X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fjalview.xsd;h=1d2235ed1a7663d0997592d703f2ac24b515d4d1;hb=14e1f9dbb9c7a4535734fd3be7ddeee2a5ae72dc;hp=e1fbb677055b34925b5f5ac382e5263f04523953;hpb=a2094092396efa4d6736b11f3b1e1415098c3d12;p=jalview.git

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index e1fbb67..1d2235e 100755
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -1,56 +1,57 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- * 
- * 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/>.
+<!-- * 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. -->
+<!-- 
+	Java JAXB binding classes are generated by running command line tool xjc:
+ 	    xjc schemas/jalview.xsd -d src -p jalview.xml.binding.jalview
+ 	Note this also generates code for included schemas
 -->
-<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" xmlns:jalview="www.jalview.org/colours" xmlns:jv="www.jalview.org" xmlns:jvws="www.jalview.org/xml/wsparamset" targetNamespace="www.jalview.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
-		<xs:import namespace="www.vamsas.ac.uk/jalview/version2" schemaLocation="vamsas.xsd"/>
-	<xs:import namespace="www.jalview.org/colours" schemaLocation="JalviewUserColours.xsd"/>
-	<xs:import namespace="www.jalview.org/xml/wsparamset" schemaLocation="JalviewWsParamSet.xsd"/>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
+	xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" xmlns:jalview="www.jalview.org/colours"
+	xmlns:jv="www.jalview.org" xmlns:jvws="www.jalview.org/xml/wsparamset"
+	targetNamespace="www.jalview.org" elementFormDefault="qualified"
+	attributeFormDefault="unqualified">
+	<xs:import namespace="www.vamsas.ac.uk/jalview/version2"
+		schemaLocation="vamsas.xsd" />
+	<xs:import namespace="www.jalview.org/colours"
+		schemaLocation="JalviewUserColours.xsd" />
+	<xs:import namespace="www.jalview.org/xml/wsparamset"
+		schemaLocation="JalviewWsParamSet.xsd" />
+	<xs:element name="JalviewModel" type="jv:JalviewModel" />
 	<xs:complexType name="JalviewModel">
 		<xs:sequence>
 			<xs:element name="creationDate" type="xs:dateTime" />
 			<xs:element name="version" type="xs:string" />
 			<xs:element name="vamsasModel" type="vamsas:VAMSAS" />
 			<xs:sequence>
-				<xs:element name="JSeq" maxOccurs="unbounded">
+				<xs:element name="JSeq" maxOccurs="unbounded" minOccurs="0">
 					<xs:complexType>
 						<xs:sequence>
-							<xs:element name="features"
-								type="jv:feature" minOccurs="0" maxOccurs="unbounded" />
-							<xs:element name="pdbids" minOccurs="0"
-								maxOccurs="unbounded">
+							<xs:element name="features" type="jv:feature"
+								minOccurs="0" maxOccurs="unbounded" />
+							<xs:element name="pdbids" minOccurs="0" maxOccurs="unbounded">
 								<xs:complexType>
 									<xs:complexContent>
-										<xs:extension
-											base="jv:pdbentry">
+										<xs:extension base="jv:pdbentry">
 											<xs:sequence>
-												<xs:element
-													name="structureState" minOccurs="0"
+												<xs:element name="structureState" minOccurs="0"
 													maxOccurs="unbounded">
 													<xs:complexType>
 														<xs:simpleContent>
-															<xs:extension
-																base="xs:string">
-																<xs:attributeGroup
-																	ref="jv:swingwindow" />
-																<xs:attribute
-																	name="visible" type="xs:boolean" />
-																<xs:attribute
-																	name="viewId" type="xs:string" use="optional">
+															<xs:extension base="xs:string">
+																<xs:attributeGroup ref="jv:swingwindow" />
+																<xs:attribute name="visible" type="xs:boolean" />
+																<xs:attribute name="viewId" type="xs:string"
+																	use="optional">
 																	<xs:annotation>
 																		<xs:documentation>
 																			additional
@@ -109,9 +110,8 @@
 																		</xs:documentation>
 																	</xs:annotation>
 																</xs:attribute>
-																<xs:attribute
-																	name="alignwithAlignPanel" type="xs:boolean"
-																	use="optional" default="true">
+																<xs:attribute name="alignwithAlignPanel"
+																	type="xs:boolean" use="optional" default="true">
 																	<xs:annotation>
 																		<xs:documentation>
 																			Flag
@@ -140,9 +140,8 @@
 																		</xs:documentation>
 																	</xs:annotation>
 																</xs:attribute>
-																<xs:attribute
-																	name="colourwithAlignPanel" type="xs:boolean"
-																	use="optional" default="false">
+																<xs:attribute name="colourwithAlignPanel"
