
@@ -504,6 +582,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
    */
   public String printJalviewFormat(SequenceI[] sequences,
           Map<String, FeatureColourI> visible,
+          Map<String, FeatureMatcherSetI> featureFilters,
           List<String> visibleFeatureGroups, boolean includeNonPositional)
   {
     if (!includeNonPositional && (visible == null || visible.isEmpty()))
@@ -531,10 +610,15 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
             .toArray(new String[visible.keySet().size()]);
 
     /*
+     * feature filters if any
+     */
+    outputFeatureFilters(out, visible, featureFilters);
+
+    /*
      * sort groups alphabetically, and ensure that features with a
      * null or empty group are output after those in named groups
      */
-    List<String> sortedGroups = new ArrayList<String>(visibleFeatureGroups);
+    List<String> sortedGroups = new ArrayList<>(visibleFeatureGroups);
     sortedGroups.remove(null);
     sortedGroups.remove("");
     Collections.sort(sortedGroups);
@@ -560,13 +644,76 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
       }
     }
 
-    for (String group : sortedGroups)
+    /*
+     * positional features within groups
+     */
+    foundSome |= outputFeaturesByGroup(out, sortedGroups, types, sequences);
+
+    return foundSome ? out.toString() : "No Features Visible";
+  }
+
+  /**
+   * Outputs any feature filters defined for visible feature types, sandwiched by
+   * STARTFILTERS and ENDFILTERS lines
+   * 
+   * @param out
+   * @param visible
+   * @param featureFilters
+   */
+  void outputFeatureFilters(StringBuilder out,
+          Map<String, FeatureColourI> visible,
+          Map<String, FeatureMatcherSetI> featureFilters)
+  {
+    if (visible == null || featureFilters == null
+            || featureFilters.isEmpty())
+    {
+      return;
+    }
+
+    boolean first = true;
+    for (String featureType : visible.keySet())
+    {
+      FeatureMatcherSetI filter = featureFilters.get(featureType);
+      if (filter != null)
+      {
+        if (first)
+        {
+          first = false;
+          out.append(newline).append(STARTFILTERS).append(newline);
+        }
+        out.append(featureType).append(TAB).append(filter.toStableString())
+                .append(newline);
+      }
+    }
+    if (!first)
+    {
+      out.append(ENDFILTERS).append(newline).append(newline);
+    }
+
+  }
+
+  /**
+   * Appends output of sequence features within feature groups to the output
+   * buffer. Groups other than the null or empty group are sandwiched by
+   * STARTGROUP and ENDGROUP lines.
+   * 
+   * @param out
+   * @param groups
+   * @param featureTypes
+   * @param sequences
+   * @return
+   */
+  private boolean outputFeaturesByGroup(StringBuilder out,
+          List<String> groups, String[] featureTypes, SequenceI[] sequences)
+  {
+    boolean foundSome = false;
+    for (String group : groups)
     {
       boolean isNamedGroup = (group != null && !"".equals(group));
       if (isNamedGroup)
       {
         out.append(newline);
-        out.append("STARTGROUP").append(TAB);
+        out.append(STARTGROUP).append(TAB);
         out.append(group);
         out.append(newline);
       }
@@ -577,11 +724,11 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
       for (int i = 0; i < sequences.length; i++)
       {
         String sequenceName = sequences[i].getName();
-        List<SequenceFeature> features = new ArrayList<SequenceFeature>();
-        if (types.length > 0)
+        List<SequenceFeature> features = new ArrayList<>();
+        if (featureTypes.length > 0)
         {
           features.addAll(sequences[i].getFeatures().getFeaturesForGroup(
-                  true, group, types));
+                  true, group, featureTypes));
         }
 
         for (SequenceFeature sequenceFeature : features)
@@ -593,13 +740,12 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
 
       if (isNamedGroup)
       {
-        out.append("ENDGROUP").append(TAB);
+        out.append(ENDGROUP).append(TAB);
         out.append(group);
         out.append(newline);
       }
     }
-
-    return foundSome ? out.toString() : "No Features Visible";
+    return foundSome;
   }
 
   /**
@@ -688,7 +834,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
       dataset = new Alignment(new SequenceI[] {});
     }
 
-    Map<String, FeatureColourI> featureColours = new HashMap<String, FeatureColourI>();
+    Map<String, FeatureColourI> featureColours = new HashMap<>();
     boolean parseResult = parse(dataset, featureColours, false, true);
     if (!parseResult)
     {
@@ -748,7 +894,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
 
     for (SequenceI seq : sequences)
     {
-      List<SequenceFeature> features = new ArrayList<SequenceFeature>();
+      List<SequenceFeature> features = new ArrayList<>();
       if (includeNonPositionalFeatures)
       {
         features.addAll(seq.getFeatures().getNonPositionalFeatures());
diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 3027ab1..7647a16 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -161,7 +161,8 @@ public class FormatAdapter extends AppletFormatAdapter
 
   public boolean getCacheSuffixDefault(FileFormatI format)
   {
-    return Cache.getDefault(format.getName() + "_JVSUFFIX", true);
+    return Cache.getDefault(format.getName().toUpperCase() + "_JVSUFFIX",
+            true);
   }
 
   public String formatSequences(FileFormatI format, AlignmentI alignment,
diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 41772d4..8a80d41 100644
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -162,7 +162,8 @@ public class AnnotationRenderer
           boolean validRes, boolean validEnd)
   {
     g.setColor(STEM_COLOUR);
-    int sCol = (lastSSX / charWidth) + startRes;
+    int sCol = (lastSSX / charWidth)
+            + hiddenColumns.adjustForHiddenColumns(startRes);
     int x1 = lastSSX;
     int x2 = (x * charWidth);
 
@@ -228,7 +229,8 @@ public class AnnotationRenderer
     // System.out.println(nonCanColor);
 
     g.setColor(nonCanColor);
-    int sCol = (lastSSX / charWidth) + startRes;
+    int sCol = (lastSSX / charWidth)
+            + hiddenColumns.adjustForHiddenColumns(startRes);
     int x1 = lastSSX;
     int x2 = (x * charWidth);
 
@@ -1147,7 +1149,8 @@ public class AnnotationRenderer
   {
     g.setColor(HELIX_COLOUR);
 
-    int sCol = (lastSSX / charWidth) + startRes;
+    int sCol = (lastSSX / charWidth)
+            + hiddenColumns.adjustForHiddenColumns(startRes);
     int x1 = lastSSX;
     int x2 = (x * charWidth);
 
diff --git a/src/jalview/schemabinding/version2/.castor.cdr b/src/jalview/schemabinding/version2/.castor.cdr
index 0a01103..e1100a8 100644
--- a/src/jalview/schemabinding/version2/.castor.cdr
+++ b/src/jalview/schemabinding/version2/.castor.cdr
@@ -1,4 +1,4 @@
-#Mon Jun 20 15:44:52 BST 2016
+#Thu Dec 14 09:10:14 GMT 2017
 jalview.schemabinding.version2.ThresholdLine=jalview.schemabinding.version2.descriptors.ThresholdLineDescriptor
 jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor
 jalview.schemabinding.version2.StructureState=jalview.schemabinding.version2.descriptors.StructureStateDescriptor
@@ -10,7 +10,9 @@ jalview.schemabinding.version2.OtherData=jalview.schemabinding.version2.descript
 jalview.schemabinding.version2.Setting=jalview.schemabinding.version2.descriptors.SettingDescriptor
 jalview.schemabinding.version2.AlcodonFrame=jalview.schemabinding.version2.descriptors.AlcodonFrameDescriptor
 jalview.schemabinding.version2.AnnotationElement=jalview.schemabinding.version2.descriptors.AnnotationElementDescriptor
+jalview.schemabinding.version2.FeatureMatcherSet=jalview.schemabinding.version2.descriptors.FeatureMatcherSetDescriptor
 jalview.schemabinding.version2.SecondaryStructure=jalview.schemabinding.version2.descriptors.SecondaryStructureDescriptor
+jalview.schemabinding.version2.MatchCondition=jalview.schemabinding.version2.descriptors.MatchConditionDescriptor
 jalview.schemabinding.version2.SequenceSet=jalview.schemabinding.version2.descriptors.SequenceSetDescriptor
 jalview.schemabinding.version2.Viewport=jalview.schemabinding.version2.descriptors.ViewportDescriptor
 jalview.schemabinding.version2.RnaViewer=jalview.schemabinding.version2.descriptors.RnaViewerDescriptor
@@ -20,31 +22,32 @@ jalview.schemabinding.version2.UserColourScheme=jalview.schemabinding.version2.d
 jalview.schemabinding.version2.DBRef=jalview.schemabinding.version2.descriptors.DBRefDescriptor
 jalview.schemabinding.version2.AlcodMap=jalview.schemabinding.version2.descriptors.AlcodMapDescriptor
 jalview.schemabinding.version2.Annotation=jalview.schemabinding.version2.descriptors.AnnotationDescriptor
-jalview.schemabinding.version2.Wsparameters=jalview.schemabinding.version2.descriptors.WsparametersDescriptor
 jalview.schemabinding.version2.JSeq=jalview.schemabinding.version2.descriptors.JSeqDescriptor
+jalview.schemabinding.version2.MatcherSet=jalview.schemabinding.version2.descriptors.MatcherSetDescriptor
 jalview.schemabinding.version2.Sequence=jalview.schemabinding.version2.descriptors.SequenceDescriptor
 jalview.schemabinding.version2.WebServiceParameterSet=jalview.schemabinding.version2.descriptors.WebServiceParameterSetDescriptor
 jalview.schemabinding.version2.Alcodon=jalview.schemabinding.version2.descriptors.AlcodonDescriptor
+jalview.schemabinding.version2.Filter=jalview.schemabinding.version2.descriptors.FilterDescriptor
 jalview.schemabinding.version2.AnnotationColours=jalview.schemabinding.version2.descriptors.AnnotationColoursDescriptor
 jalview.schemabinding.version2.Pdbids=jalview.schemabinding.version2.descriptors.PdbidsDescriptor
 jalview.schemabinding.version2.AnnotationColourScheme=jalview.schemabinding.version2.descriptors.AnnotationColourSchemeDescriptor
 jalview.schemabinding.version2.Mapping=jalview.schemabinding.version2.descriptors.MappingDescriptor
-jalview.schemabinding.version2.MappingChoice=jalview.schemabinding.version2.descriptors.MappingChoiceDescriptor
+jalview.schemabinding.version2.CompoundMatcher=jalview.schemabinding.version2.descriptors.CompoundMatcherDescriptor
+jalview.schemabinding.version2.JalviewModelSequence=jalview.schemabinding.version2.descriptors.JalviewModelSequenceDescriptor
 jalview.schemabinding.version2.Group=jalview.schemabinding.version2.descriptors.GroupDescriptor
+jalview.schemabinding.version2.MappingChoice=jalview.schemabinding.version2.descriptors.MappingChoiceDescriptor
 jalview.schemabinding.version2.Feature=jalview.schemabinding.version2.descriptors.FeatureDescriptor
-jalview.schemabinding.version2.JalviewModelSequence=jalview.schemabinding.version2.descriptors.JalviewModelSequenceDescriptor
 jalview.schemabinding.version2.UserColours=jalview.schemabinding.version2.descriptors.UserColoursDescriptor
 jalview.schemabinding.version2.Colour=jalview.schemabinding.version2.descriptors.ColourDescriptor
-jalview.schemabinding.version2.MapListFrom=jalview.schemabinding.version2.descriptors.MapListFromDescriptor
 jalview.schemabinding.version2.PdbentryItem=jalview.schemabinding.version2.descriptors.PdbentryItemDescriptor
-jalview.schemabinding.version2.JGroup=jalview.schemabinding.version2.descriptors.JGroupDescriptor
+jalview.schemabinding.version2.MapListFrom=jalview.schemabinding.version2.descriptors.MapListFromDescriptor
 jalview.schemabinding.version2.FeatureSettings=jalview.schemabinding.version2.descriptors.FeatureSettingsDescriptor
-jalview.schemabinding.version2.VamsasModel=jalview.schemabinding.version2.descriptors.VamsasModelDescriptor
-jalview.schemabinding.version2.JalviewUserColours=jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor
+jalview.schemabinding.version2.JGroup=jalview.schemabinding.version2.descriptors.JGroupDescriptor
 jalview.schemabinding.version2.MapListTo=jalview.schemabinding.version2.descriptors.MapListToDescriptor
+jalview.schemabinding.version2.JalviewUserColours=jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor
+jalview.schemabinding.version2.VamsasModel=jalview.schemabinding.version2.descriptors.VamsasModelDescriptor
 jalview.schemabinding.version2.Pdbentry=jalview.schemabinding.version2.descriptors.PdbentryDescriptor
 jalview.schemabinding.version2.HiddenColumns=jalview.schemabinding.version2.descriptors.HiddenColumnsDescriptor
 jalview.schemabinding.version2.Features=jalview.schemabinding.version2.descriptors.FeaturesDescriptor
-jalview.schemabinding.version2.DseqFor=jalview.schemabinding.version2.descriptors.DseqForDescriptor
 jalview.schemabinding.version2.VAMSAS=jalview.schemabinding.version2.descriptors.VAMSASDescriptor
-jalview.schemabinding.version2.MappingChoiceItem=jalview.schemabinding.version2.descriptors.MappingChoiceItemDescriptor
+jalview.schemabinding.version2.FeatureMatcher=jalview.schemabinding.version2.descriptors.FeatureMatcherDescriptor
diff --git a/src/jalview/schemabinding/version2/Colour.java b/src/jalview/schemabinding/version2/Colour.java
index 9d5a916..d1c7297 100644
--- a/src/jalview/schemabinding/version2/Colour.java
+++ b/src/jalview/schemabinding/version2/Colour.java
@@ -27,7 +27,8 @@ public class Colour implements java.io.Serializable
   // --------------------------/
 
   /**
-   * Field _name.
+   * Single letter residue code for an alignment colour scheme, or feature type
+   * for a feature colour scheme
    */
   private java.lang.String _name;
 
@@ -42,9 +43,15 @@ public class Colour implements java.io.Serializable
   private java.lang.String _minRGB;
 
   /**
-   * loosely specified enumeration: NONE,ABOVE, or BELOW
+   * Field _noValueColour.
    */
-  private java.lang.String _threshType;
+  private jalview.schemabinding.version2.types.NoValueColour _noValueColour = jalview.schemabinding.version2.types.NoValueColour
+          .valueOf("Min");
+
+  /**
+   * Field _threshType.
+   */
+  private jalview.schemabinding.version2.types.ColourThreshTypeType _threshType;
 
   /**
    * Field _threshold.
@@ -96,6 +103,11 @@ public class Colour implements java.io.Serializable
    */
   private boolean _has_autoScale;
 
+  /**
+   * name of feature attribute to colour by, or attribute and sub-attribute
+   */
+  private java.util.Vector _attributeNameList;
+
   // ----------------/
   // - Constructors -/
   // ----------------/
@@ -103,6 +115,9 @@ public class Colour implements java.io.Serializable
   public Colour()
   {
     super();
+    setNoValueColour(jalview.schemabinding.version2.types.NoValueColour
+            .valueOf("Min"));
+    this._attributeNameList = new java.util.Vector();
   }
 
   // -----------/
@@ -110,41 +125,140 @@ public class Colour implements java.io.Serializable
   // -----------/
 
   /**
-     */
+   * 
+   * 
+   * @param vAttributeName
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAttributeName(final java.lang.String vAttributeName)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check for the maximum size
+    if (this._attributeNameList.size() >= 2)
+    {
+      throw new IndexOutOfBoundsException(
+              "addAttributeName has a maximum of 2");
+    }
+
+    this._attributeNameList.addElement(vAttributeName);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAttributeName
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAttributeName(final int index,
+          final java.lang.String vAttributeName)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check for the maximum size
+    if (this._attributeNameList.size() >= 2)
+    {
+      throw new IndexOutOfBoundsException(
+              "addAttributeName has a maximum of 2");
+    }
+
+    this._attributeNameList.add(index, vAttributeName);
+  }
+
+  /**
+   */
   public void deleteAutoScale()
   {
     this._has_autoScale = false;
   }
 
   /**
-     */
+   */
   public void deleteColourByLabel()
   {
     this._has_colourByLabel = false;
   }
 
   /**
-     */
+   */
   public void deleteMax()
   {
     this._has_max = false;
   }
 
   /**
-     */
+   */
   public void deleteMin()
   {
     this._has_min = false;
   }
 
   /**
-     */
+   */
   public void deleteThreshold()
   {
     this._has_threshold = false;
   }
 
   /**
+   * Method enumerateAttributeName.
+   * 
+   * @return an Enumeration over all java.lang.String elements
+   */
+  public java.util.Enumeration enumerateAttributeName()
+  {
+    return this._attributeNameList.elements();
+  }
+
+  /**
+   * Method getAttributeName.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the java.lang.String at the given index
+   */
+  public java.lang.String getAttributeName(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._attributeNameList.size())
+    {
+      throw new IndexOutOfBoundsException("getAttributeName: Index value '"
+              + index + "' not in range [0.."
+              + (this._attributeNameList.size() - 1) + "]");
+    }
+
+    return (java.lang.String) _attributeNameList.get(index);
+  }
+
+  /**
+   * Method getAttributeName.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public java.lang.String[] getAttributeName()
+  {
+    java.lang.String[] array = new java.lang.String[0];
+    return (java.lang.String[]) this._attributeNameList.toArray(array);
+  }
+
+  /**
+   * Method getAttributeNameCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getAttributeNameCount()
+  {
+    return this._attributeNameList.size();
+  }
+
+  /**
    * Returns the value of field 'autoScale'.
    * 
    * @return the value of field 'AutoScale'.
@@ -195,7 +309,9 @@ public class Colour implements java.io.Serializable
   }
 
   /**
-   * Returns the value of field 'name'.
+   * Returns the value of field 'name'. The field 'name' has the following
+   * description: Single letter residue code for an alignment colour scheme, or
+   * feature type for a feature colour scheme
    * 
    * @return the value of field 'Name'.
    */
@@ -205,6 +321,16 @@ public class Colour implements java.io.Serializable
   }
 
   /**
+   * Returns the value of field 'noValueColour'.
+   * 
+   * @return the value of field 'NoValueColour'.
+   */
+  public jalview.schemabinding.version2.types.NoValueColour getNoValueColour()
+  {
+    return this._noValueColour;
+  }
+
+  /**
    * Returns the value of field 'RGB'.
    * 
    * @return the value of field 'RGB'.
@@ -215,12 +341,11 @@ public class Colour implements java.io.Serializable
   }
 
   /**
-   * Returns the value of field 'threshType'. The field 'threshType' has the
-   * following description: loosely specified enumeration: NONE,ABOVE, or BELOW
+   * Returns the value of field 'threshType'.
    * 
    * @return the value of field 'ThreshType'.
    */
-  public java.lang.String getThreshType()
+  public jalview.schemabinding.version2.types.ColourThreshTypeType getThreshType()
   {
     return this._threshType;
   }
@@ -360,6 +485,76 @@ public class Colour implements java.io.Serializable
   }
 
   /**
+   */
+  public void removeAllAttributeName()
+  {
+    this._attributeNameList.clear();
+  }
+
+  /**
+   * Method removeAttributeName.
+   * 
+   * @param vAttributeName
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeAttributeName(final java.lang.String vAttributeName)
+  {
+    boolean removed = _attributeNameList.remove(vAttributeName);
+    return removed;
+  }
+
+  /**
+   * Method removeAttributeNameAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public java.lang.String removeAttributeNameAt(final int index)
+  {
+    java.lang.Object obj = this._attributeNameList.remove(index);
+    return (java.lang.String) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAttributeName
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setAttributeName(final int index,
+          final java.lang.String vAttributeName)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._attributeNameList.size())
+    {
+      throw new IndexOutOfBoundsException("setAttributeName: Index value '"
+              + index + "' not in range [0.."
+              + (this._attributeNameList.size() - 1) + "]");
+    }
+
+    this._attributeNameList.set(index, vAttributeName);
+  }
+
+  /**
+   * 
+   * 
+   * @param vAttributeNameArray
+   */
+  public void setAttributeName(final java.lang.String[] vAttributeNameArray)
+  {
+    // -- copy array
+    _attributeNameList.clear();
+
+    for (int i = 0; i < vAttributeNameArray.length; i++)
+    {
+      this._attributeNameList.add(vAttributeNameArray[i]);
+    }
+  }
+
+  /**
    * Sets the value of field 'autoScale'.
    * 
    * @param autoScale
@@ -419,7 +614,9 @@ public class Colour implements java.io.Serializable
   }
 
   /**
-   * Sets the value of field 'name'.
+   * Sets the value of field 'name'. The field 'name' has the following
+   * description: Single letter residue code for an alignment colour scheme, or
+   * feature type for a feature colour scheme
    * 
    * @param name
    *          the value of field 'name'.
@@ -430,6 +627,18 @@ public class Colour implements java.io.Serializable
   }
 
   /**
+   * Sets the value of field 'noValueColour'.
+   * 
+   * @param noValueColour
+   *          the value of field 'noValueColour'.
+   */
+  public void setNoValueColour(
+          final jalview.schemabinding.version2.types.NoValueColour noValueColour)
+  {
+    this._noValueColour = noValueColour;
+  }
+
+  /**
    * Sets the value of field 'RGB'.
    * 
    * @param RGB
@@ -441,13 +650,13 @@ public class Colour implements java.io.Serializable
   }
 
   /**
-   * Sets the value of field 'threshType'. The field 'threshType' has the
-   * following description: loosely specified enumeration: NONE,ABOVE, or BELOW
+   * Sets the value of field 'threshType'.
    * 
    * @param threshType
    *          the value of field 'threshType'.
    */
-  public void setThreshType(final java.lang.String threshType)
+  public void setThreshType(
+          final jalview.schemabinding.version2.types.ColourThreshTypeType threshType)
   {
     this._threshType = threshType;
   }
@@ -480,8 +689,8 @@ public class Colour implements java.io.Serializable
           throws org.exolab.castor.xml.MarshalException,
           org.exolab.castor.xml.ValidationException
   {
-    return (jalview.schemabinding.version2.Colour) Unmarshaller.unmarshal(
-            jalview.schemabinding.version2.Colour.class, reader);
+    return (jalview.schemabinding.version2.Colour) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.Colour.class, reader);
   }
 