+																	type="xs:boolean" use="optional" default="false">
 																	<xs:annotation>
 																		<xs:documentation>
 																			Flag
@@ -173,9 +172,8 @@
 																		</xs:documentation>
 																	</xs:annotation>
 																</xs:attribute>
-																<xs:attribute
-																	name="colourByJmol" type="xs:boolean" use="optional"
-																	default="true">
+																<xs:attribute name="colourByJmol" type="xs:boolean"
+																	use="optional" default="true">
 																	<xs:annotation>
 																		<xs:documentation>
 																			Flag
@@ -202,6 +200,24 @@
 																		</xs:documentation>
 																	</xs:annotation>
 																</xs:attribute>
+																<xs:attribute name="type" type="xs:string"
+																	use="optional">
+																	<xs:annotation>
+																		<xs:documentation>
+																			An
+																			identifier
+																			for
+																			the
+																			viewer
+																			type,
+																			currently
+																			either
+																			JMOL
+																			or
+																			CHIMERA
+																		</xs:documentation>
+																	</xs:annotation>
+																</xs:attribute>
 
 															</xs:extension>
 														</xs:simpleContent>
@@ -212,204 +228,254 @@
 									</xs:complexContent>
 								</xs:complexType>
 							</xs:element>
-							<xs:element name="hiddenSequences"
-								type="xs:int" minOccurs="0" maxOccurs="unbounded" />
+							<xs:element name="hiddenSequences" type="xs:int"
+								minOccurs="0" maxOccurs="unbounded" />
+							<xs:element name="rnaViewer" minOccurs="0" maxOccurs="unbounded">
+								<xs:annotation>
+									<xs:documentation>Reference to a viewer showing RNA structure
+										for this sequence. Schema supports one viewer showing multiple
+										annotations for multiple sequences, though currently only one
+										annotation for one sequence (gapped or trimmed) is used
+									</xs:documentation>
+								</xs:annotation>
+								<xs:complexType>
+									<xs:sequence>
+										<xs:element name="secondaryStructure" minOccurs="1"
+											maxOccurs="unbounded">
+											<xs:complexType>
+												<xs:attribute name="title" type="xs:string" />
+												<xs:attribute name="annotationId" type="xs:string"
+													use="required">
+													<xs:annotation>
+														<xs:documentation>id attribute of Annotation in
+															vamsasModel for
+															the secondary structure annotation shown
+															in the viewer
+														</xs:documentation>
+													</xs:annotation>
+												</xs:attribute>
+												<xs:attribute name="gapped" type="xs:boolean">
+													<xs:annotation>
+														<xs:documentation>if true the RNA structure is shown with gaps, if false without
+														</xs:documentation>
+													</xs:annotation>
+												</xs:attribute>
+												<xs:attribute name="viewerState" type="xs:string">
+													<xs:annotation>
+														<xs:documentation>name of the project jar entry that holds
+															the VARNA viewer state for the structure
+														</xs:documentation>
+													</xs:annotation>
+												</xs:attribute>
+											</xs:complexType>
+										</xs:element>
+									</xs:sequence>
+									<xs:attributeGroup ref="jv:swingwindow" />
+									<xs:attribute name="title" type="xs:string" />
+									<xs:attribute name="viewId" type="xs:string">
+										<xs:annotation>
+											<xs:documentation>An id unique to the RNA viewer panel
+											</xs:documentation>
+										</xs:annotation>
+									</xs:attribute>
+									<xs:attribute name="dividerLocation" type="xs:int">
+										<xs:annotation>
+											<xs:documentation>horizontal position of split pane divider
+											</xs:documentation>
+										</xs:annotation>
+									</xs:attribute>
+									<xs:attribute name="selectedRna" type="xs:int">
+										<xs:annotation>
+											<xs:documentation>Index of the selected structure in the
+												viewer panel
+											</xs:documentation>
+										</xs:annotation>
+									</xs:attribute>
+								</xs:complexType>
+							</xs:element>
 						</xs:sequence>
-						<xs:attribute name="colour" type="xs:int"
-							use="optional" />
-						<xs:attribute name="start" type="xs:int"
-							use="required" />
-						<xs:attribute name="end" type="xs:int"
-							use="required" />
-						<xs:attribute name="id" type="xs:string"
-							use="required" />
+						<xs:attribute name="colour" type="xs:int" use="optional" />
+						<xs:attribute name="start" type="xs:int" use="required" />
+						<xs:attribute name="end" type="xs:int" use="required" />
+						<xs:attribute name="id" type="xs:string" use="required" />
 						<xs:attribute name="hidden" type="xs:boolean" />
+						<xs:attribute name="viewreference" type="xs:boolean" use="optional"/>
 					</xs:complexType>
 				</xs:element>
-				<xs:element name="JGroup" minOccurs="0"
-					maxOccurs="unbounded">
+				<xs:element name="JGroup" minOccurs="0" maxOccurs="unbounded">
 					<xs:complexType>
 						<xs:sequence>
-							<xs:element name="seq" type="xs:string"
-								maxOccurs="unbounded" />
+							<xs:element name="seq" type="xs:string" maxOccurs="unbounded" />
+							<xs:element name="annotationColours" type="jv:AnnotationColourScheme"
+								minOccurs="0" maxOccurs="1" />
 						</xs:sequence>
 						<xs:attribute name="start" type="xs:int" />
 						<xs:attribute name="end" type="xs:int" />
 						<xs:attribute name="name" type="xs:string" />
 						<xs:attribute name="colour" type="xs:string" />
-						<xs:attribute name="consThreshold"
-							type="xs:int" />
+						<xs:attribute name="consThreshold" type="xs:int" />
 						<xs:attribute name="pidThreshold" type="xs:int" />
-						<xs:attribute name="outlineColour"
-							type="xs:int" />
-						<xs:attribute name="displayBoxes"
-							type="xs:boolean" />
-						<xs:attribute name="displayText"
-							type="xs:boolean" />
-						<xs:attribute name="colourText"
-							type="xs:boolean" />
+						<xs:attribute name="outlineColour" type="xs:int" />
+						<xs:attribute name="displayBoxes" type="xs:boolean" />
+						<xs:attribute name="displayText" type="xs:boolean" />
+						<xs:attribute name="colourText" type="xs:boolean" />
 						<xs:attribute name="textCol1" type="xs:int" />
 						<xs:attribute name="textCol2" type="xs:int" />
-						<xs:attribute name="textColThreshold"
-							type="xs:int" />
-						<xs:attribute name="showUnconserved"
-							type="xs:boolean" use="optional" />
-						<xs:attribute name="ignoreGapsinConsensus"
-							type="xs:boolean" use="optional" default="true" />
-						<xs:attribute name="showConsensusHistogram"
-							type="xs:boolean" use="optional" default="true" />
-						<xs:attribute name="showSequenceLogo"
-							type="xs:boolean" use="optional" default="false" />
-						<xs:attribute name="id" type="xs:string"
-							use="optional">
+						<xs:attribute name="textColThreshold" type="xs:int" />
+						<xs:attribute name="showUnconserved" type="xs:boolean"
+							use="optional" />
+						<xs:attribute name="ignoreGapsinConsensus" type="xs:boolean"
+							use="optional" default="true" />
+						<xs:attribute name="showConsensusHistogram" type="xs:boolean"
+							use="optional" default="true" />
+						<xs:attribute name="showSequenceLogo" type="xs:boolean"
+							use="optional" default="false" />
+						<xs:attribute name="normaliseSequenceLogo" type="xs:boolean"
+							use="optional" default="false" />
+						<xs:attribute name="id" type="xs:string" use="optional">
 							<xs:annotation>
 								<xs:documentation>
 									Optional sequence group ID (only
-									needs to be unique for this
+									needs to be
+									unique for this
 									alignment)
 								</xs:documentation>
 							</xs:annotation>
 						</xs:attribute>
 					</xs:complexType>
 				</xs:element>
-				<xs:element name="Viewport" maxOccurs="unbounded">
+				<xs:element name="Viewport" maxOccurs="unbounded"
+					minOccurs="0">
 					<xs:complexType>
 						<xs:sequence>
-							<xs:element name="AnnotationColours"
-								minOccurs="0">
+							<xs:element name="AnnotationColours" type="jv:AnnotationColourScheme"
+								minOccurs="0" maxOccurs="1">
+							</xs:element>
+							<xs:element name="hiddenColumns" minOccurs="0"
+								maxOccurs="unbounded">
 								<xs:complexType>
-									<xs:attribute name="aboveThreshold"
-										type="xs:int" />
-									<xs:attribute name="annotation"
-										type="xs:string" />
-									<xs:attribute name="minColour"
-										type="xs:int" />
-									<xs:attribute name="maxColour"
-										type="xs:int" />
-									<xs:attribute name="colourScheme"
-										type="xs:string" />
-									<xs:attribute name="threshold"
-										type="xs:float" />
+									<xs:attribute name="start" type="xs:int" />
+									<xs:attribute name="end" type="xs:int" />
 								</xs:complexType>
 							</xs:element>
-							<xs:element name="hiddenColumns"
-								minOccurs="0" maxOccurs="unbounded">
+							<xs:element name="calcIdParam" minOccurs="0"
+								maxOccurs="unbounded">