   /**
diff --git a/src/jalview/schemabinding/version2/CompoundMatcher.java b/src/jalview/schemabinding/version2/CompoundMatcher.java
new file mode 100644
index 0000000..27714e2
--- /dev/null
+++ b/src/jalview/schemabinding/version2/CompoundMatcher.java
@@ -0,0 +1,374 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class CompoundMatcher.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class CompoundMatcher implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * If true, matchers are AND-ed, if false they are OR-ed
+   */
+  private boolean _and;
+
+  /**
+   * keeps track of state for field: _and
+   */
+  private boolean _has_and;
+
+  /**
+   * Field _matcherSetList.
+   */
+  private java.util.Vector _matcherSetList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public CompoundMatcher()
+  {
+    super();
+    this._matcherSetList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vMatcherSet
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addMatcherSet(
+          final jalview.schemabinding.version2.MatcherSet vMatcherSet)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check for the maximum size
+    if (this._matcherSetList.size() >= 2)
+    {
+      throw new IndexOutOfBoundsException(
+              "addMatcherSet has a maximum of 2");
+    }
+
+    this._matcherSetList.addElement(vMatcherSet);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vMatcherSet
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addMatcherSet(final int index,
+          final jalview.schemabinding.version2.MatcherSet vMatcherSet)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check for the maximum size
+    if (this._matcherSetList.size() >= 2)
+    {
+      throw new IndexOutOfBoundsException(
+              "addMatcherSet has a maximum of 2");
+    }
+
+    this._matcherSetList.add(index, vMatcherSet);
+  }
+
+  /**
+   */
+  public void deleteAnd()
+  {
+    this._has_and = false;
+  }
+
+  /**
+   * Method enumerateMatcherSet.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.MatcherSet
+   *         elements
+   */
+  public java.util.Enumeration enumerateMatcherSet()
+  {
+    return this._matcherSetList.elements();
+  }
+
+  /**
+   * Returns the value of field 'and'. The field 'and' has the following
+   * description: If true, matchers are AND-ed, if false they are OR-ed
+   * 
+   * @return the value of field 'And'.
+   */
+  public boolean getAnd()
+  {
+    return this._and;
+  }
+
+  /**
+   * Method getMatcherSet.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.MatcherSet at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.MatcherSet getMatcherSet(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._matcherSetList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "getMatcherSet: Index value '" + index + "' not in range [0.."
+                      + (this._matcherSetList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.MatcherSet) _matcherSetList
+            .get(index);
+  }
+
+  /**
+   * Method getMatcherSet.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.schemabinding.version2.MatcherSet[] getMatcherSet()
+  {
+    jalview.schemabinding.version2.MatcherSet[] array = new jalview.schemabinding.version2.MatcherSet[0];
+    return (jalview.schemabinding.version2.MatcherSet[]) this._matcherSetList
+            .toArray(array);
+  }
+
+  /**
+   * Method getMatcherSetCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getMatcherSetCount()
+  {
+    return this._matcherSetList.size();
+  }
+
+  /**
+   * Method hasAnd.
+   * 
+   * @return true if at least one And has been added
+   */
+  public boolean hasAnd()
+  {
+    return this._has_and;
+  }
+
+  /**
+   * Returns the value of field 'and'. The field 'and' has the following
+   * description: If true, matchers are AND-ed, if false they are OR-ed
+   * 
+   * @return the value of field 'And'.
+   */
+  public boolean isAnd()
+  {
+    return this._and;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   */
+  public void removeAllMatcherSet()
+  {
+    this._matcherSetList.clear();
+  }
+
+  /**
+   * Method removeMatcherSet.
+   * 
+   * @param vMatcherSet
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeMatcherSet(
+          final jalview.schemabinding.version2.MatcherSet vMatcherSet)
+  {
+    boolean removed = _matcherSetList.remove(vMatcherSet);
+    return removed;
+  }
+
+  /**
+   * Method removeMatcherSetAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.MatcherSet removeMatcherSetAt(
+          final int index)
+  {
+    java.lang.Object obj = this._matcherSetList.remove(index);
+    return (jalview.schemabinding.version2.MatcherSet) obj;
+  }
+
+  /**
+   * Sets the value of field 'and'. The field 'and' has the following
+   * description: If true, matchers are AND-ed, if false they are OR-ed
+   * 
+   * @param and
+   *          the value of field 'and'.
+   */
+  public void setAnd(final boolean and)
+  {
+    this._and = and;
+    this._has_and = true;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vMatcherSet
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setMatcherSet(final int index,
+          final jalview.schemabinding.version2.MatcherSet vMatcherSet)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._matcherSetList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "setMatcherSet: Index value '" + index + "' not in range [0.."
+                      + (this._matcherSetList.size() - 1) + "]");
+    }
+
+    this._matcherSetList.set(index, vMatcherSet);
+  }
+
+  /**
+   * 
+   * 
+   * @param vMatcherSetArray
+   */
+  public void setMatcherSet(
+          final jalview.schemabinding.version2.MatcherSet[] vMatcherSetArray)
+  {
+    // -- copy array
+    _matcherSetList.clear();
+
+    for (int i = 0; i < vMatcherSetArray.length; i++)
+    {
+      this._matcherSetList.add(vMatcherSetArray[i]);
+    }
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.CompoundMatcher
+   */
+  public static jalview.schemabinding.version2.CompoundMatcher unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.CompoundMatcher) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.CompoundMatcher.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
+
+}
diff --git a/src/jalview/schemabinding/version2/FeatureMatcher.java b/src/jalview/schemabinding/version2/FeatureMatcher.java
new file mode 100644
index 0000000..4d29cab
--- /dev/null
+++ b/src/jalview/schemabinding/version2/FeatureMatcher.java
@@ -0,0 +1,383 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class FeatureMatcher.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class FeatureMatcher implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _by.
+   */
+  private jalview.schemabinding.version2.types.FeatureMatcherByType _by;
+
+  /**
+   * name of feature attribute to filter on, or attribute and sub-attribute
+   */
+  private java.util.Vector _attributeNameList;
+
+  /**
+   * Field _condition.
+   */
+  private java.lang.String _condition;
+
+  /**
+   * Field _value.
+   */
+  private java.lang.String _value;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public FeatureMatcher()
+  {
+    super();
+    this._attributeNameList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vAttributeName
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAttributeName(final java.lang.String vAttributeName)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check for the maximum size
+    if (this._attributeNameList.size() >= 2)
+    {
+      throw new IndexOutOfBoundsException(
+              "addAttributeName has a maximum of 2");
+    }
+
+    this._attributeNameList.addElement(vAttributeName);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAttributeName
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAttributeName(final int index,
+          final java.lang.String vAttributeName)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check for the maximum size
+    if (this._attributeNameList.size() >= 2)
+    {
+      throw new IndexOutOfBoundsException(
+              "addAttributeName has a maximum of 2");
+    }
+
+    this._attributeNameList.add(index, vAttributeName);
+  }
+
+  /**
+   * Method enumerateAttributeName.
+   * 
+   * @return an Enumeration over all java.lang.String elements
+   */
+  public java.util.Enumeration enumerateAttributeName()
+  {
+    return this._attributeNameList.elements();
+  }
+
+  /**
+   * Method getAttributeName.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the java.lang.String at the given index
+   */
+  public java.lang.String getAttributeName(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._attributeNameList.size())
+    {
+      throw new IndexOutOfBoundsException("getAttributeName: Index value '"
+              + index + "' not in range [0.."
+              + (this._attributeNameList.size() - 1) + "]");
+    }
+
+    return (java.lang.String) _attributeNameList.get(index);
+  }
+
+  /**
+   * Method getAttributeName.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public java.lang.String[] getAttributeName()
+  {
+    java.lang.String[] array = new java.lang.String[0];
+    return (java.lang.String[]) this._attributeNameList.toArray(array);
+  }
+
+  /**
+   * Method getAttributeNameCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getAttributeNameCount()
+  {
+    return this._attributeNameList.size();
+  }
+
+  /**
+   * Returns the value of field 'by'.
+   * 
+   * @return the value of field 'By'.
+   */
+  public jalview.schemabinding.version2.types.FeatureMatcherByType getBy()
+  {
+    return this._by;
+  }
+
+  /**
+   * Returns the value of field 'condition'.
+   * 
+   * @return the value of field 'Condition'.
+   */
+  public java.lang.String getCondition()
+  {
+    return this._condition;
+  }
+
+  /**
+   * Returns the value of field 'value'.
+   * 
+   * @return the value of field 'Value'.
+   */
+  public java.lang.String getValue()
+  {
+    return this._value;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   */
+  public void removeAllAttributeName()
+  {
+    this._attributeNameList.clear();
+  }
+
+  /**
+   * Method removeAttributeName.
+   * 
+   * @param vAttributeName
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeAttributeName(final java.lang.String vAttributeName)
+  {
+    boolean removed = _attributeNameList.remove(vAttributeName);
+    return removed;
+  }
+
+  /**
+   * Method removeAttributeNameAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public java.lang.String removeAttributeNameAt(final int index)
+  {
+    java.lang.Object obj = this._attributeNameList.remove(index);
+    return (java.lang.String) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAttributeName
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setAttributeName(final int index,
+          final java.lang.String vAttributeName)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._attributeNameList.size())
+    {
+      throw new IndexOutOfBoundsException("setAttributeName: Index value '"
+              + index + "' not in range [0.."
+              + (this._attributeNameList.size() - 1) + "]");
+    }
+
+    this._attributeNameList.set(index, vAttributeName);
+  }
+
+  /**
+   * 
+   * 
+   * @param vAttributeNameArray
+   */
+  public void setAttributeName(final java.lang.String[] vAttributeNameArray)
+  {
+    // -- copy array
+    _attributeNameList.clear();
+
+    for (int i = 0; i < vAttributeNameArray.length; i++)
+    {
+      this._attributeNameList.add(vAttributeNameArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'by'.
+   * 
+   * @param by
+   *          the value of field 'by'.
+   */
+  public void setBy(
+          final jalview.schemabinding.version2.types.FeatureMatcherByType by)
+  {
+    this._by = by;
+  }
+
+  /**
+   * Sets the value of field 'condition'.
+   * 
+   * @param condition
+   *          the value of field 'condition'.
+   */
+  public void setCondition(final java.lang.String condition)
+  {
+    this._condition = condition;
+  }
+
+  /**
+   * Sets the value of field 'value'.
+   * 
+   * @param value
+   *          the value of field 'value'.
+   */
+  public void setValue(final java.lang.String value)
+  {
+    this._value = value;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.FeatureMatcher
+   */
+  public static jalview.schemabinding.version2.FeatureMatcher unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.FeatureMatcher) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.FeatureMatcher.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
+
+}
diff --git a/src/jalview/schemabinding/version2/FeatureMatcherSet.java b/src/jalview/schemabinding/version2/FeatureMatcherSet.java
new file mode 100644
index 0000000..2d79a98
--- /dev/null
+++ b/src/jalview/schemabinding/version2/FeatureMatcherSet.java
@@ -0,0 +1,200 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * A feature match condition, which may be simple or compound
+ * 
+ * @version $Revision$ $Date$
+ */
+public class FeatureMatcherSet implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Internal choice value storage
+   */
+  private java.lang.Object _choiceValue;
+
+  /**
+   * Field _matchCondition.
+   */
+  private MatchCondition _matchCondition;
+
+  /**
+   * Field _compoundMatcher.
+   */
+  private CompoundMatcher _compoundMatcher;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public FeatureMatcherSet()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'choiceValue'. The field 'choiceValue' has the
+   * following description: Internal choice value storage
+   * 
+   * @return the value of field 'ChoiceValue'.
+   */
+  public java.lang.Object getChoiceValue()
+  {
+    return this._choiceValue;
+  }
+
+  /**
+   * Returns the value of field 'compoundMatcher'.
+   * 
+   * @return the value of field 'CompoundMatcher'.
+   */
+  public CompoundMatcher getCompoundMatcher()
+  {
+    return this._compoundMatcher;
+  }
+
+  /**
+   * Returns the value of field 'matchCondition'.
+   * 
+   * @return the value of field 'MatchCondition'.
+   */
+  public MatchCondition getMatchCondition()
+  {
+    return this._matchCondition;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'compoundMatcher'.
+   * 
+   * @param compoundMatcher
+   *          the value of field 'compoundMatcher'.
+   */
+  public void setCompoundMatcher(final CompoundMatcher compoundMatcher)
+  {
+    this._compoundMatcher = compoundMatcher;
+    this._choiceValue = compoundMatcher;
+  }
+
+  /**
+   * Sets the value of field 'matchCondition'.
+   * 
+   * @param matchCondition
+   *          the value of field 'matchCondition'.
+   */
+  public void setMatchCondition(final MatchCondition matchCondition)
+  {
+    this._matchCondition = matchCondition;
+    this._choiceValue = matchCondition;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.FeatureMatcherSet
+   */
+  public static jalview.schemabinding.version2.FeatureMatcherSet unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.FeatureMatcherSet) Unmarshaller
+            .unmarshal(
+                    jalview.schemabinding.version2.FeatureMatcherSet.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
+
+}
diff --git a/src/jalview/schemabinding/version2/Filter.java b/src/jalview/schemabinding/version2/Filter.java
new file mode 100644
index 0000000..45323a7
--- /dev/null
+++ b/src/jalview/schemabinding/version2/Filter.java
@@ -0,0 +1,181 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class Filter.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class Filter implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _featureType.
+   */
+  private java.lang.String _featureType;
+
+  /**
+   * Field _matcherSet.
+   */
+  private jalview.schemabinding.version2.MatcherSet _matcherSet;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Filter()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Returns the value of field 'featureType'.
+   * 
+   * @return the value of field 'FeatureType'.
+   */
+  public java.lang.String getFeatureType()
+  {
+    return this._featureType;
+  }
+
+  /**
+   * Returns the value of field 'matcherSet'.
+   * 
+   * @return the value of field 'MatcherSet'.
+   */
+  public jalview.schemabinding.version2.MatcherSet getMatcherSet()
+  {
+    return this._matcherSet;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Sets the value of field 'featureType'.
+   * 
+   * @param featureType
+   *          the value of field 'featureType'.
+   */
+  public void setFeatureType(final java.lang.String featureType)
+  {
+    this._featureType = featureType;
+  }
+
+  /**
+   * Sets the value of field 'matcherSet'.
+   * 
+   * @param matcherSet
+   *          the value of field 'matcherSet'.
+   */
+  public void setMatcherSet(
+          final jalview.schemabinding.version2.MatcherSet matcherSet)
+  {
+    this._matcherSet = matcherSet;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.Filter
+   */
+  public static jalview.schemabinding.version2.Filter unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.Filter) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.Filter.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
+
+}
diff --git a/src/jalview/schemabinding/version2/JalviewUserColours.java b/src/jalview/schemabinding/version2/JalviewUserColours.java
index 042f092..c8d52ac 100644
--- a/src/jalview/schemabinding/version2/JalviewUserColours.java
+++ b/src/jalview/schemabinding/version2/JalviewUserColours.java
@@ -42,6 +42,11 @@ public class JalviewUserColours implements java.io.Serializable
    */
   private java.util.Vector _colourList;
 
+  /**
+   * Field _filterList.
+   */
+  private java.util.Vector _filterList;
+
   // ----------------/
   // - Constructors -/
   // ----------------/
@@ -50,6 +55,7 @@ public class JalviewUserColours implements java.io.Serializable
   {
     super();
     this._colourList = new java.util.Vector();
+    this._filterList = new java.util.Vector();
   }
 
   // -----------/
@@ -84,6 +90,33 @@ public class JalviewUserColours implements java.io.Serializable
   }
 
   /**
+   * 
+   * 
+   * @param vFilter
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addFilter(final Filter vFilter)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._filterList.addElement(vFilter);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vFilter
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addFilter(final int index, final Filter vFilter)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._filterList.add(index, vFilter);
+  }
+
+  /**
    * Method enumerateColour.
    * 
    * @return an Enumeration over all Colour elements
@@ -94,6 +127,16 @@ public class JalviewUserColours implements java.io.Serializable
   }
 
   /**
+   * Method enumerateFilter.
+   * 
+   * @return an Enumeration over all Filter elements
+   */
+  public java.util.Enumeration enumerateFilter()
+  {
+    return this._filterList.elements();
+  }
+
+  /**
    * Method getColour.
    * 
    * @param index
@@ -107,9 +150,9 @@ public class JalviewUserColours implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._colourList.size())
     {
-      throw new IndexOutOfBoundsException("getColour: Index value '"
-              + index + "' not in range [0.."
-              + (this._colourList.size() - 1) + "]");
+      throw new IndexOutOfBoundsException(
+              "getColour: Index value '" + index + "' not in range [0.."
+                      + (this._colourList.size() - 1) + "]");
     }
 
     return (Colour) _colourList.get(index);
@@ -141,6 +184,53 @@ public class JalviewUserColours implements java.io.Serializable
   }
 
   /**
+   * Method getFilter.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the Filter at the given index
+   */
+  public Filter getFilter(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._filterList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "getFilter: Index value '" + index + "' not in range [0.."
+                      + (this._filterList.size() - 1) + "]");
+    }
+
+    return (Filter) _filterList.get(index);
+  }
+
+  /**
+   * Method getFilter.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public Filter[] getFilter()
+  {
+    Filter[] array = new Filter[0];
+    return (Filter[]) this._filterList.toArray(array);
+  }
+
+  /**
+   * Method getFilterCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getFilterCount()
+  {
+    return this._filterList.size();
+  }
+
+  /**
    * Returns the value of field 'schemeName'.
    * 
    * @return the value of field 'SchemeName'.
@@ -217,13 +307,20 @@ public class JalviewUserColours implements java.io.Serializable
   }
 
   /**
-     */
+   */
   public void removeAllColour()
   {
     this._colourList.clear();
   }
 
   /**
+   */
+  public void removeAllFilter()
+  {
+    this._filterList.clear();
+  }
+
+  /**
    * Method removeColour.
    * 
    * @param vColour
@@ -248,6 +345,30 @@ public class JalviewUserColours implements java.io.Serializable
   }
 
   /**
+   * Method removeFilter.
+   * 
+   * @param vFilter
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeFilter(final Filter vFilter)
+  {
+    boolean removed = _filterList.remove(vFilter);
+    return removed;
+  }
+
+  /**
+   * Method removeFilterAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public Filter removeFilterAt(final int index)
+  {
+    java.lang.Object obj = this._filterList.remove(index);
+    return (Filter) obj;
+  }
+
+  /**
    * 
    * 
    * @param index
@@ -261,9 +382,9 @@ public class JalviewUserColours implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._colourList.size())
     {
-      throw new IndexOutOfBoundsException("setColour: Index value '"
-              + index + "' not in range [0.."
-              + (this._colourList.size() - 1) + "]");
+      throw new IndexOutOfBoundsException(
+              "setColour: Index value '" + index + "' not in range [0.."
+                      + (this._colourList.size() - 1) + "]");
     }
 
     this._colourList.set(index, vColour);
@@ -286,6 +407,44 @@ public class JalviewUserColours implements java.io.Serializable
   }
 