 								<xs:complexType>
-									<xs:attribute name="start"
-										type="xs:int" />
-									<xs:attribute name="end"
-										type="xs:int" />
+									<xs:complexContent>
+										<xs:extension base="jvws:WebServiceParameterSet">
+											<xs:attribute name="calcId" type="xs:string"
+												use="required">
+												<xs:annotation>
+													<xs:documentation>handle for the calculation which uses
+														this parameter set
+													</xs:documentation>
+												</xs:annotation>
+											</xs:attribute>
+											<xs:attribute name="needsUpdate" type="xs:boolean"
+												use="optional" default="false">
+												<xs:annotation>
+													<xs:documentation>should the calculation be performed
+														immediately after loading in order to refresh results
+													</xs:documentation>
+												</xs:annotation>
+											</xs:attribute>
+											<xs:attribute name="autoUpdate" type="xs:boolean"
+												use="required">
+												<xs:annotation>
+													<xs:documentation>should the calculation be automatically
+														performed on edits
+													</xs:documentation>
+												</xs:annotation>
+											</xs:attribute>
+										</xs:extension>
+									</xs:complexContent>
 								</xs:complexType>
 							</xs:element>
-							<xs:element name="calcIdParam" 
-							 
-							minOccurs="0" maxOccurs="unbounded">
-							<xs:complexType>
-							<xs:complexContent>
-							<xs:extension base="jvws:WebServiceParameterSet">
-							<xs:attribute name="calcId" type="xs:string" use="required">
-							<xs:annotation>
-							<xs:documentation>handle for the calculation which uses this parameter set</xs:documentation></xs:annotation>
-							</xs:attribute>
-							<xs:attribute name="needsUpdate" type="xs:boolean" use="optional" default="false">
-							<xs:annotation><xs:documentation>should the calculation be performed immediately after loading in order to refresh results</xs:documentation></xs:annotation>
-							</xs:attribute>
-							<xs:attribute name="autoUpdate" type="xs:boolean" use="required">
-							<xs:annotation><xs:documentation>should the calculation be automatically performed on edits</xs:documentation></xs:annotation>
-							</xs:attribute>
-							</xs:extension>
-							</xs:complexContent>
-							</xs:complexType>
-							</xs:element>
 						</xs:sequence>
 						<xs:attributeGroup ref="jv:swingwindow" />
-						<xs:attribute name="conservationSelected"
-							type="xs:boolean" />
-						<xs:attribute name="pidSelected"
-							type="xs:boolean" />
+						<xs:attribute name="conservationSelected" type="xs:boolean" />
+						<xs:attribute name="pidSelected" type="xs:boolean" />
 						<xs:attribute name="bgColour" type="xs:string" />
-						<xs:attribute name="consThreshold"
-							type="xs:int" />
+						<xs:attribute name="consThreshold" type="xs:int" />
 						<xs:attribute name="pidThreshold" type="xs:int" />
 						<xs:attribute name="title" type="xs:string" />
-						<xs:attribute name="showFullId"
-							type="xs:boolean" />
-						<xs:attribute name="rightAlignIds"
-							type="xs:boolean" />
+						<xs:attribute name="showFullId" type="xs:boolean" />
+						<xs:attribute name="rightAlignIds" type="xs:boolean" />
 						<xs:attribute name="showText" type="xs:boolean" />
-						<xs:attribute name="showColourText"
-							type="xs:boolean" />
-						<xs:attribute name="showUnconserved"
-							type="xs:boolean" use="optional" default="false" />
-						<xs:attribute name="showBoxes"
-							type="xs:boolean" />
-						<xs:attribute name="wrapAlignment"
-							type="xs:boolean" />
-						<xs:attribute name="renderGaps"
-							type="xs:boolean" />
-						<xs:attribute name="showSequenceFeatures"
-							type="xs:boolean" />
-						<xs:attribute name="showNPfeatureTooltip"
-							type="xs:boolean" use="optional" />
-						<xs:attribute name="showDbRefTooltip"
-							type="xs:boolean" use="optional" />
-						<xs:attribute name="followHighlight"
-							type="xs:boolean" use="optional" default="true" />
-						<xs:attribute name="followSelection"
-							type="xs:boolean" use="optional" default="true" />
-						<xs:attribute name="showAnnotation"
-							type="xs:boolean" />
-						<xs:attribute name="centreColumnLabels"
-							type="xs:boolean" use="optional" default="false" />
-						<xs:attribute name="showGroupConservation"
-							type="xs:boolean" use="optional" default="false" />
-						<xs:attribute name="showGroupConsensus"
-							type="xs:boolean" use="optional" default="false" />
-						<xs:attribute name="showConsensusHistogram"
-							type="xs:boolean" use="optional" default="true" />
-						<xs:attribute name="showSequenceLogo"
-							type="xs:boolean" use="optional" default="false" />
-						<xs:attribute name="ignoreGapsinConsensus"
-							type="xs:boolean" use="optional" default="true" />
-
+						<xs:attribute name="showColourText" type="xs:boolean" />
+						<xs:attribute name="showUnconserved" type="xs:boolean"
+							use="optional" default="false" />
+						<xs:attribute name="showBoxes" type="xs:boolean" />
+						<xs:attribute name="wrapAlignment" type="xs:boolean" />
+						<xs:attribute name="renderGaps" type="xs:boolean" />
+						<xs:attribute name="showSequenceFeatures" type="xs:boolean" />
+						<xs:attribute name="showNPfeatureTooltip" type="xs:boolean"
+							use="optional" />
+						<xs:attribute name="showDbRefTooltip" type="xs:boolean"
+							use="optional" />
+						<xs:attribute name="followHighlight" type="xs:boolean"
+							use="optional" default="true" />
+						<xs:attribute name="followSelection" type="xs:boolean"
+							use="optional" default="true" />
+						<xs:attribute name="showAnnotation" type="xs:boolean" />
+						<xs:attribute name="centreColumnLabels" type="xs:boolean"
+							use="optional" default="false" />
+						<xs:attribute name="showGroupConservation" type="xs:boolean"
+							use="optional" default="false" />
+						<xs:attribute name="showGroupConsensus" type="xs:boolean"
+							use="optional" default="false" />
+						<xs:attribute name="showConsensusHistogram" type="xs:boolean"
+							use="optional" default="true" />
+						<xs:attribute name="showSequenceLogo" type="xs:boolean"
+							use="optional" default="false" />
+						<xs:attribute name="normaliseSequenceLogo" type="xs:boolean"
+							use="optional" default="false" />
+						<xs:attribute name="ignoreGapsinConsensus" type="xs:boolean"
+							use="optional" default="true" />
 						<xs:attribute name="startRes" type="xs:int" />
 						<xs:attribute name="startSeq" type="xs:int" />
 						<xs:attribute name="fontName" type="xs:string" />
 						<xs:attribute name="fontSize" type="xs:int" />
 						<xs:attribute name="fontStyle" type="xs:int" />
+						<xs:attribute name="scaleProteinAsCdna" type="xs:boolean" use="optional" default="true" />
 						<xs:attribute name="viewName" type="xs:string" />
-						<xs:attribute name="sequenceSetId"
-							type="xs:string" />
-						<xs:attribute name="gatheredViews"
-							type="xs:boolean" />
+						<xs:attribute name="sequenceSetId" type="xs:string" />
+						<xs:attribute name="gatheredViews" type="xs:boolean" />
 						<xs:attribute name="textCol1" type="xs:int" />
 						<xs:attribute name="textCol2" type="xs:int" />
-						<xs:attribute name="textColThreshold"
-							type="xs:int" />
-						<xs:attribute name="id" type="xs:ID"
-							use="optional">
+						<xs:attribute name="textColThreshold" type="xs:int" />
+						<xs:attribute name="id" type="xs:ID" use="optional">
 							<xs:annotation>
 								<xs:documentation>
 									unique id used by jalview to
-									synchronize between stored and
+									synchronize
+									between stored and
 									instantiated views
 								</xs:documentation>
 							</xs:annotation>
 						</xs:attribute>
+						<xs:attribute name="complementId" type="xs:string"
+							use="optional">
+							<xs:annotation>
+								<xs:documentation>
+									The viewport id of this viewport's
+									(cdna/protein) coding complement, if any
+								</xs:documentation>
+							</xs:annotation>
+						</xs:attribute>
+						<xs:attribute name="showComplementFeatures" type="xs:boolean" use="optional" default="false" />
+						<xs:attribute name="showComplementFeaturesOnTop" type="xs:boolean" use="optional" default="false" />
 					</xs:complexType>
 				</xs:element>
-				<xs:element name="UserColours" minOccurs="0"
-					maxOccurs="unbounded">
+				<xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">
 					<xs:complexType>
 						<xs:sequence>
-							<xs:element name="UserColourScheme"
-								type="jalview:JalviewUserColours" />
+							<xs:element name="UserColourScheme" type="jalview:JalviewUserColours" />
 						</xs:sequence>
 						<xs:attribute name="id" type="xs:string" />
 					</xs:complexType>
 				</xs:element>
-				<xs:element name="tree" minOccurs="0"
-					maxOccurs="unbounded">
+				<xs:element name="tree" minOccurs="0" maxOccurs="unbounded">
 					<xs:complexType>
 						<xs:sequence minOccurs="0">
 							<xs:element name="title" type="xs:string" />
@@ -419,55 +485,104 @@
 						<xs:attribute name="fontSize" type="xs:int" />
 						<xs:attribute name="fontStyle" type="xs:int" />
 						<xs:attribute name="threshold" type="xs:float" />