   /**
+   * 
+   * 
+   * @param index
+   * @param vFilter
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setFilter(final int index, final Filter vFilter)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._filterList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "setFilter: Index value '" + index + "' not in range [0.."
+                      + (this._filterList.size() - 1) + "]");
+    }
+
+    this._filterList.set(index, vFilter);
+  }
+
+  /**
+   * 
+   * 
+   * @param vFilterArray
+   */
+  public void setFilter(final Filter[] vFilterArray)
+  {
+    // -- copy array
+    _filterList.clear();
+
+    for (int i = 0; i < vFilterArray.length; i++)
+    {
+      this._filterList.add(vFilterArray[i]);
+    }
+  }
+
+  /**
    * Sets the value of field 'schemeName'.
    * 
    * @param schemeName
diff --git a/src/jalview/schemabinding/version2/MatchCondition.java b/src/jalview/schemabinding/version2/MatchCondition.java
new file mode 100644
index 0000000..af2f3f5
--- /dev/null
+++ b/src/jalview/schemabinding/version2/MatchCondition.java
@@ -0,0 +1,126 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class MatchCondition.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class MatchCondition extends FeatureMatcher
+        implements java.io.Serializable
+{
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public MatchCondition()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.FeatureMatcher
+   */
+  public static jalview.schemabinding.version2.FeatureMatcher unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.FeatureMatcher) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.MatchCondition.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
+
+}
diff --git a/src/jalview/schemabinding/version2/MatcherSet.java b/src/jalview/schemabinding/version2/MatcherSet.java
new file mode 100644
index 0000000..6fde9e4
--- /dev/null
+++ b/src/jalview/schemabinding/version2/MatcherSet.java
@@ -0,0 +1,126 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * optional filter(s) applied to the feature type
+ * 
+ * @version $Revision$ $Date$
+ */
+public class MatcherSet extends FeatureMatcherSet
+        implements java.io.Serializable
+{
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public MatcherSet()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid()
+  {
+    try
+    {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.FeatureMatcherSet
+   */
+  public static jalview.schemabinding.version2.FeatureMatcherSet unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.FeatureMatcherSet) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.MatcherSet.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
+
+}
diff --git a/src/jalview/schemabinding/version2/OtherData.java b/src/jalview/schemabinding/version2/OtherData.java
index fb6b276..31797fe 100644
--- a/src/jalview/schemabinding/version2/OtherData.java
+++ b/src/jalview/schemabinding/version2/OtherData.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-//---------------------------------/
-//- Imported classes and packages -/
+  //---------------------------------/
+ //- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,163 +19,181 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class OtherData implements java.io.Serializable
-{
-
-  // --------------------------/
-  // - Class/Member Variables -/
-  // --------------------------/
-
-  /**
-   * Field _key.
-   */
-  private java.lang.String _key;
-
-  /**
-   * Field _value.
-   */
-  private java.lang.String _value;
-
-  // ----------------/
-  // - Constructors -/
-  // ----------------/
-
-  public OtherData()
-  {
-    super();
-  }
-
-  // -----------/
-  // - Methods -/
-  // -----------/
-
-  /**
-   * Returns the value of field 'key'.
-   * 
-   * @return the value of field 'Key'.
-   */
-  public java.lang.String getKey()
-  {
-    return this._key;
-  }
-
-  /**
-   * Returns the value of field 'value'.
-   * 
-   * @return the value of field 'Value'.
-   */
-  public java.lang.String getValue()
-  {
-    return this._value;
-  }
-
-  /**
-   * Method isValid.
-   * 
-   * @return true if this object is valid according to the schema
-   */
-  public boolean isValid()
-  {
-    try
-    {
-      validate();
-    } catch (org.exolab.castor.xml.ValidationException vex)
-    {
-      return false;
+public class OtherData implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _key.
+     */
+    private java.lang.String _key;
+
+    /**
+     * key2 may be used for a sub-attribute of key
+     */
+    private java.lang.String _key2;
+
+    /**
+     * Field _value.
+     */
+    private java.lang.String _value;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public OtherData() {
+        super();
+    }
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Returns the value of field 'key'.
+     * 
+     * @return the value of field 'Key'.
+     */
+    public java.lang.String getKey(
+    ) {
+        return this._key;
+    }
+
+    /**
+     * Returns the value of field 'key2'. The field 'key2' has the
+     * following description: key2 may be used for a sub-attribute
+     * of key
+     * 
+     * @return the value of field 'Key2'.
+     */
+    public java.lang.String getKey2(
+    ) {
+        return this._key2;
+    }
+
+    /**
+     * Returns the value of field 'value'.
+     * 
+     * @return the value of field 'Value'.
+     */
+    public java.lang.String getValue(
+    ) {
+        return this._value;
+    }
+
+    /**
+     * Method isValid.
+     * 
+     * @return true if this object is valid according to the schema
+     */
+    public boolean isValid(
+    ) {
+        try {
+            validate();
+        } catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    }
+
+    /**
+     * 
+     * 
+     * @param out
+     * @throws org.exolab.castor.xml.MarshalException if object is
+     * null or if any SAXException is thrown during marshaling
+     * @throws org.exolab.castor.xml.ValidationException if this
+     * object is an invalid instance according to the schema
+     */
+    public void marshal(
+            final java.io.Writer out)
+    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+        Marshaller.marshal(this, out);
+    }
+
+    /**
+     * 
+     * 
+     * @param handler
+     * @throws java.io.IOException if an IOException occurs during
+     * marshaling
+     * @throws org.exolab.castor.xml.ValidationException if this
+     * object is an invalid instance according to the schema
+     * @throws org.exolab.castor.xml.MarshalException if object is
+     * null or if any SAXException is thrown during marshaling
+     */
+    public void marshal(
+            final org.xml.sax.ContentHandler handler)
+    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+        Marshaller.marshal(this, handler);
+    }
+
+    /**
+     * Sets the value of field 'key'.
+     * 
+     * @param key the value of field 'key'.
+     */
+    public void setKey(
+            final java.lang.String key) {
+        this._key = key;
+    }
+
+    /**
+     * Sets the value of field 'key2'. The field 'key2' has the
+     * following description: key2 may be used for a sub-attribute
+     * of key
+     * 
+     * @param key2 the value of field 'key2'.
+     */
+    public void setKey2(
+            final java.lang.String key2) {
+        this._key2 = key2;
+    }
+
+    /**
+     * Sets the value of field 'value'.
+     * 
+     * @param value the value of field 'value'.
+     */
+    public void setValue(
+            final java.lang.String value) {
+        this._value = value;
+    }
+
+    /**
+     * Method unmarshal.
+     * 
+     * @param reader
+     * @throws org.exolab.castor.xml.MarshalException if object is
+     * null or if any SAXException is thrown during marshaling
+     * @throws org.exolab.castor.xml.ValidationException if this
+     * object is an invalid instance according to the schema
+     * @return the unmarshaled
+     * jalview.schemabinding.version2.OtherData
+     */
+    public static jalview.schemabinding.version2.OtherData unmarshal(
+            final java.io.Reader reader)
+    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+        return (jalview.schemabinding.version2.OtherData) Unmarshaller.unmarshal(jalview.schemabinding.version2.OtherData.class, reader);
+    }
+
+    /**
+     * 
+     * 
+     * @throws org.exolab.castor.xml.ValidationException if this
+     * object is an invalid instance according to the schema
+     */
+    public void validate(
+    )
+    throws org.exolab.castor.xml.ValidationException {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
     }
-    return true;
-  }
-
-  /**
-   * 
-   * 
-   * @param out
-   * @throws org.exolab.castor.xml.MarshalException
-   *           if object is null or if any SAXException is thrown during
-   *           marshaling
-   * @throws org.exolab.castor.xml.ValidationException
-   *           if this object is an invalid instance according to the schema
-   */
-  public void marshal(final java.io.Writer out)
-          throws org.exolab.castor.xml.MarshalException,
-          org.exolab.castor.xml.ValidationException
-  {
-    Marshaller.marshal(this, out);
-  }
-
-  /**
-   * 
-   * 
-   * @param handler
-   * @throws java.io.IOException
-   *           if an IOException occurs during marshaling
-   * @throws org.exolab.castor.xml.ValidationException
-   *           if this object is an invalid instance according to the schema
-   * @throws org.exolab.castor.xml.MarshalException
-   *           if object is null or if any SAXException is thrown during
-   *           marshaling
-   */
-  public void marshal(final org.xml.sax.ContentHandler handler)
-          throws java.io.IOException,
-          org.exolab.castor.xml.MarshalException,
-          org.exolab.castor.xml.ValidationException
-  {
-    Marshaller.marshal(this, handler);
-  }
-
-  /**
-   * Sets the value of field 'key'.
-   * 
-   * @param key
-   *          the value of field 'key'.
-   */
-  public void setKey(final java.lang.String key)
-  {
-    this._key = key;
-  }
-
-  /**
-   * Sets the value of field 'value'.
-   * 
-   * @param value
-   *          the value of field 'value'.
-   */
-  public void setValue(final java.lang.String value)
-  {
-    this._value = value;
-  }
-
-  /**
-   * Method unmarshal.
-   * 
-   * @param reader
-   * @throws org.exolab.castor.xml.MarshalException
-   *           if object is null or if any SAXException is thrown during
-   *           marshaling
-   * @throws org.exolab.castor.xml.ValidationException
-   *           if this object is an invalid instance according to the schema
-   * @return the unmarshaled jalview.schemabinding.version2.OtherData
-   */
-  public static jalview.schemabinding.version2.OtherData unmarshal(
-          final java.io.Reader reader)
-          throws org.exolab.castor.xml.MarshalException,
-          org.exolab.castor.xml.ValidationException
-  {
-    return (jalview.schemabinding.version2.OtherData) Unmarshaller
-            .unmarshal(jalview.schemabinding.version2.OtherData.class,
-                    reader);
-  }
-
-  /**
-   * 
-   * 
-   * @throws org.exolab.castor.xml.ValidationException
-   *           if this object is an invalid instance according to the schema
-   */
-  public void validate() throws org.exolab.castor.xml.ValidationException
-  {
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-    validator.validate(this);
-  }
 
 }
diff --git a/src/jalview/schemabinding/version2/Setting.java b/src/jalview/schemabinding/version2/Setting.java
index c458971..59e9522 100644
--- a/src/jalview/schemabinding/version2/Setting.java
+++ b/src/jalview/schemabinding/version2/Setting.java
@@ -73,6 +73,12 @@ public class Setting implements java.io.Serializable
   private boolean _has_mincolour;
 
   /**
+   * Field _noValueColour.
+   */
+  private jalview.schemabinding.version2.types.NoValueColour _noValueColour = jalview.schemabinding.version2.types.NoValueColour
+          .valueOf("Min");
+
+  /**
    * threshold value for graduated feature colour
    * 
    */
@@ -134,6 +140,16 @@ public class Setting implements java.io.Serializable
    */
   private boolean _has_autoScale;
 
+  /**
+   * name of feature attribute to colour by, or attribute and sub-attribute
+   */
+  private java.util.Vector _attributeNameList;
+
+  /**
+   * optional filter(s) applied to the feature type
+   */
+  private jalview.schemabinding.version2.MatcherSet _matcherSet;
+
   // ----------------/
   // - Constructors -/
   // ----------------/
@@ -141,6 +157,9 @@ public class Setting implements java.io.Serializable
   public Setting()
   {
     super();
+    setNoValueColour(jalview.schemabinding.version2.types.NoValueColour
+            .valueOf("Min"));
+    this._attributeNameList = new java.util.Vector();
   }
 
   // -----------/
@@ -148,76 +167,175 @@ public class Setting implements java.io.Serializable
   // -----------/
 
   /**
-     */
+   * 
+   * 
+   * @param vAttributeName
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAttributeName(final java.lang.String vAttributeName)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check for the maximum size
+    if (this._attributeNameList.size() >= 2)
+    {
+      throw new IndexOutOfBoundsException(
+              "addAttributeName has a maximum of 2");
+    }
+
+    this._attributeNameList.addElement(vAttributeName);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAttributeName
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAttributeName(final int index,
+          final java.lang.String vAttributeName)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check for the maximum size
+    if (this._attributeNameList.size() >= 2)
+    {
+      throw new IndexOutOfBoundsException(
+              "addAttributeName has a maximum of 2");
+    }
+
+    this._attributeNameList.add(index, vAttributeName);
+  }
+
+  /**
+   */
   public void deleteAutoScale()
   {
     this._has_autoScale = false;
   }
 
   /**
-     */
+   */
   public void deleteColour()
   {
     this._has_colour = false;
   }
 
   /**
-     */
+   */
   public void deleteColourByLabel()
   {
     this._has_colourByLabel = false;
   }
 
   /**
-     */
+   */
   public void deleteDisplay()
   {
     this._has_display = false;
   }
 
   /**
-     */
+   */
   public void deleteMax()
   {
     this._has_max = false;
   }
 
   /**
-     */
+   */
   public void deleteMin()
   {
     this._has_min = false;
   }
 
   /**
-     */
+   */
   public void deleteMincolour()
   {
     this._has_mincolour = false;
   }
 
   /**
-     */
+   */
   public void deleteOrder()
   {
     this._has_order = false;
   }
 
   /**
-     */
+   */
   public void deleteThreshold()
   {
     this._has_threshold = false;
   }
 
   /**
-     */
+   */
   public void deleteThreshstate()
   {
     this._has_threshstate = false;
   }
 
   /**
+   * Method enumerateAttributeName.
+   * 
+   * @return an Enumeration over all java.lang.String elements
+   */
+  public java.util.Enumeration enumerateAttributeName()
+  {
+    return this._attributeNameList.elements();
+  }
+
+  /**
+   * Method getAttributeName.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the java.lang.String at the given index
+   */
+  public java.lang.String getAttributeName(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._attributeNameList.size())
+    {
+      throw new IndexOutOfBoundsException("getAttributeName: Index value '"
+              + index + "' not in range [0.."
+              + (this._attributeNameList.size() - 1) + "]");
+    }
+
+    return (java.lang.String) _attributeNameList.get(index);
+  }
+
+  /**
+   * Method getAttributeName.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public java.lang.String[] getAttributeName()
+  {
+    java.lang.String[] array = new java.lang.String[0];
+    return (java.lang.String[]) this._attributeNameList.toArray(array);
+  }
+
+  /**
+   * Method getAttributeNameCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getAttributeNameCount()
+  {
+    return this._attributeNameList.size();
+  }
+
+  /**
    * Returns the value of field 'autoScale'.
    * 
    * @return the value of field 'AutoScale'.
@@ -258,6 +376,17 @@ public class Setting implements java.io.Serializable
   }
 
   /**
+   * Returns the value of field 'matcherSet'. The field 'matcherSet' has the
+   * following description: optional filter(s) applied to the feature type
+   * 
+   * @return the value of field 'MatcherSet'.
+   */
+  public jalview.schemabinding.version2.MatcherSet getMatcherSet()
+  {
+    return this._matcherSet;
+  }
+
+  /**
    * Returns the value of field 'max'.
    * 
    * @return the value of field 'Max'.
@@ -290,6 +419,16 @@ public class Setting implements java.io.Serializable
   }
 
   /**
+   * Returns the value of field 'noValueColour'.
+   * 
+   * @return the value of field 'NoValueColour'.
+   */
+  public jalview.schemabinding.version2.types.NoValueColour getNoValueColour()
+  {
+    return this._noValueColour;
+  }
+
+  /**
    * Returns the value of field 'order'.
    * 
    * @return the value of field 'Order'.
@@ -518,6 +657,76 @@ public class Setting implements java.io.Serializable
   }
 
   /**
+   */
+  public void removeAllAttributeName()
+  {
+    this._attributeNameList.clear();
+  }
+
+  /**
+   * Method removeAttributeName.
+   * 
+   * @param vAttributeName
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeAttributeName(final java.lang.String vAttributeName)
+  {
+    boolean removed = _attributeNameList.remove(vAttributeName);
+    return removed;
+  }
+
+  /**
+   * Method removeAttributeNameAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public java.lang.String removeAttributeNameAt(final int index)
+  {
+    java.lang.Object obj = this._attributeNameList.remove(index);
+    return (java.lang.String) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAttributeName
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setAttributeName(final int index,
+          final java.lang.String vAttributeName)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._attributeNameList.size())
+    {
+      throw new IndexOutOfBoundsException("setAttributeName: Index value '"
+              + index + "' not in range [0.."
+              + (this._attributeNameList.size() - 1) + "]");
+    }
+
+    this._attributeNameList.set(index, vAttributeName);
+  }
+
+  /**
+   * 
+   * 
+   * @param vAttributeNameArray
+   */
+  public void setAttributeName(final java.lang.String[] vAttributeNameArray)
+  {
+    // -- copy array
+    _attributeNameList.clear();
+
+    for (int i = 0; i < vAttributeNameArray.length; i++)
+    {
+      this._attributeNameList.add(vAttributeNameArray[i]);
+    }
+  }
+
+  /**
    * Sets the value of field 'autoScale'.
    * 
    * @param autoScale
@@ -566,6 +775,19 @@ public class Setting implements java.io.Serializable
   }
 
   /**
+   * Sets the value of field 'matcherSet'. The field 'matcherSet' has the
+   * following description: optional filter(s) applied to the feature type
+   * 
+   * @param matcherSet
+   *          the value of field 'matcherSet'.
+   */
+  public void setMatcherSet(
+          final jalview.schemabinding.version2.MatcherSet matcherSet)
+  {
+    this._matcherSet = matcherSet;
+  }
+
+  /**
    * Sets the value of field 'max'.
    * 
    * @param max
@@ -604,6 +826,18 @@ public class Setting implements java.io.Serializable
   }
 
   /**
+   * Sets the value of field 'noValueColour'.
+   * 
+   * @param noValueColour
+   *          the value of field 'noValueColour'.
+   */
+  public void setNoValueColour(
+          final jalview.schemabinding.version2.types.NoValueColour noValueColour)
+  {
+    this._noValueColour = noValueColour;
+  }
+
+  /**
    * Sets the value of field 'order'.
    * 
    * @param order
diff --git a/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java
index 8b1ae9e..cca4ef1 100644
--- a/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java
@@ -18,8 +18,8 @@ import jalview.schemabinding.version2.Colour;
  * 
  * @version $Revision$ $Date$
  */
-public class ColourDescriptor extends
-        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+public class ColourDescriptor
+        extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
 {
 
   // --------------------------/
@@ -55,6 +55,9 @@ public class ColourDescriptor extends
     super();
     _xmlName = "colour";
     _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
     org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
     org.exolab.castor.mapping.FieldHandler handler = null;
     org.exolab.castor.xml.FieldValidator fieldValidator = null;
@@ -197,11 +200,57 @@ public class ColourDescriptor extends
       typeValidator.setWhiteSpace("preserve");
     }
     desc.setValidator(fieldValidator);
-    // -- _threshType
+    // -- _noValueColour
     desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.String.class, "_threshType", "threshType",
+            jalview.schemabinding.version2.types.NoValueColour.class,
+            "_noValueColour", "noValueColour",
             org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Colour target = (Colour) object;
+        return target.getNoValueColour();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Colour target = (Colour) object;
+          target.setNoValueColour(
+                  (jalview.schemabinding.version2.types.NoValueColour) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    handler = new org.exolab.castor.xml.handlers.EnumFieldHandler(
+            jalview.schemabinding.version2.types.NoValueColour.class,
+            handler);
     desc.setImmutable(true);
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _noValueColour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+    }
+    desc.setValidator(fieldValidator);
+    // -- _threshType
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.types.ColourThreshTypeType.class,
+            "_threshType", "threshType",
+            org.exolab.castor.xml.NodeType.Attribute);
     handler = new org.exolab.castor.xml.XMLFieldHandler()
     {
       public java.lang.Object getValue(java.lang.Object object)
@@ -217,7 +266,8 @@ public class ColourDescriptor extends
         try
         {
           Colour target = (Colour) object;
-          target.setThreshType((java.lang.String) value);
+          target.setThreshType(
+                  (jalview.schemabinding.version2.types.ColourThreshTypeType) value);
         } catch (java.lang.Exception ex)
         {
           throw new IllegalStateException(ex.toString());
@@ -229,6 +279,10 @@ public class ColourDescriptor extends
         return null;
       }
     };
+    handler = new org.exolab.castor.xml.handlers.EnumFieldHandler(
+            jalview.schemabinding.version2.types.ColourThreshTypeType.class,
+            handler);
+    desc.setImmutable(true);
     desc.setHandler(handler);
     desc.setMultivalued(false);
     addFieldDescriptor(desc);
@@ -236,10 +290,6 @@ public class ColourDescriptor extends
     // -- validation code for: _threshType
     fieldValidator = new org.exolab.castor.xml.FieldValidator();
     { // -- local scope
-      org.exolab.castor.xml.validators.StringValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-      fieldValidator.setValidator(typeValidator);
-      typeValidator.setWhiteSpace("preserve");
     }
     desc.setValidator(fieldValidator);
     // -- _threshold
@@ -437,8 +487,8 @@ public class ColourDescriptor extends
             target.deleteColourByLabel();
             return;
           }
-          target.setColourByLabel(((java.lang.Boolean) value)
-                  .booleanValue());
+          target.setColourByLabel(
+                  ((java.lang.Boolean) value).booleanValue());
         } catch (java.lang.Exception ex)
         {
           throw new IllegalStateException(ex.toString());
@@ -518,6 +568,66 @@ public class ColourDescriptor extends
     desc.setValidator(fieldValidator);
     // -- initialize element descriptors
 
+    // -- _attributeNameList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_attributeNameList", "attributeName",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Colour target = (Colour) object;
+        return target.getAttributeName();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Colour target = (Colour) object;
+          target.addAttributeName((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public void resetValue(Object object)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Colour target = (Colour) object;
+          target.removeAllAttributeName();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _attributeNameList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    fieldValidator.setMaxOccurs(2);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
   }
 
   // -----------/
diff --git a/src/jalview/schemabinding/version2/descriptors/CompoundMatcherDescriptor.java b/src/jalview/schemabinding/version2/descriptors/CompoundMatcherDescriptor.java
new file mode 100644
index 0000000..2402d68
--- /dev/null
+++ b/src/jalview/schemabinding/version2/descriptors/CompoundMatcherDescriptor.java
@@ -0,0 +1,270 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.CompoundMatcher;
+
+/**
+ * Class CompoundMatcherDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class CompoundMatcherDescriptor
+        extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public CompoundMatcherDescriptor()
+  {
+    super();
+    _xmlName = "compoundMatcher";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _and
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_and", "and",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        CompoundMatcher target = (CompoundMatcher) object;
+        if (!target.hasAnd())
+        {
+          return null;
+        }
+        return (target.getAnd() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          CompoundMatcher target = (CompoundMatcher) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
+
+          target.setAnd(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _and
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+    // -- _matcherSetList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.MatcherSet.class,
+            "_matcherSetList", "matcherSet",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        CompoundMatcher target = (CompoundMatcher) object;
+        return target.getMatcherSet();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          CompoundMatcher target = (CompoundMatcher) object;
+          target.addMatcherSet(
+                  (jalview.schemabinding.version2.MatcherSet) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public void resetValue(Object object)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          CompoundMatcher target = (CompoundMatcher) object;
+          target.removeAllMatcherSet();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.MatcherSet();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _matcherSetList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(2);
+    fieldValidator.setMaxOccurs(2);
+    { // -- local scope
+    }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.CompoundMatcher.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
+
+}
diff --git a/src/jalview/schemabinding/version2/descriptors/FeatureMatcherDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeatureMatcherDescriptor.java
new file mode 100644
index 0000000..2df2f5b
--- /dev/null
+++ b/src/jalview/schemabinding/version2/descriptors/FeatureMatcherDescriptor.java
@@ -0,0 +1,356 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.FeatureMatcher;
+
+/**
+ * Class FeatureMatcherDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class FeatureMatcherDescriptor
+        extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public FeatureMatcherDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org/colours";
+    _xmlName = "FeatureMatcher";
+    _elementDefinition = false;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _by
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.types.FeatureMatcherByType.class,
+            "_by", "by", org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        FeatureMatcher target = (FeatureMatcher) object;
+        return target.getBy();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          FeatureMatcher target = (FeatureMatcher) object;
+          target.setBy(
+                  (jalview.schemabinding.version2.types.FeatureMatcherByType) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    handler = new org.exolab.castor.xml.handlers.EnumFieldHandler(
+            jalview.schemabinding.version2.types.FeatureMatcherByType.class,
+            handler);
+    desc.setImmutable(true);
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _by
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+    }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+    // -- _attributeNameList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_attributeNameList", "attributeName",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        FeatureMatcher target = (FeatureMatcher) object;
+        return target.getAttributeName();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          FeatureMatcher target = (FeatureMatcher) object;
+          target.addAttributeName((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public void resetValue(Object object)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          FeatureMatcher target = (FeatureMatcher) object;
+          target.removeAllAttributeName();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _attributeNameList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    fieldValidator.setMaxOccurs(2);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _condition
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_condition", "condition",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        FeatureMatcher target = (FeatureMatcher) object;
+        return target.getCondition();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          FeatureMatcher target = (FeatureMatcher) object;
+          target.setCondition((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _condition
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _value
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_value", "value",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        FeatureMatcher target = (FeatureMatcher) object;
+        return target.getValue();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          FeatureMatcher target = (FeatureMatcher) object;
+          target.setValue((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _value
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.FeatureMatcher.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
+
+}
diff --git a/src/jalview/schemabinding/version2/descriptors/FeatureMatcherSetDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeatureMatcherSetDescriptor.java
new file mode 100644
index 0000000..b3d19bb
--- /dev/null
+++ b/src/jalview/schemabinding/version2/descriptors/FeatureMatcherSetDescriptor.java
@@ -0,0 +1,258 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+import jalview.schemabinding.version2.CompoundMatcher;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.FeatureMatcherSet;
+import jalview.schemabinding.version2.MatchCondition;
+
+/**
+ * Class FeatureMatcherSetDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class FeatureMatcherSetDescriptor
+        extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public FeatureMatcherSetDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org/colours";
+    _xmlName = "FeatureMatcherSet";
+    _elementDefinition = false;
+
+    // -- set grouping compositor
+    setCompositorAsChoice();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- initialize element descriptors
+
+    // -- _matchCondition
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            MatchCondition.class, "_matchCondition", "matchCondition",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      @Override
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        FeatureMatcherSet target = (FeatureMatcherSet) object;
+        return target.getMatchCondition();
+      }
+
+      @Override
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          FeatureMatcherSet target = (FeatureMatcherSet) object;
+          target.setMatchCondition((MatchCondition) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      @Override
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new MatchCondition();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _matchCondition
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+    }
+    desc.setValidator(fieldValidator);
+    // -- _compoundMatcher
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            CompoundMatcher.class, "_compoundMatcher", "compoundMatcher",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      @Override
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        FeatureMatcherSet target = (FeatureMatcherSet) object;
+        return target.getCompoundMatcher();
+      }
+
+      @Override
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          FeatureMatcherSet target = (FeatureMatcherSet) object;
+          target.setCompoundMatcher((CompoundMatcher) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      @Override
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new CompoundMatcher();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _compoundMatcher
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+    }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  @Override
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  @Override
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  @Override
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.FeatureMatcherSet.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  @Override
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  @Override
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  @Override
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  @Override
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  @Override
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
+
+}
diff --git a/src/jalview/schemabinding/version2/descriptors/FilterDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FilterDescriptor.java
new file mode 100644
index 0000000..f58f9ae
--- /dev/null
+++ b/src/jalview/schemabinding/version2/descriptors/FilterDescriptor.java
@@ -0,0 +1,246 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.Filter;
+
+/**
+ * Class FilterDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class FilterDescriptor
+        extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public FilterDescriptor()
+  {
+    super();
+    _xmlName = "filter";
+    _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
+    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+    org.exolab.castor.mapping.FieldHandler handler = null;
+    org.exolab.castor.xml.FieldValidator fieldValidator = null;
+    // -- initialize attribute descriptors
+
+    // -- _featureType
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_featureType", "featureType",
+            org.exolab.castor.xml.NodeType.Attribute);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Filter target = (Filter) object;
+        return target.getFeatureType();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Filter target = (Filter) object;
+          target.setFeatureType((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _featureType
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+    // -- _matcherSet
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.MatcherSet.class, "_matcherSet",
+            "matcherSet", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Filter target = (Filter) object;
+        return target.getMatcherSet();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Filter target = (Filter) object;
+          target.setMatcherSet(
+                  (jalview.schemabinding.version2.MatcherSet) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.MatcherSet();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _matcherSet
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+    }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.Filter.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
+
+}
diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java
index d65de13..459d645 100644
--- a/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java
@@ -7,11 +7,13 @@
 
 package jalview.schemabinding.version2.descriptors;
 
+import jalview.schemabinding.version2.Colour;
+import jalview.schemabinding.version2.Filter;
+
 //---------------------------------/
 //- Imported classes and packages -/
 //---------------------------------/
 
-import jalview.schemabinding.version2.Colour;
 import jalview.schemabinding.version2.JalviewUserColours;
 
 /**
@@ -19,8 +21,8 @@ import jalview.schemabinding.version2.JalviewUserColours;
  * 
  * @version $Revision$ $Date$
  */
-public class JalviewUserColoursDescriptor extends
-        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+public class JalviewUserColoursDescriptor
+        extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
 {
 
   // --------------------------/
@@ -192,8 +194,8 @@ public class JalviewUserColoursDescriptor extends
       }
 
       @Override
-      public void resetValue(Object object) throws IllegalStateException,
-              IllegalArgumentException
+      public void resetValue(Object object)
+              throws IllegalStateException, IllegalArgumentException
       {
         try
         {
@@ -221,6 +223,64 @@ public class JalviewUserColoursDescriptor extends
     { // -- local scope
     }
     desc.setValidator(fieldValidator);
+    // -- _filterList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            Filter.class, "_filterList", "filter",
+            org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      @Override
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JalviewUserColours target = (JalviewUserColours) object;
+        return target.getFilter();
+      }
+
+      @Override
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JalviewUserColours target = (JalviewUserColours) object;
+          target.addFilter((Filter) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      @Override
+      public void resetValue(Object object)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JalviewUserColours target = (JalviewUserColours) object;
+          target.removeAllFilter();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      @Override
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new Filter();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _filterList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
+    }
+    desc.setValidator(fieldValidator);
   }
 
   // -----------/
diff --git a/src/jalview/schemabinding/version2/descriptors/MatchConditionDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MatchConditionDescriptor.java
new file mode 100644
index 0000000..8373421
--- /dev/null
+++ b/src/jalview/schemabinding/version2/descriptors/MatchConditionDescriptor.java
@@ -0,0 +1,148 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.MatchCondition;
+
+/**
+ * Class MatchConditionDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class MatchConditionDescriptor extends
+        jalview.schemabinding.version2.descriptors.FeatureMatcherDescriptor
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public MatchConditionDescriptor()
+  {
+    super();
+    setExtendsWithoutFlatten(
+            new jalview.schemabinding.version2.descriptors.FeatureMatcherDescriptor());
+    _xmlName = "matchCondition";
+    _elementDefinition = true;
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.MatchCondition.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
+
+}
diff --git a/src/jalview/schemabinding/version2/descriptors/MatcherSetDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MatcherSetDescriptor.java
new file mode 100644
index 0000000..2807f92
--- /dev/null
+++ b/src/jalview/schemabinding/version2/descriptors/MatcherSetDescriptor.java
@@ -0,0 +1,148 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.MatcherSet;
+
+/**
+ * Class MatcherSetDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class MatcherSetDescriptor extends
+        jalview.schemabinding.version2.descriptors.FeatureMatcherSetDescriptor
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public MatcherSetDescriptor()
+  {
+    super();
+    setExtendsWithoutFlatten(
+            new jalview.schemabinding.version2.descriptors.FeatureMatcherSetDescriptor());
+    _xmlName = "matcherSet";
+    _elementDefinition = true;
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.MatcherSet.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
+
+}
diff --git a/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java b/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java
index f582311..ab7a626 100644
--- a/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-//---------------------------------/
-//- Imported classes and packages -/
+  //---------------------------------/
+ //- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.OtherData;
@@ -18,231 +18,255 @@ import jalview.schemabinding.version2.OtherData;
  * 
  * @version $Revision$ $Date$
  */
-public class OtherDataDescriptor extends
-        org.exolab.castor.xml.util.XMLClassDescriptorImpl
-{
-
-  // --------------------------/
-  // - Class/Member Variables -/
-  // --------------------------/
-
-  /**
-   * Field _elementDefinition.
-   */
-  private boolean _elementDefinition;
-
-  /**
-   * Field _nsPrefix.
-   */
-  private java.lang.String _nsPrefix;
-
-  /**
-   * Field _nsURI.
-   */
-  private java.lang.String _nsURI;
-
-  /**
-   * Field _xmlName.
-   */
-  private java.lang.String _xmlName;
-
-  // ----------------/
-  // - Constructors -/
-  // ----------------/
-
-  public OtherDataDescriptor()
-  {
-    super();
-    _nsURI = "www.jalview.org";
-    _xmlName = "otherData";
-    _elementDefinition = true;
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
-    org.exolab.castor.mapping.FieldHandler handler = null;
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;
-    // -- initialize attribute descriptors
-
-    // -- _key
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.String.class, "_key", "key",
-            org.exolab.castor.xml.NodeType.Attribute);
-    desc.setImmutable(true);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        OtherData target = (OtherData) object;
-        return target.getKey();
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          OtherData target = (OtherData) object;
-          target.setKey((java.lang.String) value);
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
+public class OtherDataDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _elementDefinition.
+     */
+    private boolean _elementDefinition;
+
+    /**
+     * Field _nsPrefix.
+     */
+    private java.lang.String _nsPrefix;
+
+    /**
+     * Field _nsURI.
+     */
+    private java.lang.String _nsURI;
+
+    /**
+     * Field _xmlName.
+     */
+    private java.lang.String _xmlName;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public OtherDataDescriptor() {
+        super();
+        _nsURI = "www.jalview.org";
+        _xmlName = "otherData";
+        _elementDefinition = true;
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.mapping.FieldHandler             handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _key
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_key", "key", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                OtherData target = (OtherData) object;
+                return target.getKey();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    OtherData target = (OtherData) object;
+                    target.setKey( (java.lang.String) value);
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _key
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            org.exolab.castor.xml.validators.StringValidator typeValidator;
+            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+            fieldValidator.setValidator(typeValidator);
+            typeValidator.setWhiteSpace("preserve");
+        }
+        desc.setValidator(fieldValidator);
+        //-- _key2
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_key2", "key2", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                OtherData target = (OtherData) object;
+                return target.getKey2();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    OtherData target = (OtherData) object;
+                    target.setKey2( (java.lang.String) value);
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _key2
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            org.exolab.castor.xml.validators.StringValidator typeValidator;
+            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+            fieldValidator.setValidator(typeValidator);
+            typeValidator.setWhiteSpace("preserve");
+        }
+        desc.setValidator(fieldValidator);
+        //-- _value
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                OtherData target = (OtherData) object;
+                return target.getValue();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    OtherData target = (OtherData) object;
+                    target.setValue( (java.lang.String) value);
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _value
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            org.exolab.castor.xml.validators.StringValidator typeValidator;
+            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+            fieldValidator.setValidator(typeValidator);
+            typeValidator.setWhiteSpace("preserve");
         }
-      }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+    }
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
 
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
+    /**
+     * Method getAccessMode.
+     * 
+     * @return the access mode specified for this class.
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode(
+    ) {
         return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setRequired(true);
-    desc.setMultivalued(false);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _key
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    fieldValidator.setMinOccurs(1);
-    { // -- local scope
-      org.exolab.castor.xml.validators.StringValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-      fieldValidator.setValidator(typeValidator);
-      typeValidator.setWhiteSpace("preserve");
     }
-    desc.setValidator(fieldValidator);
-    // -- _value
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.String.class, "_value", "value",
-            org.exolab.castor.xml.NodeType.Attribute);
-    desc.setImmutable(true);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        OtherData target = (OtherData) object;
-        return target.getValue();
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          OtherData target = (OtherData) object;
-          target.setValue((java.lang.String) value);
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
 
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setRequired(true);
-    desc.setMultivalued(false);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _value
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    fieldValidator.setMinOccurs(1);
-    { // -- local scope
-      org.exolab.castor.xml.validators.StringValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-      fieldValidator.setValidator(typeValidator);
-      typeValidator.setWhiteSpace("preserve");
+    /**
+     * Method getIdentity.
+     * 
+     * @return the identity field, null if this class has no
+     * identity.
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
+    ) {
+        return super.getIdentity();
+    }
+
+    /**
+     * Method getJavaClass.
+     * 
+     * @return the Java class represented by this descriptor.
+     */
+    public java.lang.Class getJavaClass(
+    ) {
+        return jalview.schemabinding.version2.OtherData.class;
+    }
+
+    /**
+     * Method getNameSpacePrefix.
+     * 
+     * @return the namespace prefix to use when marshaling as XML.
+     */
+    public java.lang.String getNameSpacePrefix(
+    ) {
+        return _nsPrefix;
+    }
+
+    /**
+     * Method getNameSpaceURI.
+     * 
+     * @return the namespace URI used when marshaling and
+     * unmarshaling as XML.
+     */
+    public java.lang.String getNameSpaceURI(
+    ) {
+        return _nsURI;
+    }
+
+    /**
+     * Method getValidator.
+     * 
+     * @return a specific validator for the class described by this
+     * ClassDescriptor.
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator(
+    ) {
+        return this;
+    }
+
+    /**
+     * Method getXMLName.
+     * 
+     * @return the XML Name for the Class being described.
+     */
+    public java.lang.String getXMLName(
+    ) {
+        return _xmlName;
+    }
+
+    /**
+     * Method isElementDefinition.
+     * 
+     * @return true if XML schema definition of this Class is that
+     * of a global
+     * element or element with anonymous type definition.
+     */
+    public boolean isElementDefinition(
+    ) {
+        return _elementDefinition;
     }
-    desc.setValidator(fieldValidator);
-    // -- initialize element descriptors
-
-  }
-
-  // -----------/
-  // - Methods -/
-  // -----------/
-
-  /**
-   * Method getAccessMode.
-   * 
-   * @return the access mode specified for this class.
-   */
-  public org.exolab.castor.mapping.AccessMode getAccessMode()
-  {
-    return null;
-  }
-
-  /**
-   * Method getIdentity.
-   * 
-   * @return the identity field, null if this class has no identity.
-   */
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-  {
-    return super.getIdentity();
-  }
-
-  /**
-   * Method getJavaClass.
-   * 
-   * @return the Java class represented by this descriptor.
-   */
-  public java.lang.Class getJavaClass()
-  {
-    return jalview.schemabinding.version2.OtherData.class;
-  }
-
-  /**
-   * Method getNameSpacePrefix.
-   * 
-   * @return the namespace prefix to use when marshaling as XML.
-   */
-  public java.lang.String getNameSpacePrefix()
-  {
-    return _nsPrefix;
-  }
-
-  /**
-   * Method getNameSpaceURI.
-   * 
-   * @return the namespace URI used when marshaling and unmarshaling as XML.
-   */
-  public java.lang.String getNameSpaceURI()
-  {
-    return _nsURI;
-  }
-
-  /**
-   * Method getValidator.
-   * 
-   * @return a specific validator for the class described by this
-   *         ClassDescriptor.
-   */
-  public org.exolab.castor.xml.TypeValidator getValidator()
-  {
-    return this;
-  }
-
-  /**
-   * Method getXMLName.
-   * 
-   * @return the XML Name for the Class being described.
-   */
-  public java.lang.String getXMLName()
-  {
-    return _xmlName;
-  }
-
-  /**
-   * Method isElementDefinition.
-   * 
-   * @return true if XML schema definition of this Class is that of a global
-   *         element or element with anonymous type definition.
-   */
-  public boolean isElementDefinition()
-  {
-    return _elementDefinition;
-  }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java
index 4703f46..c816e43 100644
--- a/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java
@@ -18,8 +18,8 @@ import jalview.schemabinding.version2.Setting;
  * 
  * @version $Revision$ $Date$
  */
-public class SettingDescriptor extends
-        org.exolab.castor.xml.util.XMLClassDescriptorImpl
+public class SettingDescriptor
+        extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
 {
 
   // --------------------------/
@@ -56,6 +56,9 @@ public class SettingDescriptor extends
     _nsURI = "www.jalview.org";
     _xmlName = "setting";
     _elementDefinition = true;
+
+    // -- set grouping compositor
+    setCompositorAsSequence();
     org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
     org.exolab.castor.mapping.FieldHandler handler = null;
     org.exolab.castor.xml.FieldValidator fieldValidator = null;
@@ -331,6 +334,52 @@ public class SettingDescriptor extends
       typeValidator.setMaxInclusive(2147483647);
     }
     desc.setValidator(fieldValidator);
+    // -- _noValueColour
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.types.NoValueColour.class,
+            "_noValueColour", "noValueColour",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Setting target = (Setting) object;
+        return target.getNoValueColour();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Setting target = (Setting) object;
+          target.setNoValueColour(
+                  (jalview.schemabinding.version2.types.NoValueColour) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    handler = new org.exolab.castor.xml.handlers.EnumFieldHandler(
+            jalview.schemabinding.version2.types.NoValueColour.class,
+            handler);
+    desc.setImmutable(true);
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _noValueColour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+    }
+    desc.setValidator(fieldValidator);
     // -- _threshold
     desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
             java.lang.Float.TYPE, "_threshold", "threshold",
@@ -581,8 +630,8 @@ public class SettingDescriptor extends
             target.deleteColourByLabel();
             return;
           }
-          target.setColourByLabel(((java.lang.Boolean) value)
-                  .booleanValue());
+          target.setColourByLabel(
+                  ((java.lang.Boolean) value).booleanValue());
         } catch (java.lang.Exception ex)
         {
           throw new IllegalStateException(ex.toString());
@@ -662,6 +711,109 @@ public class SettingDescriptor extends
     desc.setValidator(fieldValidator);
     // -- initialize element descriptors
 
+    // -- _attributeNameList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_attributeNameList", "attributeName",
+            org.exolab.castor.xml.NodeType.Element);
+    desc.setImmutable(true);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Setting target = (Setting) object;
+        return target.getAttributeName();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Setting target = (Setting) object;
+          target.addAttributeName((java.lang.String) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public void resetValue(Object object)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Setting target = (Setting) object;
+          target.removeAllAttributeName();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _attributeNameList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    fieldValidator.setMaxOccurs(2);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _matcherSet
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.MatcherSet.class, "_matcherSet",
+            "matcherSet", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        Setting target = (Setting) object;
+        return target.getMatcherSet();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          Setting target = (Setting) object;
+          target.setMatcherSet(
+                  (jalview.schemabinding.version2.MatcherSet) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.MatcherSet();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _matcherSet
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+    }
+    desc.setValidator(fieldValidator);
   }
 