-						<xs:attribute name="showBootstrap"
-							type="xs:boolean" />
-						<xs:attribute name="showDistances"
-							type="xs:boolean" />
-						<xs:attribute name="markUnlinked"
-							type="xs:boolean" />
-						<xs:attribute name="fitToWindow"
-							type="xs:boolean" />
-						<xs:attribute name="currentTree"
-							type="xs:boolean" />
-						<xs:attribute name="id" type="xs:ID"
-							use="optional">
+						<xs:attribute name="showBootstrap" type="xs:boolean" />
+						<xs:attribute name="showDistances" type="xs:boolean" />
+						<xs:attribute name="markUnlinked" type="xs:boolean" />
+						<xs:attribute name="fitToWindow" type="xs:boolean" />
+						<xs:attribute name="currentTree" type="xs:boolean" />
+						<xs:attribute name="id" type="xs:ID" use="optional">
 							<xs:annotation>
 								<xs:documentation>
 									Tree ID added for binding tree
-									visualization settings to vamsas
+									visualization
+									settings to vamsas
 									document trees in jalview 2.4.1
 								</xs:documentation>
 							</xs:annotation>
 						</xs:attribute>
 						<xs:attributeGroup ref="jv:swingwindow" />
+						<xs:attribute name="linkToAllViews" use="optional" default="false" type="xs:boolean" />
+					</xs:complexType>
+				</xs:element>
+				<xs:element name="PcaViewer" minOccurs="0" maxOccurs="unbounded">
+					<xs:complexType>
+						<xs:sequence>
+							<xs:element name="sequencePoint" minOccurs="1" maxOccurs="unbounded">
+								<xs:complexType>
+									<xs:attribute name="sequenceRef" type="xs:string" />
+									<xs:attributeGroup ref="jv:position" />
+								</xs:complexType>
+							</xs:element>
+							<xs:element name="axis" minOccurs="3" maxOccurs="3">
+								<xs:annotation>
+									<xs:documentation>
+										endpoints of X, Y and Z axes in that order
+									</xs:documentation>
+								</xs:annotation>
+								<xs:complexType>
+									<xs:attributeGroup ref="jv:position" />
+								</xs:complexType>
+							</xs:element>
+							<xs:element name="seqPointMin">
+								<xs:complexType>
+									<xs:attributeGroup ref="jv:position" />
+								</xs:complexType>
+							</xs:element>
+							<xs:element name="seqPointMax">
+								<xs:complexType>
+									<xs:attributeGroup ref="jv:position" />
+								</xs:complexType>
+							</xs:element>
+							<xs:element name="pcaData" type="jv:PcaDataType" />
+						</xs:sequence>
+						<xs:attribute name="title" type="xs:string" />
+						<xs:attribute name="scoreModelName" type="xs:string" />
+						<xs:attribute name="xDim" type="xs:int" />
+						<xs:attribute name="yDim" type="xs:int" />
+						<xs:attribute name="zDim" type="xs:int" />
+						<xs:attribute name="bgColour" type="xs:int" />
+						<xs:attribute name="scaleFactor" type="xs:float" />
+						<xs:attribute name="showLabels" type="xs:boolean" />
+						<xs:attribute name="linkToAllViews" type="xs:boolean" />
+						<xs:attributeGroup ref="jv:SimilarityParams" />
+						<xs:attributeGroup ref="jv:swingwindow" />
 					</xs:complexType>
 				</xs:element>
 				<xs:element name="FeatureSettings" minOccurs="0">
 					<xs:complexType>
 						<xs:sequence>
-							<xs:element name="setting" minOccurs="0"
-								maxOccurs="unbounded">
+							<xs:element name="setting" minOccurs="0" maxOccurs="unbounded">
 								<xs:complexType>
-									<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" use="required" />
-									<xs:attribute name="order"
-										type="xs:float" use="optional" />
-									<xs:attribute name="mincolour"
-										type="xs:int" use="optional">
+									<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"
+										use="required" />
+									<xs:attribute name="order" type="xs:float" use="optional" />
+									<xs:attribute name="mincolour" type="xs:int" use="optional">
 										<xs:annotation>
 											<xs:documentation>
 												Optional minimum colour
-												for graduated feature
+												for graduated
+												feature
 												colour
 											</xs:documentation>
 										</xs:annotation>
 									</xs:attribute>
-									<xs:attribute name="threshold"
-										type="xs:float" use="optional">
+									<xs:attribute name="noValueColour" use="optional" type="jalview:NoValueColour" default="Min" />
+									<xs:attribute name="threshold" type="xs:float"
+										use="optional">
 										<xs:annotation>
 											<xs:documentation>
 												threshold value for
@@ -475,8 +590,8 @@
 											</xs:documentation>
 										</xs:annotation>
 									</xs:attribute>
-									<xs:attribute name="threshstate"
-										type="xs:int" use="optional">
+									<xs:attribute name="threshstate" type="xs:int"