   // -----------/
diff --git a/src/jalview/schemabinding/version2/types/.castor.cdr b/src/jalview/schemabinding/version2/types/.castor.cdr
new file mode 100644
index 0000000..d9874b6
--- /dev/null
+++ b/src/jalview/schemabinding/version2/types/.castor.cdr
@@ -0,0 +1,5 @@
+#Thu Dec 14 15:28:22 GMT 2017
+jalview.schemabinding.version2.types.ColourNoValueColourType=jalview.schemabinding.version2.types.descriptors.ColourNoValueColourTypeDescriptor
+jalview.schemabinding.version2.types.FeatureMatcherByType=jalview.schemabinding.version2.types.descriptors.FeatureMatcherByTypeDescriptor
+jalview.schemabinding.version2.types.NoValueColour=jalview.schemabinding.version2.types.descriptors.NoValueColourDescriptor
+jalview.schemabinding.version2.types.ColourThreshTypeType=jalview.schemabinding.version2.types.descriptors.ColourThreshTypeTypeDescriptor
diff --git a/src/jalview/schemabinding/version2/types/ColourThreshTypeType.java b/src/jalview/schemabinding/version2/types/ColourThreshTypeType.java
new file mode 100644
index 0000000..0330411
--- /dev/null
+++ b/src/jalview/schemabinding/version2/types/ColourThreshTypeType.java
@@ -0,0 +1,168 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.types;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.util.Hashtable;
+
+/**
+ * Class ColourThreshTypeType.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class ColourThreshTypeType implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * The NONE type
+     */
+    public static final int NONE_TYPE = 0;
+
+    /**
+     * The instance of the NONE type
+     */
+    public static final ColourThreshTypeType NONE = new ColourThreshTypeType(NONE_TYPE, "NONE");
+
+    /**
+     * The ABOVE type
+     */
+    public static final int ABOVE_TYPE = 1;
+
+    /**
+     * The instance of the ABOVE type
+     */
+    public static final ColourThreshTypeType ABOVE = new ColourThreshTypeType(ABOVE_TYPE, "ABOVE");
+
+    /**
+     * The BELOW type
+     */
+    public static final int BELOW_TYPE = 2;
+
+    /**
+     * The instance of the BELOW type
+     */
+    public static final ColourThreshTypeType BELOW = new ColourThreshTypeType(BELOW_TYPE, "BELOW");
+
+    /**
+     * Field _memberTable.
+     */
+    private static java.util.Hashtable _memberTable = init();
+
+    /**
+     * Field type.
+     */
+    private int type = -1;
+
+    /**
+     * Field stringValue.
+     */
+    private java.lang.String stringValue = null;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    private ColourThreshTypeType(final int type, final java.lang.String value) {
+        super();
+        this.type = type;
+        this.stringValue = value;
+    }
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method enumerate.Returns an enumeration of all possible
+     * instances of ColourThreshTypeType
+     * 
+     * @return an Enumeration over all possible instances of
+     * ColourThreshTypeType
+     */
+    public static java.util.Enumeration enumerate(
+    ) {
+        return _memberTable.elements();
+    }
+
+    /**
+     * Method getType.Returns the type of this ColourThreshTypeType
+     * 
+     * @return the type of this ColourThreshTypeType
+     */
+    public int getType(
+    ) {
+        return this.type;
+    }
+
+    /**
+     * Method init.
+     * 
+     * @return the initialized Hashtable for the member table
+     */
+    private static java.util.Hashtable init(
+    ) {
+        Hashtable members = new Hashtable();
+        members.put("NONE", NONE);
+        members.put("ABOVE", ABOVE);
+        members.put("BELOW", BELOW);
+        return members;
+    }
+
+    /**
+     * Method readResolve. will be called during deserialization to
+     * replace the deserialized object with the correct constant
+     * instance.
+     * 
+     * @return this deserialized object
+     */
+    private java.lang.Object readResolve(
+    ) {
+        return valueOf(this.stringValue);
+    }
+
+    /**
+     * Method toString.Returns the String representation of this
+     * ColourThreshTypeType
+     * 
+     * @return the String representation of this ColourThreshTypeTyp
+     */
+    public java.lang.String toString(
+    ) {
+        return this.stringValue;
+    }
+
+    /**
+     * Method valueOf.Returns a new ColourThreshTypeType based on
+     * the given String value.
+     * 
+     * @param string
+     * @return the ColourThreshTypeType value of parameter 'string'
+     */
+    public static jalview.schemabinding.version2.types.ColourThreshTypeType valueOf(
+            final java.lang.String string) {
+        java.lang.Object obj = null;
+        if (string != null) {
+            obj = _memberTable.get(string);
+        }
+        if (obj == null) {
+            String err = "" + string + " is not a valid ColourThreshTypeType";
+            throw new IllegalArgumentException(err);
+        }
+        return (ColourThreshTypeType) obj;
+    }
+
+}
diff --git a/src/jalview/schemabinding/version2/types/FeatureMatcherByType.java b/src/jalview/schemabinding/version2/types/FeatureMatcherByType.java
new file mode 100644
index 0000000..6e97332
--- /dev/null
+++ b/src/jalview/schemabinding/version2/types/FeatureMatcherByType.java
@@ -0,0 +1,168 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.types;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.util.Hashtable;
+
+/**
+ * Class FeatureMatcherByType.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class FeatureMatcherByType implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * The byLabel type
+     */
+    public static final int BYLABEL_TYPE = 0;
+
+    /**
+     * The instance of the byLabel type
+     */
+    public static final FeatureMatcherByType BYLABEL = new FeatureMatcherByType(BYLABEL_TYPE, "byLabel");
+
+    /**
+     * The byScore type
+     */
+    public static final int BYSCORE_TYPE = 1;
+
+    /**
+     * The instance of the byScore type
+     */
+    public static final FeatureMatcherByType BYSCORE = new FeatureMatcherByType(BYSCORE_TYPE, "byScore");
+
+    /**
+     * The byAttribute type
+     */
+    public static final int BYATTRIBUTE_TYPE = 2;
+
+    /**
+     * The instance of the byAttribute type
+     */
+    public static final FeatureMatcherByType BYATTRIBUTE = new FeatureMatcherByType(BYATTRIBUTE_TYPE, "byAttribute");
+
+    /**
+     * Field _memberTable.
+     */
+    private static java.util.Hashtable _memberTable = init();
+
+    /**
+     * Field type.
+     */
+    private int type = -1;
+
+    /**
+     * Field stringValue.
+     */
+    private java.lang.String stringValue = null;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    private FeatureMatcherByType(final int type, final java.lang.String value) {
+        super();
+        this.type = type;
+        this.stringValue = value;
+    }
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method enumerate.Returns an enumeration of all possible
+     * instances of FeatureMatcherByType
+     * 
+     * @return an Enumeration over all possible instances of
+     * FeatureMatcherByType
+     */
+    public static java.util.Enumeration enumerate(
+    ) {
+        return _memberTable.elements();
+    }
+
+    /**
+     * Method getType.Returns the type of this FeatureMatcherByType
+     * 
+     * @return the type of this FeatureMatcherByType
+     */
+    public int getType(
+    ) {
+        return this.type;
+    }
+
+    /**
+     * Method init.
+     * 
+     * @return the initialized Hashtable for the member table
+     */
+    private static java.util.Hashtable init(
+    ) {
+        Hashtable members = new Hashtable();
+        members.put("byLabel", BYLABEL);
+        members.put("byScore", BYSCORE);
+        members.put("byAttribute", BYATTRIBUTE);
+        return members;
+    }
+
+    /**
+     * Method readResolve. will be called during deserialization to
+     * replace the deserialized object with the correct constant
+     * instance.
+     * 
+     * @return this deserialized object
+     */
+    private java.lang.Object readResolve(
+    ) {
+        return valueOf(this.stringValue);
+    }
+
+    /**
+     * Method toString.Returns the String representation of this
+     * FeatureMatcherByType
+     * 
+     * @return the String representation of this FeatureMatcherByTyp
+     */
+    public java.lang.String toString(
+    ) {
+        return this.stringValue;
+    }
+
+    /**
+     * Method valueOf.Returns a new FeatureMatcherByType based on
+     * the given String value.
+     * 
+     * @param string
+     * @return the FeatureMatcherByType value of parameter 'string'
+     */
+    public static jalview.schemabinding.version2.types.FeatureMatcherByType valueOf(
+            final java.lang.String string) {
+        java.lang.Object obj = null;
+        if (string != null) {
+            obj = _memberTable.get(string);
+        }
+        if (obj == null) {
+            String err = "" + string + " is not a valid FeatureMatcherByType";
+            throw new IllegalArgumentException(err);
+        }
+        return (FeatureMatcherByType) obj;
+    }
+
+}
diff --git a/src/jalview/schemabinding/version2/types/NoValueColour.java b/src/jalview/schemabinding/version2/types/NoValueColour.java
new file mode 100644
index 0000000..bbef3d7
--- /dev/null
+++ b/src/jalview/schemabinding/version2/types/NoValueColour.java
@@ -0,0 +1,169 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.types;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import java.util.Hashtable;
+
+/**
+ * Graduated feature colour if no score (or attribute) value
+ * 
+ * @version $Revision$ $Date$
+ */
+public class NoValueColour implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * The None type
+   */
+  public static final int NONE_TYPE = 0;
+
+  /**
+   * The instance of the None type
+   */
+  public static final NoValueColour NONE = new NoValueColour(NONE_TYPE,
+          "None");
+
+  /**
+   * The Min type
+   */
+  public static final int MIN_TYPE = 1;
+
+  /**
+   * The instance of the Min type
+   */
+  public static final NoValueColour MIN = new NoValueColour(MIN_TYPE,
+          "Min");
+
+  /**
+   * The Max type
+   */
+  public static final int MAX_TYPE = 2;
+
+  /**
+   * The instance of the Max type
+   */
+  public static final NoValueColour MAX = new NoValueColour(MAX_TYPE,
+          "Max");
+
+  /**
+   * Field _memberTable.
+   */
+  private static java.util.Hashtable _memberTable = init();
+
+  /**
+   * Field type.
+   */
+  private int type = -1;
+
+  /**
+   * Field stringValue.
+   */
+  private java.lang.String stringValue = null;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  private NoValueColour(final int type, final java.lang.String value)
+  {
+    super();
+    this.type = type;
+    this.stringValue = value;
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method enumerate.Returns an enumeration of all possible instances of
+   * NoValueColour
+   * 
+   * @return an Enumeration over all possible instances of NoValueColour
+   */
+  public static java.util.Enumeration enumerate()
+  {
+    return _memberTable.elements();
+  }
+
+  /**
+   * Method getType.Returns the type of this NoValueColour
+   * 
+   * @return the type of this NoValueColour
+   */
+  public int getType()
+  {
+    return this.type;
+  }
+
+  /**
+   * Method init.
+   * 
+   * @return the initialized Hashtable for the member table
+   */
+  private static java.util.Hashtable init()
+  {
+    Hashtable members = new Hashtable();
+    members.put("None", NONE);
+    members.put("Min", MIN);
+    members.put("Max", MAX);
+    return members;
+  }
+
+  /**
+   * Method readResolve. will be called during deserialization to replace the
+   * deserialized object with the correct constant instance.
+   * 
+   * @return this deserialized object
+   */
+  private java.lang.Object readResolve()
+  {
+    return valueOf(this.stringValue);
+  }
+
+  /**
+   * Method toString.Returns the String representation of this NoValueColour
+   * 
+   * @return the String representation of this NoValueColour
+   */
+  public java.lang.String toString()
+  {
+    return this.stringValue;
+  }
+
+  /**
+   * Method valueOf.Returns a new NoValueColour based on the given String value.
+   * 
+   * @param string
+   * @return the NoValueColour value of parameter 'string'
+   */
+  public static jalview.schemabinding.version2.types.NoValueColour valueOf(
+          final java.lang.String string)
+  {
+    java.lang.Object obj = null;
+    if (string != null)
+    {
+      obj = _memberTable.get(string);
+    }
+    if (obj == null)
+    {
+      String err = "" + string + " is not a valid NoValueColour";
+      throw new IllegalArgumentException(err);
+    }
+    return (NoValueColour) obj;
+  }
+
+}
diff --git a/src/jalview/schemabinding/version2/types/descriptors/ColourThreshTypeTypeDescriptor.java b/src/jalview/schemabinding/version2/types/descriptors/ColourThreshTypeTypeDescriptor.java
new file mode 100644
index 0000000..f978363
--- /dev/null
+++ b/src/jalview/schemabinding/version2/types/descriptors/ColourThreshTypeTypeDescriptor.java
@@ -0,0 +1,150 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.types.descriptors;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.types.ColourThreshTypeType;
+
+/**
+ * Class ColourThreshTypeTypeDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class ColourThreshTypeTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _elementDefinition.
+     */
+    private boolean _elementDefinition;
+
+    /**
+     * Field _nsPrefix.
+     */
+    private java.lang.String _nsPrefix;
+
+    /**
+     * Field _nsURI.
+     */
+    private java.lang.String _nsURI;
+
+    /**
+     * Field _xmlName.
+     */
+    private java.lang.String _xmlName;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public ColourThreshTypeTypeDescriptor() {
+        super();
+        _nsURI = "www.jalview.org/colours";
+        _xmlName = "ColourThreshTypeType";
+        _elementDefinition = false;
+    }
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode.
+     * 
+     * @return the access mode specified for this class.
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode(
+    ) {
+        return null;
+    }
+
+    /**
+     * Method getIdentity.
+     * 
+     * @return the identity field, null if this class has no
+     * identity.
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
+    ) {
+        return super.getIdentity();
+    }
+
+    /**
+     * Method getJavaClass.
+     * 
+     * @return the Java class represented by this descriptor.
+     */
+    public java.lang.Class getJavaClass(
+    ) {
+        return jalview.schemabinding.version2.types.ColourThreshTypeType.class;
+    }
+
+    /**
+     * Method getNameSpacePrefix.
+     * 
+     * @return the namespace prefix to use when marshaling as XML.
+     */
+    public java.lang.String getNameSpacePrefix(
+    ) {
+        return _nsPrefix;
+    }
+
+    /**
+     * Method getNameSpaceURI.
+     * 
+     * @return the namespace URI used when marshaling and
+     * unmarshaling as XML.
+     */
+    public java.lang.String getNameSpaceURI(
+    ) {
+        return _nsURI;
+    }
+
+    /**
+     * Method getValidator.
+     * 
+     * @return a specific validator for the class described by this
+     * ClassDescriptor.
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator(
+    ) {
+        return this;
+    }
+
+    /**
+     * Method getXMLName.
+     * 
+     * @return the XML Name for the Class being described.
+     */
+    public java.lang.String getXMLName(
+    ) {
+        return _xmlName;
+    }
+
+    /**
+     * Method isElementDefinition.
+     * 
+     * @return true if XML schema definition of this Class is that
+     * of a global
+     * element or element with anonymous type definition.
+     */
+    public boolean isElementDefinition(
+    ) {
+        return _elementDefinition;
+    }
+
+}
diff --git a/src/jalview/schemabinding/version2/types/descriptors/FeatureMatcherByTypeDescriptor.java b/src/jalview/schemabinding/version2/types/descriptors/FeatureMatcherByTypeDescriptor.java
new file mode 100644
index 0000000..e392e76
--- /dev/null
+++ b/src/jalview/schemabinding/version2/types/descriptors/FeatureMatcherByTypeDescriptor.java
@@ -0,0 +1,150 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.types.descriptors;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.types.FeatureMatcherByType;
+
+/**
+ * Class FeatureMatcherByTypeDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class FeatureMatcherByTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _elementDefinition.
+     */
+    private boolean _elementDefinition;
+
+    /**
+     * Field _nsPrefix.
+     */
+    private java.lang.String _nsPrefix;
+
+    /**
+     * Field _nsURI.
+     */
+    private java.lang.String _nsURI;
+
+    /**
+     * Field _xmlName.
+     */
+    private java.lang.String _xmlName;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public FeatureMatcherByTypeDescriptor() {
+        super();
+        _nsURI = "www.jalview.org/colours";
+        _xmlName = "FeatureMatcherByType";
+        _elementDefinition = false;
+    }
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode.
+     * 
+     * @return the access mode specified for this class.
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode(
+    ) {
+        return null;
+    }
+
+    /**
+     * Method getIdentity.
+     * 
+     * @return the identity field, null if this class has no
+     * identity.
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
+    ) {
+        return super.getIdentity();
+    }
+
+    /**
+     * Method getJavaClass.
+     * 
+     * @return the Java class represented by this descriptor.
+     */
+    public java.lang.Class getJavaClass(
+    ) {
+        return jalview.schemabinding.version2.types.FeatureMatcherByType.class;
+    }
+
+    /**
+     * Method getNameSpacePrefix.
+     * 
+     * @return the namespace prefix to use when marshaling as XML.
+     */
+    public java.lang.String getNameSpacePrefix(
+    ) {
+        return _nsPrefix;
+    }
+
+    /**
+     * Method getNameSpaceURI.
+     * 
+     * @return the namespace URI used when marshaling and
+     * unmarshaling as XML.
+     */
+    public java.lang.String getNameSpaceURI(
+    ) {
+        return _nsURI;
+    }
+
+    /**
+     * Method getValidator.
+     * 
+     * @return a specific validator for the class described by this
+     * ClassDescriptor.
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator(
+    ) {
+        return this;
+    }
+
+    /**
+     * Method getXMLName.
+     * 
+     * @return the XML Name for the Class being described.
+     */
+    public java.lang.String getXMLName(
+    ) {
+        return _xmlName;
+    }
+
+    /**
+     * Method isElementDefinition.
+     * 
+     * @return true if XML schema definition of this Class is that
+     * of a global
+     * element or element with anonymous type definition.
+     */
+    public boolean isElementDefinition(
+    ) {
+        return _elementDefinition;
+    }
+
+}
diff --git a/src/jalview/schemabinding/version2/types/descriptors/NoValueColourDescriptor.java b/src/jalview/schemabinding/version2/types/descriptors/NoValueColourDescriptor.java
new file mode 100644
index 0000000..14c58ed
--- /dev/null
+++ b/src/jalview/schemabinding/version2/types/descriptors/NoValueColourDescriptor.java
@@ -0,0 +1,147 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.types.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.types.NoValueColour;
+
+/**
+ * Class NoValueColourDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class NoValueColourDescriptor
+        extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _elementDefinition.
+   */
+  private boolean _elementDefinition;
+
+  /**
+   * Field _nsPrefix.
+   */
+  private java.lang.String _nsPrefix;
+
+  /**
+   * Field _nsURI.
+   */
+  private java.lang.String _nsURI;
+
+  /**
+   * Field _xmlName.
+   */
+  private java.lang.String _xmlName;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public NoValueColourDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org/colours";
+    _xmlName = "NoValueColour";
+    _elementDefinition = false;
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * Method getAccessMode.
+   * 
+   * @return the access mode specified for this class.
+   */
+  public org.exolab.castor.mapping.AccessMode getAccessMode()
+  {
+    return null;
+  }
+
+  /**
+   * Method getIdentity.
+   * 
+   * @return the identity field, null if this class has no identity.
+   */
+  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+  {
+    return super.getIdentity();
+  }
+
+  /**
+   * Method getJavaClass.
+   * 
+   * @return the Java class represented by this descriptor.
+   */
+  public java.lang.Class getJavaClass()
+  {
+    return jalview.schemabinding.version2.types.NoValueColour.class;
+  }
+
+  /**
+   * Method getNameSpacePrefix.
+   * 
+   * @return the namespace prefix to use when marshaling as XML.
+   */
+  public java.lang.String getNameSpacePrefix()
+  {
+    return _nsPrefix;
+  }
+
+  /**
+   * Method getNameSpaceURI.
+   * 
+   * @return the namespace URI used when marshaling and unmarshaling as XML.
+   */
+  public java.lang.String getNameSpaceURI()
+  {
+    return _nsURI;
+  }
+
+  /**
+   * Method getValidator.
+   * 
+   * @return a specific validator for the class described by this
+   *         ClassDescriptor.
+   */
+  public org.exolab.castor.xml.TypeValidator getValidator()
+  {
+    return this;
+  }
+
+  /**
+   * Method getXMLName.
+   * 
+   * @return the XML Name for the Class being described.
+   */
+  public java.lang.String getXMLName()
+  {
+    return _xmlName;
+  }
+
+  /**
+   * Method isElementDefinition.
+   * 
+   * @return true if XML schema definition of this Class is that of a global
+   *         element or element with anonymous type definition.
+   */
+  public boolean isElementDefinition()
+  {
+    return _elementDefinition;
+  }
+
+}
diff --git a/src/jalview/schemes/FeatureColour.java b/src/jalview/schemes/FeatureColour.java
index aa0b640..7d14662 100644
--- a/src/jalview/schemes/FeatureColour.java
+++ b/src/jalview/schemes/FeatureColour.java
@@ -22,6 +22,7 @@ package jalview.schemes;
 
 import jalview.api.FeatureColourI;
 import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.features.FeatureMatcher;
 import jalview.util.ColorUtils;
 import jalview.util.Format;
 
@@ -49,6 +50,27 @@ import java.util.StringTokenizer;
  */
 public class FeatureColour implements FeatureColourI
 {
+  private static final String ABSOLUTE = "abso";
+
+  private static final String ABOVE = "above";
+
+  private static final String BELOW = "below";
+
+  /*
+   * constants used to read or write a Jalview Features file
+   */
+  private static final String LABEL = "label";
+
+  private static final String SCORE = "score";
+
+  private static final String ATTRIBUTE = "attribute";
+
+  private static final String NO_VALUE_MIN = "noValueMin";
+
+  private static final String NO_VALUE_MAX = "noValueMax";
+
+  private static final String NO_VALUE_NONE = "noValueNone";
+
   static final Color DEFAULT_NO_COLOUR = null;
 
   private static final String BAR = "|";
@@ -111,16 +133,29 @@ public class FeatureColour implements FeatureColourI
 
   /**
    * Parses a Jalview features file format colour descriptor
-   * [label|][mincolour|maxcolour
-   * |[absolute|]minvalue|maxvalue|thresholdtype|thresholdvalue] Examples:
+   * <p>
+   * <code>
+   * [label|score|[attribute|attributeName]|][mincolour|maxcolour|
+   * [absolute|]minvalue|maxvalue|[noValueOption|]thresholdtype|thresholdvalue]</code>
+   * <p>
+   * 'Score' is optional (default) for a graduated colour. An attribute with
+   * sub-attribute should be written as (for example) CSQ:Consequence.
+   * noValueOption is one of <code>noValueMin, noValueMax, noValueNone</code>
+   * with default noValueMin.
+   * <p>
+   * Examples:
    * <ul>
    * <li>red</li>
    * <li>a28bbb</li>
    * <li>25,125,213</li>
    * <li>label</li>
+   * <li>attribute|CSQ:PolyPhen</li>
    * <li>label|||0.0|0.0|above|12.5</li>
    * <li>label|||0.0|0.0|below|12.5</li>
    * <li>red|green|12.0|26.0|none</li>
+   * <li>score|red|green|12.0|26.0|none</li>
+   * <li>attribute|AF|red|green|12.0|26.0|none</li>
+   * <li>attribute|AF|red|green|noValueNone|12.0|26.0|none</li>
    * <li>a28bbb|3eb555|12.0|26.0|above|12.5</li>
    * <li>a28bbb|3eb555|abso|12.0|26.0|below|12.5</li>
    * </ul>
@@ -130,34 +165,71 @@ public class FeatureColour implements FeatureColourI
    * @throws IllegalArgumentException
    *           if not parseable
    */
-  public static FeatureColour parseJalviewFeatureColour(String descriptor)
+  public static FeatureColourI parseJalviewFeatureColour(String descriptor)
   {
-    StringTokenizer gcol = new StringTokenizer(descriptor, "|", true);
+    StringTokenizer gcol = new StringTokenizer(descriptor, BAR, true);
     float min = Float.MIN_VALUE;
     float max = Float.MAX_VALUE;
-    boolean labelColour = false;
+    boolean byLabel = false;
+    boolean byAttribute = false;
+    String attName = null;
+    String mincol = null;
+    String maxcol = null;
 
-    String mincol = gcol.nextToken();
-    if (mincol == "|")
+    /*
+     * first token should be 'label', or 'score', or an
+     * attribute name, or simple colour, or minimum colour
+     */
+    String nextToken = gcol.nextToken();
+    if (nextToken == BAR)
     {
       throw new IllegalArgumentException(
               "Expected either 'label' or a colour specification in the line: "
                       + descriptor);
     }
-    String maxcol = null;
-    if (mincol.toLowerCase().indexOf("label") == 0)
+    if (nextToken.toLowerCase().startsWith(LABEL))
     {
-      labelColour = true;
+      byLabel = true;
+      // get the token after the next delimiter:
       mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
-      // skip '|'
       mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
     }
+    else if (nextToken.toLowerCase().startsWith(SCORE))
+    {
+      mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
+      mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
+    }
+    else if (nextToken.toLowerCase().startsWith(ATTRIBUTE))
+    {
+      byAttribute = true;
+      attName = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
+      attName = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
+      mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
+      mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
+    }
+    else
+    {
+      mincol = nextToken;
+    }
 
-    if (!labelColour && !gcol.hasMoreTokens())
+    /*
+     * if only one token, it can validly be label, attributeName,
+     * or a plain colour value
+     */
+    if (!gcol.hasMoreTokens())
     {
-      /*
-       * only a simple colour specification - parse it
-       */
+      if (byLabel || byAttribute)
+      {
+        FeatureColourI fc = new FeatureColour();
+        fc.setColourByLabel(true);
+        if (byAttribute)
+        {
+          fc.setAttributeName(
+                  FeatureMatcher.fromAttributeDisplayName(attName));
+        }
+        return fc;
+      }
+
       Color colour = ColorUtils.parseColourString(descriptor);
       if (colour == null)
       {
@@ -168,34 +240,64 @@ public class FeatureColour implements FeatureColourI
     }
 
     /*
+     * continue parsing for min/max/no colour (if graduated)
+     * and for threshold (colour by text or graduated)
+     */
+
+    /*
      * autoScaled == true: colours range over actual score range
      * autoScaled == false ('abso'): colours range over min/max range
      */
     boolean autoScaled = true;
     String tok = null, minval, maxval;
+    String noValueColour = NO_VALUE_MIN;
+
     if (mincol != null)
     {
       // at least four more tokens
-      if (mincol.equals("|"))
+      if (mincol.equals(BAR))
       {
-        mincol = "";
+        mincol = null;
       }
       else
       {
         gcol.nextToken(); // skip next '|'
       }
       maxcol = gcol.nextToken();
-      if (maxcol.equals("|"))
+      if (maxcol.equals(BAR))
       {
-        maxcol = "";
+        maxcol = null;
       }
       else
       {
         gcol.nextToken(); // skip next '|'
       }
       tok = gcol.nextToken();
+
+      /*
+       * check for specifier for colour for no attribute value
+       * (new in 2.11, defaults to minColour if not specified)
+       */
+      if (tok.equalsIgnoreCase(NO_VALUE_MIN))
+      {
+        tok = gcol.nextToken();
+        tok = gcol.nextToken();
+      }
+      else if (tok.equalsIgnoreCase(NO_VALUE_MAX))
+      {
+        noValueColour = NO_VALUE_MAX;
+        tok = gcol.nextToken();
+        tok = gcol.nextToken();
+      }
+      else if (tok.equalsIgnoreCase(NO_VALUE_NONE))
+      {
+        noValueColour = NO_VALUE_NONE;
+        tok = gcol.nextToken();
+        tok = gcol.nextToken();
+      }
+
       gcol.nextToken(); // skip next '|'
-      if (tok.toLowerCase().startsWith("abso"))
+      if (tok.toLowerCase().startsWith(ABSOLUTE))
       {
         minval = gcol.nextToken();
         gcol.nextToken(); // skip next '|'
@@ -237,34 +339,45 @@ public class FeatureColour implements FeatureColourI
     }
     else
     {
-      // add in some dummy min/max colours for the label-only
-      // colourscheme.
-      mincol = "FFFFFF";
-      maxcol = "000000";
+      /*
+       * dummy min/max colours for colour by text
+       * (label or attribute value)
+       */
+      mincol = "white";
+      maxcol = "black";
+      byLabel = true;
     }
 