+										use="optional">
 										<xs:annotation>
 											<xs:documentation>
 												threshold type for
@@ -484,23 +599,19 @@
 											</xs:documentation>
 										</xs:annotation>
 									</xs:attribute>
-									<xs:attribute name="max"
-										type="xs:float" use="optional" />
-									<xs:attribute name="min"
-										type="xs:float" use="optional" />
-									<xs:attribute name="colourByLabel"
-										type="xs:boolean" use="optional" />
-									<xs:attribute name="autoScale"
-										type="xs:boolean" use="optional" />
+									<xs:attribute name="max" type="xs:float" use="optional" />
+									<xs:attribute name="min" type="xs:float" use="optional" />
+									<xs:attribute name="colourByLabel" type="xs:boolean"
+										use="optional" />
+									<xs:attribute name="autoScale" type="xs:boolean"
+										use="optional" />
 								</xs:complexType>
 							</xs:element>
-							<xs:element name="group" minOccurs="0"
-								maxOccurs="unbounded">
+							<xs:element name="group" minOccurs="0" maxOccurs="unbounded">
 								<xs:complexType>
-									<xs:attribute name="name"
-										type="xs:string" use="required" />
-									<xs:attribute name="display"
-										type="xs:boolean" use="required" />
+									<xs:attribute name="name" type="xs:string" use="required" />
+									<xs:attribute name="display" type="xs:boolean"
+										use="required" />
 								</xs:complexType>
 							</xs:element>
 						</xs:sequence>
@@ -513,53 +624,106 @@
 		<xs:sequence>
 			<xs:element name="otherData" minOccurs="0" maxOccurs="unbounded">
 				<xs:complexType>
-					<xs:attribute name="key" type="xs:string" use="required"/>
-					<xs:attribute name="value" type="xs:string" use="required"/>
+					<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>
 		</xs:sequence>
-		<xs:attribute name="begin" type="xs:int" use="required"/>
-		<xs:attribute name="end" type="xs:int" use="required"/>
-		<xs:attribute name="type" type="xs:string" use="required"/>
-		<xs:attribute name="description" type="xs:string" use="optional"/>
-		<xs:attribute name="status" type="xs:string" use="optional"/>
-		<xs:attribute name="featureGroup" type="xs:string" use="optional"/>
-		<xs:attribute name="score" type="xs:float" use="optional"/>
+		<xs:attribute name="begin" type="xs:int" use="required" />
+		<xs:attribute name="end" type="xs:int" use="required" />
+		<xs:attribute name="type" type="xs:string" use="required" />
+		<xs:attribute name="description" type="xs:string" use="optional" />
+		<xs:attribute name="status" type="xs:string" use="optional" />
+		<xs:attribute name="featureGroup" type="xs:string" use="optional" />
+		<xs:attribute name="score" type="xs:float" use="optional" />
 	</xs:complexType>
 	<xs:complexType name="pdbentry">
 		<xs:sequence minOccurs="0" maxOccurs="unbounded">
 			<xs:element name="property" minOccurs="0" maxOccurs="unbounded">
 				<xs:complexType>
-					<xs:attribute name="name" type="xs:string" use="required"/>
-					<xs:attribute name="value" type="xs:string" use="required"/>
+					<xs:attribute name="name" type="xs:string" use="required" />
+					<xs:attribute name="value" type="xs:string" use="required" />
 				</xs:complexType>
 			</xs:element>
 		</xs:sequence>
-		<xs:attribute name="id" type="xs:string" use="required"/>
-		<xs:attribute name="type" type="xs:string" use="optional"/>
-		<xs:attribute name="file" type="xs:string"/>
+		<xs:attribute name="id" type="xs:string" use="required" />
+		<xs:attribute name="type" type="xs:string" use="optional" />
+		<xs:attribute name="file" type="xs:string" />
 	</xs:complexType>
-	<!-- 
-	<xs:complexType name="reportWindow">
-	<xs:annotation>
-	<xs:documentation>Generic type for windows containing mime-typed data associated with other jalview windows</xs:documentation>
-	</xs:annotation>
-	<xs:sequence>
-	</xs:sequence>
-    <xs:attribute name="id" type="xs:string" use="required"/>
-    <xs:attribute name="type" type="xs:string" use="optional"/>
-    <xs:attribute name="file" type="xs:string" use="optional"/>
+	<!-- <xs:complexType name="reportWindow"> <xs:annotation> <xs:documentation>Generic 
+		type for windows containing mime-typed data associated with other jalview 
+		windows</xs:documentation> </xs:annotation> <xs:sequence> </xs:sequence> 
+		<xs:attribute name="id" type="xs:string" use="required"/> <xs:attribute name="type" 
+		type="xs:string" use="optional"/> <xs:attribute name="file" type="xs:string" 
+		use="optional"/> </xs:complexType> -->
+	<xs:attributeGroup name="swingwindow">
+		<xs:annotation>
+			<xs:documentation>
+				base attributes for windows displayed in Jalview
+				desktop.