     /*
-     * construct the FeatureColour
+     * construct the FeatureColour!
      */
     FeatureColour featureColour;
     try
     {
       Color minColour = ColorUtils.parseColourString(mincol);
       Color maxColour = ColorUtils.parseColourString(maxcol);
-      featureColour = new FeatureColour(minColour, maxColour, min, max);
-      featureColour.setColourByLabel(labelColour);
+      Color noColour = noValueColour.equals(NO_VALUE_MAX) ? maxColour
+              : (noValueColour.equals(NO_VALUE_NONE) ? null : minColour);
+      featureColour = new FeatureColour(minColour, maxColour, noColour, min,
+              max);
+      featureColour.setColourByLabel(minColour == null);
       featureColour.setAutoScaled(autoScaled);
+      if (byAttribute)
+      {
+        featureColour.setAttributeName(
+                FeatureMatcher.fromAttributeDisplayName(attName));
+      }
       // add in any additional parameters
       String ttype = null, tval = null;
       if (gcol.hasMoreTokens())
       {
         // threshold type and possibly a threshold value
         ttype = gcol.nextToken();
-        if (ttype.toLowerCase().startsWith("below"))
+        if (ttype.toLowerCase().startsWith(BELOW))
         {
           featureColour.setBelowThreshold(true);
         }
-        else if (ttype.toLowerCase().startsWith("above"))
+        else if (ttype.toLowerCase().startsWith(ABOVE))
         {
           featureColour.setAboveThreshold(true);
         }
@@ -296,7 +409,7 @@ public class FeatureColour implements FeatureColourI
                 "Ignoring additional tokens in parameters in graduated colour specification\n");
         while (gcol.hasMoreTokens())
         {
-          System.err.println("|" + gcol.nextToken());
+          System.err.println(BAR + gcol.nextToken());
         }
         System.err.println("\n");
       }
@@ -698,21 +811,43 @@ public class FeatureColour implements FeatureColourI
     else
     {
       StringBuilder sb = new StringBuilder(32);
-      if (isColourByLabel())
+      if (isColourByAttribute())
       {
-        sb.append("label");
-        if (hasThreshold())
-        {
-          sb.append(BAR).append(BAR).append(BAR);
-        }
+        sb.append(ATTRIBUTE).append(BAR);
+        sb.append(
+                FeatureMatcher.toAttributeDisplayName(getAttributeName()));
+      }
+      else if (isColourByLabel())
+      {
+        sb.append(LABEL);
+      }
+      else
+      {
+        sb.append(SCORE);
       }
       if (isGraduatedColour())
       {
-        sb.append(Format.getHexString(getMinColour())).append(BAR);
+        sb.append(BAR).append(Format.getHexString(getMinColour()))
+                .append(BAR);
         sb.append(Format.getHexString(getMaxColour())).append(BAR);
+        String noValue = minColour.equals(noColour) ? NO_VALUE_MIN
+                : (maxColour.equals(noColour) ? NO_VALUE_MAX
+                        : NO_VALUE_NONE);
+        sb.append(noValue).append(BAR);
         if (!isAutoScaled())
         {
-          sb.append("abso").append(BAR);
+          sb.append(ABSOLUTE).append(BAR);
+        }
+      }
+      else
+      {
+        /*
+         * colour by text with score threshold: empty fields for
+         * minColour and maxColour (not used)
+         */
+        if (hasThreshold())
+        {
+          sb.append(BAR).append(BAR).append(BAR);
         }
       }
       if (hasThreshold() || isGraduatedColour())
@@ -721,11 +856,11 @@ public class FeatureColour implements FeatureColourI
         sb.append(getMax()).append(BAR);
         if (isBelowThreshold())
         {
-          sb.append("below").append(BAR).append(getThreshold());
+          sb.append(BELOW).append(BAR).append(getThreshold());
         }
         else if (isAboveThreshold())
         {
-          sb.append("above").append(BAR).append(getThreshold());
+          sb.append(ABOVE).append(BAR).append(getThreshold());
         }
         else
         {
diff --git a/src/jalview/util/matcher/Condition.java b/src/jalview/util/matcher/Condition.java
index 3047802..8816a7f 100644
--- a/src/jalview/util/matcher/Condition.java
+++ b/src/jalview/util/matcher/Condition.java
@@ -8,19 +8,55 @@ import jalview.util.MessageManager;
  */
 public enum Condition
 {
-  Contains(false, true), NotContains(false, true), Matches(false, true),
-  NotMatches(false, true), Present(false, false), NotPresent(false, false),
-  EQ(true, true), NE(true, true), LT(true, true), LE(true, true),
-  GT(true, true), GE(true, true);
-  
+  Contains(false, true, "Contains"),
+  NotContains(false, true, "NotContains"), Matches(false, true, "Matches"),
+  NotMatches(false, true, "NotMatches"), Present(false, false, "Present"),
+  NotPresent(false, false, "NotPresent"), EQ(true, true, "EQ"),
+  NE(true, true, "NE"), LT(true, true, "LT"), LE(true, true, "LE"),
+  GT(true, true, "GT"), GE(true, true, "GE");
+
   private boolean numeric;
 
   private boolean needsAPattern;
 
-  Condition(boolean isNumeric, boolean needsPattern)
+  /*
+   * value used to save a Condition to the 
+   * Jalview project file or restore it from project; 
+   * it should not be changed even if enum names change in future
+   */
+  private String stableName;
+
+  /**
+   * Answers the enum value whose 'stable name' matches the argument (not case
+   * sensitive), or null if no match
+   * 
+   * @param stableName
+   * @return
+   */
+  public static Condition fromString(String stableName)
+  {
+    for (Condition c : values())
+    {
+      if (c.stableName.equalsIgnoreCase(stableName))
+      {
+        return c;
+      }
+    }
+    return null;
+  }
+
+  /**
+   * Constructor
+   * 
+   * @param isNumeric
+   * @param needsPattern
+   * @param stablename
+   */
+  Condition(boolean isNumeric, boolean needsPattern, String stablename)
   {
     numeric = isNumeric;
     needsAPattern = needsPattern;
+    stableName = stablename;
   }
 
   /**
@@ -45,6 +81,11 @@ public enum Condition
     return needsAPattern;
   }
 
+  public String getStableName()
+  {
+    return stableName;
+  }
+
   /**
    * Answers a display name for the match condition, suitable for showing in
    * drop-down menus. The value may be internationalized using the resource key
diff --git a/src/jalview/util/matcher/Matcher.java b/src/jalview/util/matcher/Matcher.java
index 353df83..0792509 100644
--- a/src/jalview/util/matcher/Matcher.java
+++ b/src/jalview/util/matcher/Matcher.java
@@ -42,8 +42,8 @@ public class Matcher implements MatcherI
    * @param compareTo
    * @return
    * @throws NumberFormatException
-   *           if a numerical condition is specified with a non-numeric comparison
-   *           value
+   *           if a numerical condition is specified with a non-numeric
+   *           comparison value
    * @throws NullPointerException
    *           if a null condition or comparison string is specified
    */
diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index c58461e..e4d9d88 100644
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -1070,7 +1070,7 @@ public abstract class FeatureRendererModel
   @Override
   public Map<String, FeatureMatcherSetI> getFeatureFilters()
   {
-    return new HashMap<>(featureFilters);
+    return featureFilters;
   }
 
   @Override
@@ -1100,8 +1100,8 @@ public abstract class FeatureRendererModel
 
   /**
    * Answers the colour for the feature, or null if the feature is excluded by
-   * feature type or group visibility, by filters, or by colour threshold
-   * settings
+   * feature group visibility, by filters, or by colour threshold settings. This
+   * method does not take feature visibility into account.
    * 
    * @param sf
    * @param fc
@@ -1110,14 +1110,6 @@ public abstract class FeatureRendererModel
   public Color getColor(SequenceFeature sf, FeatureColourI fc)
   {
     /*
-     * is the feature type displayed?
-     */
-    if (!showFeatureOfType(sf.getType()))
-    {
-      return null;
-    }
-
-    /*
      * is the feature group displayed?
      */
     if (featureGroupNotShown(sf))
diff --git a/test/jalview/datamodel/features/FeatureAttributesTest.java b/test/jalview/datamodel/features/FeatureAttributesTest.java
index 4b7a435..e47c787 100644
--- a/test/jalview/datamodel/features/FeatureAttributesTest.java
+++ b/test/jalview/datamodel/features/FeatureAttributesTest.java
@@ -12,6 +12,7 @@ import java.util.HashMap;
 import java.util.Map;
 
 import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 import junit.extensions.PA;
@@ -20,6 +21,16 @@ public class FeatureAttributesTest
 {
 
   /**
+   * clear down attributes map before tests
+   */
+  @BeforeClass
+  public void setUp()
+  {
+    FeatureAttributes fa = FeatureAttributes.getInstance();
+    ((Map<?, ?>) PA.getValue(fa, "attributes")).clear();
+  }
+
+  /**
    * clear down attributes map after tests
    */
   @AfterMethod
@@ -56,7 +67,7 @@ public class FeatureAttributesTest
         "csq", "AF" }) < 0);
   }
 
-  @Test
+  @Test(groups = "Functional")
   public void testGetMinMax()
   {
     SequenceFeature sf = new SequenceFeature("Pfam", "desc", 10, 20,
@@ -88,7 +99,7 @@ public class FeatureAttributesTest
    * Test the method that returns an attribute description, provided it is
    * recorded and unique
    */
-  @Test
+  @Test(groups = "Functional")
   public void testGetDescription()
   {
     FeatureAttributes fa = FeatureAttributes.getInstance();
@@ -102,7 +113,7 @@ public class FeatureAttributesTest
     assertNull(fa.getDescription("Pfam", "kd"));
   }
 
-  @Test
+  @Test(groups = "Functional")
   public void testDatatype()
   {
     FeatureAttributes fa = FeatureAttributes.getInstance();
diff --git a/test/jalview/datamodel/features/FeatureMatcherSetTest.java b/test/jalview/datamodel/features/FeatureMatcherSetTest.java
index 56644fd..a2d2c9a 100644
--- a/test/jalview/datamodel/features/FeatureMatcherSetTest.java
+++ b/test/jalview/datamodel/features/FeatureMatcherSetTest.java
@@ -2,6 +2,7 @@ package jalview.datamodel.features;
 
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 import static org.testng.Assert.fail;
@@ -103,7 +104,8 @@ public class FeatureMatcherSetTest
      * OR failed attribute and score conditions with matched label condition
      */
     fms = new FeatureMatcherSet();
-    fms.or(fm2).or(byScoreFail);
+    fms.or(fm2);
+    fms.or(byScoreFail);
     assertFalse(fms.matches(sf));
     fms.or(byLabelPass);
     assertTrue(fms.matches(sf));
@@ -127,7 +129,7 @@ public class FeatureMatcherSetTest
     FeatureMatcherSetI fms = new FeatureMatcherSet();
     assertEquals(fms.toString(), "");
     fms.and(fm1);
-    assertEquals(fms.toString(), "(AF < 1.2)");
+    assertEquals(fms.toString(), "AF < 1.2");
     fms.and(fm2);
     assertEquals(fms.toString(),
             "(AF < 1.2) and (CLIN_SIG does not contain 'path')");
@@ -138,7 +140,7 @@ public class FeatureMatcherSetTest
     fms = new FeatureMatcherSet();
     assertEquals(fms.toString(), "");
     fms.or(fm1);
-    assertEquals(fms.toString(), "(AF < 1.2)");
+    assertEquals(fms.toString(), "AF < 1.2");
     fms.or(fm2);
     assertEquals(fms.toString(),
             "(AF < 1.2) or (CLIN_SIG does not contain 'path')");
@@ -282,4 +284,136 @@ public class FeatureMatcherSetTest
     csq.put("Consequence", "Catastrophic");
     assertTrue(fms.matches(sf));
   }
+
+  /**
+   * Tests for toStableString which (unlike toString) does not i18n the
+   * conditions
+   * 
+   * @see FeatureMatcherTest#testToStableString()
+   */
+  @Test(groups = "Functional")
+  public void testToStableString()
+  {
+    FeatureMatcherI fm1 = FeatureMatcher.byAttribute(Condition.LT, "1.2",
+            "AF");
+    assertEquals(fm1.toStableString(), "AF LT 1.2");
+  
+    FeatureMatcher fm2 = FeatureMatcher.byAttribute(Condition.NotContains,
+            "path", "CLIN_SIG");
+    assertEquals(fm2.toStableString(), "CLIN_SIG NotContains path");
+  
+    /*
+     * AND them
+     */
+    FeatureMatcherSetI fms = new FeatureMatcherSet();
+    assertEquals(fms.toStableString(), "");
+    fms.and(fm1);
+    // no brackets needed if a single condition
+    assertEquals(fms.toStableString(), "AF LT 1.2");
+    // brackets if more than one condition
+    fms.and(fm2);
+    assertEquals(fms.toStableString(),
+            "(AF LT 1.2) AND (CLIN_SIG NotContains path)");
+  
+    /*
+     * OR them
+     */
+    fms = new FeatureMatcherSet();
+    assertEquals(fms.toStableString(), "");
+    fms.or(fm1);
+    assertEquals(fms.toStableString(), "AF LT 1.2");
+    fms.or(fm2);
+    assertEquals(fms.toStableString(),
+            "(AF LT 1.2) OR (CLIN_SIG NotContains path)");
+  
+    /*
+     * attribute or value including space is quoted
+     */
+    FeatureMatcher fm3 = FeatureMatcher.byAttribute(Condition.NotMatches,
+            "foo bar", "CSQ", "Poly Phen");
+    assertEquals(fm3.toStableString(),
+            "'CSQ:Poly Phen' NotMatches 'foo bar'");
+    fms.or(fm3);
+    assertEquals(fms.toStableString(),
+            "(AF LT 1.2) OR (CLIN_SIG NotContains path) OR ('CSQ:Poly Phen' NotMatches 'foo bar')");
+
+    try
+    {
+      fms.and(fm1);
+      fail("Expected exception");
+    } catch (IllegalStateException e)
+    {
+      // expected
+    }
+  }
+
+  /**
+   * Tests for parsing a string representation of a FeatureMatcherSet
+   * 
+   * @see FeatureMatcherSetTest#testToStableString()
+   */
+  @Test(groups = "Functional")
+  public void testFromString()
+  {
+    String descriptor = "AF LT 1.2";
+    FeatureMatcherSetI fms = FeatureMatcherSet.fromString(descriptor);
+
+    /*
+     * shortcut asserts by verifying a 'roundtrip', 
+     * which we trust if other tests pass :-)
+     */
+    assertEquals(fms.toStableString(), descriptor);
+
+    // brackets optional, quotes optional, condition case insensitive
+    fms = FeatureMatcherSet.fromString("('AF' lt '1.2')");
+    assertEquals(fms.toStableString(), descriptor);
+
+    descriptor = "(AF LT 1.2) AND (CLIN_SIG NotContains path)";
+    fms = FeatureMatcherSet.fromString(descriptor);
+    assertEquals(fms.toStableString(), descriptor);
+
+    // AND is not case-sensitive
+    fms = FeatureMatcherSet
+            .fromString("(AF LT 1.2) and (CLIN_SIG NotContains path)");
+    assertEquals(fms.toStableString(), descriptor);
+  
+    descriptor = "(AF LT 1.2) OR (CLIN_SIG NotContains path)";
+    fms = FeatureMatcherSet.fromString(descriptor);
+    assertEquals(fms.toStableString(), descriptor);
+
+    // OR is not case-sensitive
+    fms = FeatureMatcherSet
+            .fromString("(AF LT 1.2) or (CLIN_SIG NotContains path)");
+    assertEquals(fms.toStableString(), descriptor);
+
+    // can get away without brackets on last match condition
+    fms = FeatureMatcherSet
+            .fromString("(AF LT 1.2) or CLIN_SIG NotContains path");
+    assertEquals(fms.toStableString(), descriptor);
+  
+    descriptor = "(AF LT 1.2) OR (CLIN_SIG NotContains path) OR ('CSQ:Poly Phen' NotMatches 'foo bar')";
+    fms = FeatureMatcherSet.fromString(descriptor);
+    assertEquals(fms.toStableString(), descriptor);
+
+    // can't mix OR and AND
+    descriptor = "(AF LT 1.2) OR (CLIN_SIG NotContains path) AND ('CSQ:Poly Phen' NotMatches 'foo bar')";
+    assertNull(FeatureMatcherSet.fromString(descriptor));
+
+    // can't mix AND and OR
+    descriptor = "(AF LT 1.2) and (CLIN_SIG NotContains path) or ('CSQ:Poly Phen' NotMatches 'foo bar')";
+    assertNull(FeatureMatcherSet.fromString(descriptor));
+
+    // brackets missing
+    assertNull(FeatureMatcherSet
+            .fromString("AF LT 1.2 or CLIN_SIG NotContains path"));
+
+    // invalid conjunction
+    assertNull(FeatureMatcherSet.fromString("(AF LT 1.2) but (AF GT -2)"));
+
+    // unbalanced quote (1)
+    assertNull(FeatureMatcherSet.fromString("('AF lt '1.2')"));
+
+    // unbalanced quote (2)
+    assertNull(FeatureMatcherSet.fromString("('AF' lt '1.2)"));
+  }
 }
diff --git a/test/jalview/datamodel/features/FeatureMatcherTest.java b/test/jalview/datamodel/features/FeatureMatcherTest.java
index 62b03a3..4bd34cb 100644
--- a/test/jalview/datamodel/features/FeatureMatcherTest.java
+++ b/test/jalview/datamodel/features/FeatureMatcherTest.java
@@ -3,6 +3,7 @@ package jalview.datamodel.features;
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
 import jalview.datamodel.SequenceFeature;
@@ -15,7 +16,7 @@ import org.testng.annotations.Test;
 
 public class FeatureMatcherTest
 {
-  @Test
+  @Test(groups = "Functional")
   public void testMatches_byLabel()
   {
     SequenceFeature sf = new SequenceFeature("Cath", "this is my label", 11,
@@ -62,7 +63,7 @@ public class FeatureMatcherTest
             FeatureMatcher.byLabel(Condition.NotPresent, "").matches(sf));
   }
 
-  @Test
+  @Test(groups = "Functional")
   public void testMatches_byScore()
   {
     SequenceFeature sf = new SequenceFeature("Cath", "this is my label", 11,
@@ -87,7 +88,8 @@ public class FeatureMatcherTest
     assertFalse(FeatureMatcher.byScore(Condition.GT, "3.2").matches(sf));
     assertTrue(FeatureMatcher.byScore(Condition.GT, "2.2").matches(sf));
   }
-  @Test
+
+  @Test(groups = "Functional")
   public void testMatches_byAttribute()
   {
     /*
@@ -127,7 +129,7 @@ public class FeatureMatcherTest
     assertFalse(fm.matches(sf));
   }
 
-  @Test
+  @Test(groups = "Functional")
   public void testToString()
   {
     Locale.setDefault(Locale.ENGLISH);
@@ -162,7 +164,7 @@ public class FeatureMatcherTest
             MessageManager.getString("label.score") + " >= 12.2");
   }
 
-  @Test
+  @Test(groups = "Functional")
   public void testGetAttribute()
   {
     FeatureMatcherI fm = FeatureMatcher.byAttribute(Condition.GE, "-2",
@@ -184,7 +186,17 @@ public class FeatureMatcherTest
     assertNull(FeatureMatcher.byScore(Condition.LE, "-1").getAttribute());
   }
 
-  @Test
+  @Test(groups = "Functional")
+  public void testIsByAttribute()
+  {
+    assertFalse(FeatureMatcher.byLabel(Condition.NotContains, "foo")
+            .isByAttribute());
+    assertFalse(FeatureMatcher.byScore(Condition.LE, "-1").isByAttribute());
+    assertTrue(FeatureMatcher.byAttribute(Condition.LE, "-1", "AC")
+            .isByAttribute());
+  }
+
+  @Test(groups = "Functional")
   public void testIsByLabel()
   {
     assertTrue(FeatureMatcher.byLabel(Condition.NotContains, "foo")
@@ -194,7 +206,7 @@ public class FeatureMatcherTest
             .isByLabel());
   }
 
-  @Test
+  @Test(groups = "Functional")
   public void testIsByScore()
   {
     assertFalse(FeatureMatcher.byLabel(Condition.NotContains, "foo")
@@ -204,7 +216,7 @@ public class FeatureMatcherTest
             .isByScore());
   }
 