+			</xs:documentation>
+		</xs:annotation>
+		<xs:attribute name="width" type="xs:int" />
+		<xs:attribute name="height" type="xs:int" />
+		<xs:attribute name="xpos" type="xs:int" />
+		<xs:attribute name="ypos" type="xs:int" />
+	</xs:attributeGroup>
+	<xs:complexType name="AnnotationColourScheme">
+		<xs:attribute name="aboveThreshold" type="xs:int" />
+		<xs:attribute name="annotation" type="xs:string" />
+		<xs:attribute name="minColour" type="xs:int" />
+		<xs:attribute name="maxColour" type="xs:int" />
+		<xs:attribute name="colourScheme" type="xs:string" />
+		<xs:attribute name="threshold" type="xs:float" />
+		<xs:attribute name="perSequence" type="xs:boolean" use="optional" />
+		<xs:attribute name="predefinedColours" type="xs:boolean"
+			use="optional" />
+	</xs:complexType>
+	<xs:attributeGroup name="SimilarityParams">
+		<xs:annotation>
+			<xs:documentation>
+				parameters that condition a similarity score calculation
+			</xs:documentation>
+		</xs:annotation>
+		<xs:attribute name="includeGaps" type="xs:boolean" />
+		<xs:attribute name="matchGaps" type="xs:boolean" />
+		<xs:attribute name="includeGappedColumns" type="xs:boolean" />
+		<xs:attribute name="denominateByShortestLength" type="xs:boolean" />
+	</xs:attributeGroup>
+	<xs:attributeGroup name="position">
+		<xs:attribute name="xPos" type="xs:float" />
+		<xs:attribute name="yPos" type="xs:float" />
+		<xs:attribute name="zPos" type="xs:float" />
+	</xs:attributeGroup>
+	<xs:complexType name="PcaDataType">
+		<xs:annotation>
+			<xs:documentation>
+				The results of a PCA calculation
+			</xs:documentation>
+		</xs:annotation>
+		<xs:sequence>
+			<xs:element name="pairwiseMatrix" type="jv:DoubleMatrix" />
+			<xs:element name="tridiagonalMatrix" type="jv:DoubleMatrix" />
+			<xs:element name="eigenMatrix" type="jv:DoubleMatrix" />
+		</xs:sequence>
+	</xs:complexType>
+	<xs:complexType name="DoubleVector">
+		<xs:sequence>
+			<xs:element name="v" type="xs:double" minOccurs="0" maxOccurs="unbounded" />
+		</xs:sequence>
+	</xs:complexType>
+	<xs:complexType name="DoubleMatrix">
+		<xs:sequence>
+			<xs:element name="row" type="jv:DoubleVector" minOccurs="0" maxOccurs="unbounded" />
+			<xs:element name="D" minOccurs="0" type="jv:DoubleVector" />
+			<xs:element name="E" minOccurs="0" type="jv:DoubleVector" />
+		</xs:sequence>
+		<xs:attribute name="rows"  type="xs:int" />
+		<xs:attribute name="columns" type="xs:int" />
 	</xs:complexType>
- -->
-    <xs:attributeGroup name="swingwindow">
-    <xs:annotation>
-    <xs:documentation>
-      base attributes for windows displayed in Jalview desktop.
-    </xs:documentation>
-    </xs:annotation>
-      <xs:attribute name="width" type="xs:int"/>
-      <xs:attribute name="height" type="xs:int"/>
-      <xs:attribute name="xpos" type="xs:int"/>
-      <xs:attribute name="ypos" type="xs:int"/>
-    </xs:attributeGroup>
 </xs:schema>