-  @Test
+  @Test(groups = "Functional")
   public void testGetMatcher()
   {
     FeatureMatcherI fm = FeatureMatcher.byAttribute(Condition.GE, "-2f",
@@ -213,4 +225,128 @@ public class FeatureMatcherTest
     assertEquals(fm.getMatcher().getFloatValue(), -2F);
     assertEquals(fm.getMatcher().getPattern(), "-2.0");
   }
+
+  @Test(groups = "Functional")
+  public void testFromString()
+  {
+    FeatureMatcherI fm = FeatureMatcher.fromString("'AF' LT 1.2");
+    assertFalse(fm.isByLabel());
+    assertFalse(fm.isByScore());
+    assertEquals(fm.getAttribute(), new String[] { "AF" });
+    assertSame(Condition.LT, fm.getMatcher().getCondition());
+    assertEquals(fm.getMatcher().getFloatValue(), 1.2f);
+    assertEquals(fm.getMatcher().getPattern(), "1.2");
+
+    // quotes are optional, condition is not case sensitive
+    fm = FeatureMatcher.fromString("AF lt '1.2'");
+    assertFalse(fm.isByLabel());
+    assertFalse(fm.isByScore());
+    assertEquals(fm.getAttribute(), new String[] { "AF" });
+    assertSame(Condition.LT, fm.getMatcher().getCondition());
+    assertEquals(fm.getMatcher().getFloatValue(), 1.2f);
+    assertEquals(fm.getMatcher().getPattern(), "1.2");
+
+    fm = FeatureMatcher.fromString("'AF' Present");
+    assertFalse(fm.isByLabel());
+    assertFalse(fm.isByScore());
+    assertEquals(fm.getAttribute(), new String[] { "AF" });
+    assertSame(Condition.Present, fm.getMatcher().getCondition());
+
+    fm = FeatureMatcher.fromString("CSQ:Consequence contains damaging");
+    assertFalse(fm.isByLabel());
+    assertFalse(fm.isByScore());
+    assertEquals(fm.getAttribute(), new String[] { "CSQ", "Consequence" });
+    assertSame(Condition.Contains, fm.getMatcher().getCondition());
+    assertEquals(fm.getMatcher().getPattern(), "damaging");
+
+    // keyword Label is not case sensitive
+    fm = FeatureMatcher.fromString("LABEL Matches 'foobar'");
+    assertTrue(fm.isByLabel());
+    assertFalse(fm.isByScore());
+    assertNull(fm.getAttribute());
+    assertSame(Condition.Matches, fm.getMatcher().getCondition());
+    assertEquals(fm.getMatcher().getPattern(), "foobar");
+
+    fm = FeatureMatcher.fromString("'Label' matches 'foo bar'");
+    assertTrue(fm.isByLabel());
+    assertFalse(fm.isByScore());
+    assertNull(fm.getAttribute());
+    assertSame(Condition.Matches, fm.getMatcher().getCondition());
+    assertEquals(fm.getMatcher().getPattern(), "foo bar");
+
+    // quotes optional on pattern
+    fm = FeatureMatcher.fromString("'Label' matches foo bar");
+    assertTrue(fm.isByLabel());
+    assertFalse(fm.isByScore());
+    assertNull(fm.getAttribute());
+    assertSame(Condition.Matches, fm.getMatcher().getCondition());
+    assertEquals(fm.getMatcher().getPattern(), "foo bar");
+
+    fm = FeatureMatcher.fromString("Score GE 12.2");
+    assertFalse(fm.isByLabel());
+    assertTrue(fm.isByScore());
+    assertNull(fm.getAttribute());
+    assertSame(Condition.GE, fm.getMatcher().getCondition());
+    assertEquals(fm.getMatcher().getPattern(), "12.2");
+    assertEquals(fm.getMatcher().getFloatValue(), 12.2f);
+
+    // keyword Score is not case sensitive
+    fm = FeatureMatcher.fromString("'SCORE' ge '12.2'");
+    assertFalse(fm.isByLabel());
+    assertTrue(fm.isByScore());
+    assertNull(fm.getAttribute());
+    assertSame(Condition.GE, fm.getMatcher().getCondition());
+    assertEquals(fm.getMatcher().getPattern(), "12.2");
+    assertEquals(fm.getMatcher().getFloatValue(), 12.2f);
+
+    // invalid numeric pattern
+    assertNull(FeatureMatcher.fromString("Score eq twelve"));
+    // unbalanced opening quote
+    assertNull(FeatureMatcher.fromString("'Score ge 12.2"));
+    // unbalanced pattern quote
+    assertNull(FeatureMatcher.fromString("'Score' ge '12.2"));
+    // pattern missing
+    assertNull(FeatureMatcher.fromString("Score ge"));
+    // condition and pattern missing
+    assertNull(FeatureMatcher.fromString("Score"));
+    // everything missing
+    assertNull(FeatureMatcher.fromString(""));
+  }
+
+  /**
+   * Tests for toStableString which (unlike toString) does not i18n the
+   * conditions
+   */
+  @Test(groups = "Functional")
+  public void testToStableString()
+  {
+    // attribute name not quoted unless it contains space
+    FeatureMatcherI fm = FeatureMatcher.byAttribute(Condition.LT, "1.2",
+            "AF");
+    assertEquals(fm.toStableString(), "AF LT 1.2");
+
+    /*
+     * Present / NotPresent omit the value pattern
+     */
+    fm = FeatureMatcher.byAttribute(Condition.Present, "", "AF");
+    assertEquals(fm.toStableString(), "AF Present");
+    fm = FeatureMatcher.byAttribute(Condition.NotPresent, "", "AF");
+    assertEquals(fm.toStableString(), "AF NotPresent");
+
+    /*
+     * by Label
+     * pattern not quoted unless it contains space
+     */
+    fm = FeatureMatcher.byLabel(Condition.Matches, "foobar");
+    assertEquals(fm.toStableString(), "Label Matches foobar");
+
+    fm = FeatureMatcher.byLabel(Condition.Matches, "foo bar");
+    assertEquals(fm.toStableString(), "Label Matches 'foo bar'");
+
+    /*
+     * by Score
+     */
+    fm = FeatureMatcher.byScore(Condition.GE, "12.2");
+    assertEquals(fm.toStableString(), "Score GE 12.2");
+  }
 }
diff --git a/test/jalview/gui/AnnotationColumnChooserTest.java b/test/jalview/gui/AnnotationColumnChooserTest.java
new file mode 100644
index 0000000..06478d5
--- /dev/null
+++ b/test/jalview/gui/AnnotationColumnChooserTest.java
@@ -0,0 +1,176 @@
+/*
+ * 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.gui;
+
+import static org.testng.Assert.assertFalse;
+import static org.testng.AssertJUnit.assertEquals;
+
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
+
+import java.io.IOException;
+import java.util.List;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+/**
+ * Unit tests for AnnotationChooser
+ * 
+ * @author kmourao
+ *
+ */
+public class AnnotationColumnChooserTest
+{
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  // 4 sequences x 13 positions
+  final static String TEST_DATA = ">FER_CAPAA Ferredoxin\n"
+          + "TIETHKEAELVG-\n"
+          + ">FER_CAPAN Ferredoxin, chloroplast precursor\n"
+          + "TIETHKEAELVG-\n"
+          + ">FER1_SOLLC Ferredoxin-1, chloroplast precursor\n"
+          + "TIETHKEEELTA-\n" + ">Q93XJ9_SOLTU Ferredoxin I precursor\n"
+          + "TIETHKEEELTA-\n";
+
+  AnnotationChooser testee;
+
+  AlignmentPanel parentPanel;
+
+  AlignFrame af;
+
+  @BeforeMethod(alwaysRun = true)
+  public void setUp() throws IOException
+  {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    // pin down annotation sort order for test
+    Cache.applicationProperties.setProperty(Preferences.SORT_ANNOTATIONS,
+            SequenceAnnotationOrder.NONE.name());
+    final String TRUE = Boolean.TRUE.toString();
+    Cache.applicationProperties.setProperty(Preferences.SHOW_AUTOCALC_ABOVE,
+            TRUE);
+    Cache.applicationProperties.setProperty("SHOW_QUALITY", TRUE);
+    Cache.applicationProperties.setProperty("SHOW_CONSERVATION", TRUE);
+    Cache.applicationProperties.setProperty("SHOW_IDENTITY", TRUE);
+
+    AlignmentI al = new FormatAdapter().readFile(TEST_DATA,
+            DataSourceType.PASTE, FileFormat.Fasta);
+    af = new AlignFrame(al, 700, 500);
+    parentPanel = new AlignmentPanel(af, af.getViewport());
+    addAnnotations();
+  }
+
+  /**
+   * Add 4 annotations, 3 of them sequence-specific.
+   * 
+   * <PRE>
+   * ann1 - for sequence 0 - label 'IUPRED' ann2 - not sequence related - label
+   * 'Beauty' ann3 - for sequence 3 - label 'JMol' ann4 - for sequence 2 - label
+   * 'IUPRED' ann5 - for sequence 1 - label 'JMol'
+   */
+  private void addAnnotations()
+  {
+    Annotation an = new Annotation(2f);
+    Annotation[] anns = new Annotation[] { an, an, an };
+    AlignmentAnnotation ann0 = new AlignmentAnnotation("IUPRED", "", anns);
+    AlignmentAnnotation ann1 = new AlignmentAnnotation("Beauty", "", anns);
+    AlignmentAnnotation ann2 = new AlignmentAnnotation("JMol", "", anns);
+    AlignmentAnnotation ann3 = new AlignmentAnnotation("IUPRED", "", anns);
+    AlignmentAnnotation ann4 = new AlignmentAnnotation("JMol", "", anns);
+    SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray();
+    ann0.setSequenceRef(seqs[0]);
+    ann2.setSequenceRef(seqs[3]);
+    ann3.setSequenceRef(seqs[2]);
+    ann4.setSequenceRef(seqs[1]);
+    parentPanel.getAlignment().addAnnotation(ann0);
+    parentPanel.getAlignment().addAnnotation(ann1);
+    parentPanel.getAlignment().addAnnotation(ann2);
+    parentPanel.getAlignment().addAnnotation(ann3);
+    parentPanel.getAlignment().addAnnotation(ann4);
+  }
+
+  /**
+   * Test reset
+   */
+  @Test(groups = { "Functional" })
+  public void testReset()
+  {
+    AnnotationColumnChooser acc = new AnnotationColumnChooser(
+            af.getViewport(), af.alignPanel);
+
+    HiddenColumns oldhidden = new HiddenColumns();
+    oldhidden.hideColumns(10, 20);
+    acc.setOldHiddenColumns(oldhidden);
+
+    HiddenColumns newHidden = new HiddenColumns();
+    newHidden.hideColumns(0, 3);
+    newHidden.hideColumns(22, 25);
+    af.getViewport().setHiddenColumns(newHidden);
+
+    HiddenColumns currentHidden = af.getViewport().getAlignment()
+            .getHiddenColumns();
+    List<int[]> regions = currentHidden.getHiddenColumnsCopy();
+    assertEquals(regions.get(0)[0], 0);
+    assertEquals(regions.get(0)[1], 3);
+    assertEquals(regions.get(1)[0], 22);
+    assertEquals(regions.get(1)[1], 25);
+
+    // now reset hidden columns
+    acc.reset();
+    currentHidden = af.getViewport().getAlignment().getHiddenColumns();
+    regions = currentHidden.getHiddenColumnsCopy();
+    assertEquals(regions.get(0)[0], 10);
+    assertEquals(regions.get(0)[1], 20);
+
+    // check works with empty hidden columns as old columns
+    oldhidden = new HiddenColumns();
+    acc.setOldHiddenColumns(oldhidden);
+    acc.reset();
+    currentHidden = af.getViewport().getAlignment().getHiddenColumns();
+    assertFalse(currentHidden.hasHiddenColumns());
+
+    // check works with empty hidden columns as new columns
+    oldhidden.hideColumns(10, 20);
+    acc.setOldHiddenColumns(oldhidden);
+    currentHidden = af.getViewport().getAlignment().getHiddenColumns();
+    assertFalse(currentHidden.hasHiddenColumns());
+
+    acc.reset();
+    currentHidden = af.getViewport().getAlignment().getHiddenColumns();
+    regions = currentHidden.getHiddenColumnsCopy();
+    assertEquals(regions.get(0)[0], 10);
+    assertEquals(regions.get(0)[1], 20);
+  }
+}
diff --git a/test/jalview/gui/FeatureSettingsTest.java b/test/jalview/gui/FeatureSettingsTest.java
new file mode 100644
index 0000000..6ddebf8
--- /dev/null
+++ b/test/jalview/gui/FeatureSettingsTest.java
@@ -0,0 +1,191 @@
+package jalview.gui;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertTrue;
+
+import jalview.api.FeatureColourI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcher;
+import jalview.datamodel.features.FeatureMatcherSet;
+import jalview.datamodel.features.FeatureMatcherSetI;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+import jalview.schemes.FeatureColour;
+import jalview.util.matcher.Condition;
+
+import java.awt.Color;
+import java.io.File;
+import java.io.IOException;
+import java.util.HashMap;
+
+import org.testng.annotations.Test;
+
+public class FeatureSettingsTest
+{
+  /**
+   * Test a roundtrip of save and reload of feature colours and filters as XML
+   * 
+   * @throws IOException
+   */
+  @Test(groups = "Functional")
+  public void testSaveLoad() throws IOException
+  {
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
+    SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0);
+
+    /*
+     * add some features to the sequence
+     */
+    int score = 1;
+    addFeatures(seq1, "type1", score++);
+    addFeatures(seq1, "type2", score++);
+    addFeatures(seq1, "type3", score++);
+    addFeatures(seq1, "type4", score++);
+    addFeatures(seq1, "type5", score++);
+
+    /*
+     * set colour schemes for features
+     */
+    FeatureRenderer fr = af.getFeatureRenderer();
+
+    // type1: red
+    fr.setColour("type1", new FeatureColour(Color.red));
+
+    // type2: by label
+    FeatureColourI byLabel = new FeatureColour();
+    byLabel.setColourByLabel(true);
+    fr.setColour("type2", byLabel);
+
+    // type3: by score above threshold
+    FeatureColourI byScore = new FeatureColour(Color.BLACK, Color.BLUE, 1,
+            10);
+    byScore.setAboveThreshold(true);
+    byScore.setThreshold(2f);
+    fr.setColour("type3", byScore);
+
+    // type4: by attribute AF
+    FeatureColourI byAF = new FeatureColour();
+    byAF.setColourByLabel(true);
+    byAF.setAttributeName("AF");
+    fr.setColour("type4", byAF);
+
+    // type5: by attribute CSQ:PolyPhen below threshold
+    FeatureColourI byPolyPhen = new FeatureColour(Color.BLACK, Color.BLUE,
+            1, 10);
+    byPolyPhen.setBelowThreshold(true);
+    byPolyPhen.setThreshold(3f);
+    byPolyPhen.setAttributeName("CSQ", "PolyPhen");
+    fr.setColour("type5", byPolyPhen);
+
+    /*
+     * set filters for feature types
+     */
+
+    // filter type1 features by (label contains "x")
+    FeatureMatcherSetI filterByX = new FeatureMatcherSet();
+    filterByX.and(FeatureMatcher.byLabel(Condition.Contains, "x"));
+    fr.setFeatureFilter("type1", filterByX);
+
+    // filter type2 features by (score <= 2.4 and score > 1.1)
+    FeatureMatcherSetI filterByScore = new FeatureMatcherSet();
+    filterByScore.and(FeatureMatcher.byScore(Condition.LE, "2.4"));
+    filterByScore.and(FeatureMatcher.byScore(Condition.GT, "1.1"));
+    fr.setFeatureFilter("type2", filterByScore);
+
+    // filter type3 features by (AF contains X OR CSQ:PolyPhen != 0)
+    FeatureMatcherSetI filterByXY = new FeatureMatcherSet();
+    filterByXY
+            .and(FeatureMatcher.byAttribute(Condition.Contains, "X", "AF"));
+    filterByXY.or(FeatureMatcher.byAttribute(Condition.NE, "0", "CSQ",
+            "PolyPhen"));
+    fr.setFeatureFilter("type3", filterByXY);
+
+    /*
+     * save colours and filters to an XML file
+     */
+    File coloursFile = File.createTempFile("testSaveLoad", ".fc");
+    coloursFile.deleteOnExit();
+    FeatureSettings fs = new FeatureSettings(af);
+    fs.save(coloursFile);
+
+    /*
+     * change feature colours and filters
+     */
+    FeatureColourI pink = new FeatureColour(Color.pink);
+    fr.setColour("type1", pink);
+    fr.setColour("type2", pink);
+    fr.setColour("type3", pink);
+    fr.setColour("type4", pink);
+    fr.setColour("type5", pink);
+
+    FeatureMatcherSetI filter2 = new FeatureMatcherSet();
+    filter2.and(FeatureMatcher.byLabel(Condition.NotContains, "y"));
+    fr.setFeatureFilter("type1", filter2);
+    fr.setFeatureFilter("type2", filter2);
+    fr.setFeatureFilter("type3", filter2);
+    fr.setFeatureFilter("type4", filter2);
+    fr.setFeatureFilter("type5", filter2);
+
+    /*
+     * reload colours and filters from file and verify they are restored
+     */
+    fs.load(coloursFile);
+    FeatureColourI fc = fr.getFeatureStyle("type1");
+    assertTrue(fc.isSimpleColour());
+    assertEquals(fc.getColour(), Color.red);
+    fc = fr.getFeatureStyle("type2");
+    assertTrue(fc.isColourByLabel());
+    fc = fr.getFeatureStyle("type3");
+    assertTrue(fc.isGraduatedColour());
+    assertNull(fc.getAttributeName());
+    assertTrue(fc.isAboveThreshold());
+    assertEquals(fc.getThreshold(), 2f);
+    fc = fr.getFeatureStyle("type4");
+    assertTrue(fc.isColourByLabel());
+    assertTrue(fc.isColourByAttribute());
+    assertEquals(fc.getAttributeName(), new String[] { "AF" });
+    fc = fr.getFeatureStyle("type5");
+    assertTrue(fc.isGraduatedColour());
+    assertTrue(fc.isColourByAttribute());
+    assertEquals(fc.getAttributeName(), new String[] { "CSQ", "PolyPhen" });
+    assertTrue(fc.isBelowThreshold());
+    assertEquals(fc.getThreshold(), 3f);
+
+    assertEquals(fr.getFeatureFilter("type1").toStableString(), "Label Contains x");
+    assertEquals(fr.getFeatureFilter("type2").toStableString(),
+            "(Score LE 2.4) AND (Score GT 1.1)");
+    assertEquals(fr.getFeatureFilter("type3").toStableString(),
+            "(AF Contains X) OR (CSQ:PolyPhen NE 0.0)");
+  }
+
+  /**
+   * Adds two features of the given type to the given sequence, also setting the
+   * score as the value of attribute "AF" and sub-attribute "CSQ:PolyPhen"
+   * 
+   * @param seq
+   * @param featureType
+   * @param score
+   */
+  private void addFeatures(SequenceI seq, String featureType, int score)
+  {
+    addFeature(seq, featureType, score++);
+    addFeature(seq, featureType, score);
+  }
+
+  private void addFeature(SequenceI seq, String featureType, int score)
+  {
+    SequenceFeature sf = new SequenceFeature(featureType, "desc", 1, 2,
+            score, "grp");
+    sf.setValue("AF", score);
+    sf.setValue("CSQ", new HashMap<String, String>()
+    {
+      {
+        put("PolyPhen", Integer.toString(score));
+      }
+    });
+    seq.addSequenceFeature(sf);
+  }
+}
diff --git a/test/jalview/gui/StructureViewerTest.java b/test/jalview/gui/StructureViewerTest.java
index 4d5b114..86342d2 100644
--- a/test/jalview/gui/StructureViewerTest.java
+++ b/test/jalview/gui/StructureViewerTest.java
@@ -39,8 +39,10 @@ public class StructureViewerTest
     PDBEntry pdbe4 = new PDBEntry("1GAQ", "A", Type.PDB, null);
     PDBEntry pdbe5 = new PDBEntry("3A6S", "B", Type.PDB, "path2");
     PDBEntry pdbe6 = new PDBEntry("1GAQ", "B", Type.PDB, null);
+    PDBEntry pdbe7 = new PDBEntry("1FOO", "Q", Type.PDB, null);
+
     PDBEntry[] pdbs = new PDBEntry[] { pdbe1, pdbe2, pdbe3, pdbe4, pdbe5,
-        pdbe6 };
+        pdbe6, pdbe7 };
 
     /*
      * seq1 ... seq6 associated with pdbe1 ... pdbe6
@@ -61,6 +63,7 @@ public class StructureViewerTest
     assertTrue(uniques.containsKey(pdbe4));
     assertFalse(uniques.containsKey(pdbe5));
     assertFalse(uniques.containsKey(pdbe6));
+    assertTrue(uniques.containsKey(pdbe7));
 
     // 1A70 associates with seq1 and seq3
     SequenceI[] ss = uniques.get(pdbe1);
@@ -79,5 +82,10 @@ public class StructureViewerTest
     assertEquals(ss.length, 2);
     assertSame(seqs[3], ss[0]);
     assertSame(seqs[5], ss[1]);
+
+    // 1FOO has seq7
+    ss = uniques.get(pdbe7);
+    assertEquals(ss.length, 1);
+    assertSame(seqs[6], ss[0]);
   }
 }
diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java
index 152ab84..32ca841 100644
--- a/test/jalview/io/FeaturesFileTest.java
+++ b/test/jalview/io/FeaturesFileTest.java
@@ -23,7 +23,9 @@ package jalview.io;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
 import jalview.api.FeatureColourI;
 import jalview.api.FeatureRenderer;
@@ -32,11 +34,17 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceDummy;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcher;
+import jalview.datamodel.features.FeatureMatcherI;
+import jalview.datamodel.features.FeatureMatcherSet;
+import jalview.datamodel.features.FeatureMatcherSetI;
 import jalview.datamodel.features.SequenceFeatures;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
+import jalview.schemes.FeatureColour;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.matcher.Condition;
 
 import java.awt.Color;
 import java.io.File;
@@ -44,6 +52,7 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
@@ -467,10 +476,10 @@ public class FeaturesFileTest
      */
     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
     Map<String, FeatureColourI> visible = fr.getDisplayedFeatureCols();
-    List<String> visibleGroups = new ArrayList<String>(
+    List<String> visibleGroups = new ArrayList<>(
             Arrays.asList(new String[] {}));
     String exported = featuresFile.printJalviewFormat(
-            al.getSequencesArray(), visible, visibleGroups, false);
+            al.getSequencesArray(), visible, null, visibleGroups, false);
     String expected = "No Features Visible";
     assertEquals(expected, exported);
 
@@ -479,7 +488,7 @@ public class FeaturesFileTest
      */
     visibleGroups.add("uniprot");
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
-            visible, visibleGroups, true);
+            visible, null, visibleGroups, true);
     expected = "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
             + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n"
             + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n" // NaN is not output
@@ -493,9 +502,9 @@ public class FeaturesFileTest
     fr.setVisible("GAMMA-TURN");
     visible = fr.getDisplayedFeatureCols();
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
-            visible, visibleGroups, false);
+            visible, null, visibleGroups, false);
     expected = "METAL\tcc9900\n"
-            + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
+            + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
             + "\nSTARTGROUP\tuniprot\n"
             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
@@ -508,13 +517,13 @@ public class FeaturesFileTest
     fr.setVisible("Pfam");
     visible = fr.getDisplayedFeatureCols();
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
-            visible, visibleGroups, false);
+            visible, null, visibleGroups, false);
     /*
      * features are output within group, ordered by sequence and by type
      */
     expected = "METAL\tcc9900\n"
             + "Pfam\tff0000\n"
-            + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
+            + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
             + "\nSTARTGROUP\tuniprot\n"
             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
@@ -539,8 +548,8 @@ public class FeaturesFileTest
      */
     FeaturesFile featuresFile = new FeaturesFile();
     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
-    Map<String, FeatureColourI> visible = new HashMap<String, FeatureColourI>();
-    List<String> visibleGroups = new ArrayList<String>(
+    Map<String, FeatureColourI> visible = new HashMap<>();
+    List<String> visibleGroups = new ArrayList<>(
             Arrays.asList(new String[] {}));
     String exported = featuresFile.printGffFormat(al.getSequencesArray(),
             visible, visibleGroups, false);
@@ -623,4 +632,79 @@ public class FeaturesFileTest
             + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n";
     assertEquals(expected, exported);
   }
+
+  /**
+   * Test for parsing of feature filters as represented in a Jalview features
+   * file
+   * 
+   * @throws Exception
+   */
+  @Test(groups = { "Functional" })
+  public void testParseFilters() throws Exception
+  {
+    Map<String, FeatureMatcherSetI> filters = new HashMap<>();
+    String text = "sequence_variant\tCSQ:PolyPhen NotContains 'damaging'\n"
+            + "missense_variant\t(label contains foobar) and (Score lt 1.3)";
+    FeaturesFile featuresFile = new FeaturesFile(text,
+            DataSourceType.PASTE);
+    featuresFile.parseFilters(filters);
+    assertEquals(filters.size(), 2);
+
+    FeatureMatcherSetI fm = filters.get("sequence_variant");
+    assertNotNull(fm);
+    Iterator<FeatureMatcherI> matchers = fm.getMatchers().iterator();
+    FeatureMatcherI matcher = matchers.next();
+    assertFalse(matchers.hasNext());
+    String[] attributes = matcher.getAttribute();
+    assertArrayEquals(attributes, new String[] { "CSQ", "PolyPhen" });
+    assertSame(matcher.getMatcher().getCondition(), Condition.NotContains);
+    assertEquals(matcher.getMatcher().getPattern(), "damaging");
+
+    fm = filters.get("missense_variant");
+    assertNotNull(fm);
+    matchers = fm.getMatchers().iterator();
+    matcher = matchers.next();
+    assertTrue(matcher.isByLabel());
+    assertSame(matcher.getMatcher().getCondition(), Condition.Contains);
+    assertEquals(matcher.getMatcher().getPattern(), "foobar");
+    matcher = matchers.next();
+    assertTrue(matcher.isByScore());
+    assertSame(matcher.getMatcher().getCondition(), Condition.LT);
+    assertEquals(matcher.getMatcher().getPattern(), "1.3");
+    assertEquals(matcher.getMatcher().getFloatValue(), 1.3f);
+
+    assertFalse(matchers.hasNext());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testOutputFeatureFilters()
+  {
+    FeaturesFile ff = new FeaturesFile();
+    StringBuilder sb = new StringBuilder();
+    Map<String, FeatureColourI> visible = new HashMap<>();
+    visible.put("pfam", new FeatureColour(Color.red));
+    Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
+
+    // with no filters, nothing is output
+    ff.outputFeatureFilters(sb, visible, featureFilters);
+    assertEquals("", sb.toString());
+
+    // with filter for not visible features only, nothing is output
+    FeatureMatcherSet filter = new FeatureMatcherSet();
+    filter.and(FeatureMatcher.byLabel(Condition.Present, null));
+    featureFilters.put("foobar", filter);
+    ff.outputFeatureFilters(sb, visible, featureFilters);
+    assertEquals("", sb.toString());
+
+    // with filters for visible feature types
+    FeatureMatcherSet filter2 = new FeatureMatcherSet();
+    filter2.and(FeatureMatcher.byAttribute(Condition.Present, null, "CSQ",
+            "PolyPhen"));
+    filter2.and(FeatureMatcher.byScore(Condition.LE, "-2.4"));
+    featureFilters.put("pfam", filter2);
+    visible.put("foobar", new FeatureColour(Color.blue));
+    ff.outputFeatureFilters(sb, visible, featureFilters);
+    String expected = "\nSTARTFILTERS\nfoobar\tLabel Present\npfam\t(CSQ:PolyPhen Present) AND (Score LE -2.4)\nENDFILTERS\n\n";
+    assertEquals(expected, sb.toString());
+  }
 }
diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index 6abb7e5..e9e0782 100644
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -23,11 +23,13 @@ package jalview.io;
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureColourI;
 import jalview.api.ViewStyleI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -35,12 +37,17 @@ import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcher;
+import jalview.datamodel.features.FeatureMatcherSet;
+import jalview.datamodel.features.FeatureMatcherSetI;
 import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.Desktop;
+import jalview.gui.FeatureRenderer;
 import jalview.gui.Jalview2XML;
 import jalview.gui.JvOptionPane;
 import jalview.gui.PopupMenu;
@@ -50,13 +57,16 @@ import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.BuriedColourScheme;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.FeatureColour;
 import jalview.schemes.JalviewColourScheme;
 import jalview.schemes.RNAHelicesColour;
 import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.structure.StructureImportSettings;
+import jalview.util.matcher.Condition;
 import jalview.viewmodel.AlignmentViewport;
 
+import java.awt.Color;
 import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
@@ -413,7 +423,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     String afid = af.getViewport().getSequenceSetId();
 
     // remember reference sequence for each panel
-    Map<String, SequenceI> refseqs = new HashMap<String, SequenceI>();
+    Map<String, SequenceI> refseqs = new HashMap<>();
 
     /*
      * mark sequence 2, 3, 4.. in panels 1, 2, 3...
@@ -551,8 +561,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
      * remember representative and hidden sequences marked 
      * on each panel
      */
-    Map<String, SequenceI> repSeqs = new HashMap<String, SequenceI>();
-    Map<String, List<String>> hiddenSeqNames = new HashMap<String, List<String>>();
+    Map<String, SequenceI> repSeqs = new HashMap<>();
+    Map<String, List<String>> hiddenSeqNames = new HashMap<>();
 
     /*
      * mark sequence 2, 3, 4.. in panels 1, 2, 3...
@@ -568,7 +578,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
       repIndex = Math.max(repIndex, 1);
       SequenceI repSeq = alignment.getSequenceAt(repIndex);
       repSeqs.put(ap.getViewName(), repSeq);
-      List<String> hiddenNames = new ArrayList<String>();
+      List<String> hiddenNames = new ArrayList<>();
       hiddenSeqNames.put(ap.getViewName(), hiddenNames);
 
       /*
@@ -841,4 +851,163 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     assertTrue(rs.conservationApplied());
     assertEquals(rs.getConservationInc(), 30);
   }
+
+  /**
+   * Test save and reload of feature colour schemes and filter settings
+   * 
+   * @throws IOException
+   */
+  @Test(groups = { "Functional" })
+  public void testSaveLoadFeatureColoursAndFilters() throws IOException
+  {
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
+    SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0);
+
+    /*
+     * add some features to the sequence
+     */
+    int score = 1;
+    addFeatures(seq1, "type1", score++);
+    addFeatures(seq1, "type2", score++);
+    addFeatures(seq1, "type3", score++);
+    addFeatures(seq1, "type4", score++);
+    addFeatures(seq1, "type5", score++);
+
+    /*
+     * set colour schemes for features
+     */
+    FeatureRenderer fr = af.getFeatureRenderer();
+    fr.findAllFeatures(true);
+
+    // type1: red
+    fr.setColour("type1", new FeatureColour(Color.red));
+
+    // type2: by label
+    FeatureColourI byLabel = new FeatureColour();
+    byLabel.setColourByLabel(true);
+    fr.setColour("type2", byLabel);
+
+    // type3: by score above threshold
+    FeatureColourI byScore = new FeatureColour(Color.BLACK, Color.BLUE, 1,
+            10);
+    byScore.setAboveThreshold(true);
+    byScore.setThreshold(2f);
+    fr.setColour("type3", byScore);
+
+    // type4: by attribute AF
+    FeatureColourI byAF = new FeatureColour();
+    byAF.setColourByLabel(true);
+    byAF.setAttributeName("AF");
+    fr.setColour("type4", byAF);
+
+    // type5: by attribute CSQ:PolyPhen below threshold
+    FeatureColourI byPolyPhen = new FeatureColour(Color.BLACK, Color.BLUE,
+            1, 10);
+    byPolyPhen.setBelowThreshold(true);
+    byPolyPhen.setThreshold(3f);
+    byPolyPhen.setAttributeName("CSQ", "PolyPhen");
+    fr.setColour("type5", byPolyPhen);
+
+    /*
+     * set filters for feature types
+     */
+
+    // filter type1 features by (label contains "x")
+    FeatureMatcherSetI filterByX = new FeatureMatcherSet();
+    filterByX.and(FeatureMatcher.byLabel(Condition.Contains, "x"));
+    fr.setFeatureFilter("type1", filterByX);
+
+    // filter type2 features by (score <= 2.4 and score > 1.1)
+    FeatureMatcherSetI filterByScore = new FeatureMatcherSet();
+    filterByScore.and(FeatureMatcher.byScore(Condition.LE, "2.4"));
+    filterByScore.and(FeatureMatcher.byScore(Condition.GT, "1.1"));
+    fr.setFeatureFilter("type2", filterByScore);
+
+    // filter type3 features by (AF contains X OR CSQ:PolyPhen != 0)
+    FeatureMatcherSetI filterByXY = new FeatureMatcherSet();
+    filterByXY
+            .and(FeatureMatcher.byAttribute(Condition.Contains, "X", "AF"));
+    filterByXY.or(FeatureMatcher.byAttribute(Condition.NE, "0", "CSQ",
+            "PolyPhen"));
+    fr.setFeatureFilter("type3", filterByXY);
+
+    /*
+     * save as Jalview project
+     */
+    File tfile = File.createTempFile("JalviewTest", ".jvp");
+    tfile.deleteOnExit();
+    String filePath = tfile.getAbsolutePath();
+    assertTrue(af.saveAlignment(filePath, FileFormat.Jalview),
+            "Failed to store as a project.");
+
+    /*
+     * close current alignment and load the saved project
+     */
+    af.closeMenuItem_actionPerformed(true);
+    af = null;
+    af = new FileLoader()
+            .LoadFileWaitTillLoaded(filePath, DataSourceType.FILE);
+    assertNotNull(af, "Failed to import new project");
+
+    /*
+     * verify restored feature colour schemes and filters
+     */
+    fr = af.getFeatureRenderer();
+    FeatureColourI fc = fr.getFeatureStyle("type1");
+    assertTrue(fc.isSimpleColour());
+    assertEquals(fc.getColour(), Color.red);
+    fc = fr.getFeatureStyle("type2");
+    assertTrue(fc.isColourByLabel());
+    fc = fr.getFeatureStyle("type3");
+    assertTrue(fc.isGraduatedColour());
+    assertNull(fc.getAttributeName());
+    assertTrue(fc.isAboveThreshold());
+    assertEquals(fc.getThreshold(), 2f);
+    fc = fr.getFeatureStyle("type4");
+    assertTrue(fc.isColourByLabel());
+    assertTrue(fc.isColourByAttribute());
+    assertEquals(fc.getAttributeName(), new String[] { "AF" });
+    fc = fr.getFeatureStyle("type5");
+    assertTrue(fc.isGraduatedColour());
+    assertTrue(fc.isColourByAttribute());
+    assertEquals(fc.getAttributeName(), new String[] { "CSQ", "PolyPhen" });
+    assertTrue(fc.isBelowThreshold());
+    assertEquals(fc.getThreshold(), 3f);
+
+    assertEquals(fr.getFeatureFilter("type1").toStableString(),
+            "Label Contains x");
+    assertEquals(fr.getFeatureFilter("type2").toStableString(),
+            "(Score LE 2.4) AND (Score GT 1.1)");
+    assertEquals(fr.getFeatureFilter("type3").toStableString(),
+            "(AF Contains X) OR (CSQ:PolyPhen NE 0.0)");
+  }
+
+  private void addFeature(SequenceI seq, String featureType, int score)
+  {
+    SequenceFeature sf = new SequenceFeature(featureType, "desc", 1, 2,
+            score, "grp");
+    sf.setValue("AF", score);
+    sf.setValue("CSQ", new HashMap<String, String>()
+    {
+      {
+        put("PolyPhen", Integer.toString(score));
+      }
+    });
+    seq.addSequenceFeature(sf);
+  }
+
+  /**
+   * Adds two features of the given type to the given sequence, also setting the
+   * score as the value of attribute "AF" and sub-attribute "CSQ:PolyPhen"
+   * 
+   * @param seq
+   * @param featureType
+   * @param score
+   */
+  private void addFeatures(SequenceI seq, String featureType, int score)
+  {
+    addFeature(seq, featureType, score++);
+    addFeature(seq, featureType, score);
+  }
 }
diff --git a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
index 03398c0..cebef11 100644
--- a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
@@ -378,11 +378,12 @@ public class FeatureRendererTest
 
     /*
      * hide feature type, then unhide
+     * - feature type visibility should not affect the result
      */
     FeatureSettingsBean[] data = new FeatureSettingsBean[1];
     data[0] = new FeatureSettingsBean("Cath", fc, null, false);
     fr.setFeaturePriority(data);
-    assertNull(fr.getColour(sf1));
+    assertEquals(fr.getColour(sf1), Color.red);
     data[0] = new FeatureSettingsBean("Cath", fc, null, true);
     fr.setFeaturePriority(data);
     assertEquals(fr.getColour(sf1), Color.red);
diff --git a/test/jalview/schemes/FeatureColourTest.java b/test/jalview/schemes/FeatureColourTest.java
index 72c29d3..2eb718b 100644
--- a/test/jalview/schemes/FeatureColourTest.java
+++ b/test/jalview/schemes/FeatureColourTest.java
@@ -27,6 +27,7 @@ import static org.testng.AssertJUnit.assertTrue;
 import static org.testng.AssertJUnit.fail;
 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
+import jalview.api.FeatureColourI;
 import jalview.datamodel.SequenceFeature;
 import jalview.gui.JvOptionPane;
 import jalview.util.ColorUtils;
@@ -325,20 +326,29 @@ public class FeatureColourTest
     assertEquals("domain\tlabel", fc.toJalviewFormat("domain"));
 
     /*
+     * colour by attribute text (no threshold)
+     */
+    fc = new FeatureColour();
+    fc.setColourByLabel(true);
+    fc.setAttributeName("CLIN_SIG");
+    assertEquals("domain\tattribute|CLIN_SIG", fc.toJalviewFormat("domain"));
+    
+    /*
      * colour by label (autoscaled) (an odd state you can reach by selecting
      * 'above threshold', then deselecting 'threshold is min/max' then 'colour
      * by label')
      */
+    fc.setAttributeName((String[]) null);
     fc.setAutoScaled(true);
     assertEquals("domain\tlabel", fc.toJalviewFormat("domain"));
 
     /*
-     * colour by label (above threshold) (min/max values are output though not
-     * used by this scheme)
+     * colour by label (above threshold) 
      */
     fc.setAutoScaled(false);
     fc.setThreshold(12.5f);
     fc.setAboveThreshold(true);
+    // min/max values are output though not used by this scheme
     assertEquals("domain\tlabel|||0.0|0.0|above|12.5",
             fc.toJalviewFormat("domain"));
 
@@ -350,38 +360,80 @@ public class FeatureColourTest
             fc.toJalviewFormat("domain"));
 
     /*
-     * graduated colour, no threshold
+     * colour by attributes text (below threshold)
+     */
+    fc.setBelowThreshold(true);
+    fc.setAttributeName("CSQ", "Consequence");
+    assertEquals("domain\tattribute|CSQ:Consequence|||0.0|0.0|below|12.5",
+            fc.toJalviewFormat("domain"));
+
+    /*
+     * graduated colour by score, no threshold
+     * - default constructor sets noValueColor = minColor
      */
     fc = new FeatureColour(Color.GREEN, Color.RED, 12f, 25f);
     String greenHex = Format.getHexString(Color.GREEN);
-    String expected = String.format("domain\t%s|%s|abso|12.0|25.0|none",
-            greenHex, redHex);
+    String expected = String.format(
+            "domain\tscore|%s|%s|noValueMin|abso|12.0|25.0|none", greenHex,
+            redHex);
     assertEquals(expected, fc.toJalviewFormat("domain"));
 
     /*
+     * graduated colour by score, no threshold, no value gets min colour
+     */
+    fc = new FeatureColour(Color.GREEN, Color.RED, Color.GREEN, 12f, 25f);
+    expected = String.format(
+            "domain\tscore|%s|%s|noValueMin|abso|12.0|25.0|none", greenHex,
+            redHex);
+    assertEquals(expected, fc.toJalviewFormat("domain"));
+
+    /*
+     * graduated colour by score, no threshold, no value gets max colour
+     */
+    fc = new FeatureColour(Color.GREEN, Color.RED, Color.RED, 12f, 25f);
+    expected = String.format(
+            "domain\tscore|%s|%s|noValueMax|abso|12.0|25.0|none", greenHex,
+            redHex);
+    assertEquals(expected, fc.toJalviewFormat("domain"));
+    
+    /*
      * colour ranges over the actual score ranges (not min/max)
      */
     fc.setAutoScaled(true);
-    expected = String.format("domain\t%s|%s|12.0|25.0|none", greenHex,
+    expected = String.format(
+            "domain\tscore|%s|%s|noValueMax|12.0|25.0|none", greenHex,
             redHex);
     assertEquals(expected, fc.toJalviewFormat("domain"));
 
     /*
-     * graduated colour below threshold
+     * graduated colour by score, below threshold
      */
     fc.setThreshold(12.5f);
     fc.setBelowThreshold(true);
-    expected = String.format("domain\t%s|%s|12.0|25.0|below|12.5",
+    expected = String.format(
+            "domain\tscore|%s|%s|noValueMax|12.0|25.0|below|12.5",
             greenHex, redHex);
     assertEquals(expected, fc.toJalviewFormat("domain"));
 
     /*
-     * graduated colour above threshold
+     * graduated colour by score, above threshold
      */
     fc.setThreshold(12.5f);
     fc.setAboveThreshold(true);
     fc.setAutoScaled(false);
-    expected = String.format("domain\t%s|%s|abso|12.0|25.0|above|12.5",
+    expected = String.format(
+            "domain\tscore|%s|%s|noValueMax|abso|12.0|25.0|above|12.5",
+            greenHex, redHex);
+    assertEquals(expected, fc.toJalviewFormat("domain"));
+
+    /*
+     * graduated colour by attribute, above threshold
+     */
+    fc.setAttributeName("CSQ", "AF");
+    fc.setAboveThreshold(true);
+    fc.setAutoScaled(false);
+    expected = String.format(
+            "domain\tattribute|CSQ:AF|%s|%s|noValueMax|abso|12.0|25.0|above|12.5",
             greenHex, redHex);
     assertEquals(expected, fc.toJalviewFormat("domain"));
   }
@@ -395,7 +447,7 @@ public class FeatureColourTest
     /*
      * simple colour by name
      */
-    FeatureColour fc = FeatureColour.parseJalviewFeatureColour("red");
+    FeatureColourI fc = FeatureColour.parseJalviewFeatureColour("red");
     assertTrue(fc.isSimpleColour());
     assertEquals(Color.RED, fc.getColour());
 
@@ -443,7 +495,28 @@ public class FeatureColourTest
     assertEquals(12.0f, fc.getThreshold());
 
     /*
-     * graduated colour (by name) (no threshold)
+     * colour by attribute text (no threshold)
+     */
+    fc = FeatureColour.parseJalviewFeatureColour("attribute|CLIN_SIG");
+    assertTrue(fc.isColourByAttribute());
+    assertTrue(fc.isColourByLabel());
+    assertFalse(fc.hasThreshold());
+    assertArrayEquals(new String[] { "CLIN_SIG" }, fc.getAttributeName());
+
+    /*
+     * colour by attributes text (with score threshold)
+     */
+    fc = FeatureColour.parseJalviewFeatureColour(
+            "attribute|CSQ:Consequence|||0.0|0.0|above|12.0");
+    assertTrue(fc.isColourByLabel());
+    assertTrue(fc.isColourByAttribute());
+    assertArrayEquals(new String[] { "CSQ", "Consequence" },
+            fc.getAttributeName());
+    assertTrue(fc.isAboveThreshold());
+    assertEquals(12.0f, fc.getThreshold());
+
+    /*
+     * graduated colour by score (with colour names) (no threshold)
      */
     fc = FeatureColour.parseJalviewFeatureColour("red|green|10.0|20.0");
     assertTrue(fc.isGraduatedColour());
@@ -455,7 +528,35 @@ public class FeatureColourTest
     assertTrue(fc.isAutoScaled());
 
     /*
-     * graduated colour (by hex code) (above threshold)
+     * graduated colour (explicitly by 'score') (no threshold)
+     */
+    fc = FeatureColour
+            .parseJalviewFeatureColour("Score|red|green|10.0|20.0");
+    assertTrue(fc.isGraduatedColour());
+    assertFalse(fc.hasThreshold());
+    assertEquals(Color.RED, fc.getMinColour());
+    assertEquals(Color.GREEN, fc.getMaxColour());
+    assertEquals(10f, fc.getMin());
+    assertEquals(20f, fc.getMax());
+    assertTrue(fc.isAutoScaled());
+
+    /*
+     * graduated colour by attribute (no threshold)
+     */
+    fc = FeatureColour
+            .parseJalviewFeatureColour("attribute|AF|red|green|10.0|20.0");
+    assertTrue(fc.isGraduatedColour());
+    assertTrue(fc.isColourByAttribute());
+    assertArrayEquals(new String[] { "AF" }, fc.getAttributeName());
+    assertFalse(fc.hasThreshold());
+    assertEquals(Color.RED, fc.getMinColour());
+    assertEquals(Color.GREEN, fc.getMaxColour());
+    assertEquals(10f, fc.getMin());
+    assertEquals(20f, fc.getMax());
+    assertTrue(fc.isAutoScaled());
+
+    /*
+     * graduated colour by score (colours by hex code) (above threshold)
      */
     String descriptor = String.format("%s|%s|10.0|20.0|above|15",
             Format.getHexString(Color.RED),
@@ -472,9 +573,26 @@ public class FeatureColourTest
     assertTrue(fc.isAutoScaled());
 
     /*
+     * graduated colour by attributes (below threshold)
+     */
+    fc = FeatureColour.parseJalviewFeatureColour(
+            "attribute|CSQ:AF|red|green|10.0|20.0|below|13");
+    assertTrue(fc.isGraduatedColour());
+    assertTrue(fc.isColourByAttribute());
+    assertArrayEquals(new String[] { "CSQ", "AF" }, fc.getAttributeName());
+    assertTrue(fc.hasThreshold());
+    assertTrue(fc.isBelowThreshold());
+    assertEquals(13f, fc.getThreshold());
+    assertEquals(Color.RED, fc.getMinColour());
+    assertEquals(Color.GREEN, fc.getMaxColour());
+    assertEquals(10f, fc.getMin());
+    assertEquals(20f, fc.getMax());
+    assertTrue(fc.isAutoScaled());
+
+    /*
      * graduated colour (by RGB triplet) (below threshold), absolute scale
      */
-    descriptor = String.format("255,0,0|0,255,0|abso|10.0|20.0|below|15");
+    descriptor = "255,0,0|0,255,0|abso|10.0|20.0|below|15";
     fc = FeatureColour.parseJalviewFeatureColour(descriptor);
     assertTrue(fc.isGraduatedColour());
     assertFalse(fc.isAutoScaled());
@@ -486,8 +604,7 @@ public class FeatureColourTest
     assertEquals(10f, fc.getMin());
     assertEquals(20f, fc.getMax());
 
-    descriptor = String
-            .format("blue|255,0,255|absolute|20.0|95.0|below|66.0");
+    descriptor = "blue|255,0,255|absolute|20.0|95.0|below|66.0";
     fc = FeatureColour.parseJalviewFeatureColour(descriptor);
     assertTrue(fc.isGraduatedColour());
   }
diff --git a/test/jalview/util/matcher/ConditionTest.java b/test/jalview/util/matcher/ConditionTest.java
index 883596a..2a12534 100644
--- a/test/jalview/util/matcher/ConditionTest.java
+++ b/test/jalview/util/matcher/ConditionTest.java
@@ -1,6 +1,7 @@
 package jalview.util.matcher;
 
 import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNull;
 
 import java.util.Locale;
 
@@ -30,4 +31,46 @@ public class ConditionTest
      */
     assertEquals(Condition.NE.toString(), "not =");
   }
+
+  @Test(groups = "Functional")
+  public void testGetStableName()
+  {
+    assertEquals(Condition.Contains.getStableName(), "Contains");
+    assertEquals(Condition.NotContains.getStableName(), "NotContains");
+    assertEquals(Condition.Matches.getStableName(), "Matches");
+    assertEquals(Condition.NotMatches.getStableName(), "NotMatches");
+    assertEquals(Condition.Present.getStableName(), "Present");
+    assertEquals(Condition.NotPresent.getStableName(), "NotPresent");
+    assertEquals(Condition.LT.getStableName(), "LT");
+    assertEquals(Condition.LE.getStableName(), "LE");
+    assertEquals(Condition.GT.getStableName(), "GT");
+    assertEquals(Condition.GE.getStableName(), "GE");
+    assertEquals(Condition.EQ.getStableName(), "EQ");
+    assertEquals(Condition.NE.getStableName(), "NE");
+  }
+
+  @Test(groups = "Functional")
+  public void testFromString()
+  {
+    assertEquals(Condition.fromString("Contains"), Condition.Contains);
+    // not case sensitive
+    assertEquals(Condition.fromString("contains"), Condition.Contains);
+    assertEquals(Condition.fromString("CONTAINS"), Condition.Contains);
+    assertEquals(Condition.fromString("NotContains"),
+            Condition.NotContains);
+    assertEquals(Condition.fromString("Matches"), Condition.Matches);
+    assertEquals(Condition.fromString("NotMatches"), Condition.NotMatches);
+    assertEquals(Condition.fromString("Present"), Condition.Present);
+    assertEquals(Condition.fromString("NotPresent"), Condition.NotPresent);
+    assertEquals(Condition.fromString("LT"), Condition.LT);
+    assertEquals(Condition.fromString("LE"), Condition.LE);
+    assertEquals(Condition.fromString("GT"), Condition.GT);
+    assertEquals(Condition.fromString("GE"), Condition.GE);
+    assertEquals(Condition.fromString("EQ"), Condition.EQ);
+    assertEquals(Condition.fromString("NE"), Condition.NE);
+
+    assertNull(Condition.fromString("Equals"));
+    assertNull(Condition.fromString(""));
+    assertNull(Condition.fromString(null));
+  }
 }
