X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fjalview.xsd;h=d643648c08a2122f78d8ab7c27258ff7ac2297f4;hb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;hp=c847b6d3604d742e2a84fb1ab4e53193bac72a0d;hpb=f25d2c93b2a8c381d35e7ae1ab7b3bb20d33a1a3;p=jalview.git

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index c847b6d..d643648 100755
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -1,59 +1,209 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.
 -->
-<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" targetNamespace="www.jalview.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
+<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: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: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" maxOccurs="unbounded">
+												<xs:element
+													name="structureState" minOccurs="0"
+													maxOccurs="unbounded">
 													<xs:complexType>
 														<xs:simpleContent>
-															<xs:extension base="xs:string">
-																<xs:attribute name="visible" type="xs:boolean"/>
-																<xs:attribute name="xpos" type="xs:int"/>
-																<xs:attribute name="ypos" type="xs:int"/>
-																<xs:attribute name="width" type="xs:int"/>
-																<xs:attribute name="height" type="xs:int"/>
-																<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 identifier which properly disambiguates
-																		the structure view from any other view with the same attributes. This is not an ID,
-																		because it is possible to have many references to the same physical structure view
-																		from different sequences in an alignment. A structureState element citing the same
-																		viewId will appear for each instance.</xs:documentation>
+																		<xs:documentation>
+																			additional
+																			identifier
+																			which
+																			properly
+																			disambiguates
+																			the
+																			structure
+																			view
+																			from
+																			any
+																			other
+																			view
+																			with
+																			the
+																			same
+																			attributes.
+																			This
+																			is
+																			not
+																			an
+																			ID,
+																			because
+																			it
+																			is
+																			possible
+																			to
+																			have
+																			many
+																			references
+																			to
+																			the
+																			same
+																			physical
+																			structure
+																			view
+																			from
+																			different
+																			sequences
+																			in
+																			an
+																			alignment.
+																			A
+																			structureState
+																			element
+																			citing
+																			the
+																			same
+																			viewId
+																			will
+																			appear
+																			for
+																			each
+																			instance.
+																		</xs:documentation>
 																	</xs:annotation>
 																</xs:attribute>
-																	
-																
+																<xs:attribute
+																	name="alignwithAlignPanel" type="xs:boolean"
+																	use="optional" default="true">
+																	<xs:annotation>
+																		<xs:documentation>
+																			Flag
+																			set
+																			if
+																			the
+																			alignment
+																			panel
+																			containing
+																			this
+																			JSeq
+																			should
+																			be
+																			included
+																			in
+																			those
+																			used
+																			to
+																			perform
+																			a
+																			structure
+																			superposition
+																			(since
+																			Jalview
+																			2.7).
+																		</xs:documentation>
+																	</xs:annotation>
+																</xs:attribute>
+																<xs:attribute
+																	name="colourwithAlignPanel" type="xs:boolean"
+																	use="optional" default="false">
+																	<xs:annotation>
+																		<xs:documentation>
+																			Flag
+																			set
+																			if
+																			the
+																			alignment
+																			panel
+																			containing
+																			this
+																			JSeq
+																			should
+																			be
+																			included
+																			in
+																			those
+																			used
+																			to
+																			colour
+																			its
+																			associated
+																			sequences
+																			in
+																			this
+																			structureState(since
+																			Jalview
+																			2.7).
+																		</xs:documentation>
+																	</xs:annotation>
+																</xs:attribute>
+																<xs:attribute
+																	name="colourByJmol" type="xs:boolean" use="optional"
+																	default="true">
+																	<xs:annotation>
+																		<xs:documentation>
+																			Flag
+																			set
+																			if
+																			the
+																			structure
+																			display
+																			is
+																			coloured
+																			by
+																			the
+																			Jmol
+																			state,
+																			rather
+																			than
+																			by
+																			one
+																			or
+																			more
+																			linked
+																			alignment
+																			views.
+																		</xs:documentation>
+																	</xs:annotation>
+																</xs:attribute>
+
 															</xs:extension>
 														</xs:simpleContent>
 													</xs:complexType>
@@ -63,175 +213,293 @@
 									</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: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="hidden" type="xs:boolean"/>
+						<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: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:sequence>
+							<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="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="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:annotation>
-						<xs:documentation>
-						Optional sequence group ID (only needs to be unique for this alignment)
-						</xs:documentation>
-						</xs:annotation></xs:attribute>
+						<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="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="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="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
+									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: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:complexType>
+							<xs:element name="AnnotationColours" type="jv:AnnotationColourScheme" 
+								minOccurs="0" maxOccurs="1">
 							</xs:element>
-							<xs:element name="hiddenColumns" minOccurs="0" maxOccurs="unbounded">
+							<xs:element name="hiddenColumns"
+								minOccurs="0" maxOccurs="unbounded">
 								<xs:complexType>
-									<xs:attribute name="start" type="xs:int"/>
-									<xs:attribute name="end" type="xs:int"/>
+									<xs:attribute name="start"
+										type="xs:int" />
+									<xs:attribute name="end"
+										type="xs:int" />
 								</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: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="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="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="xpos" type="xs:int"/>
-						<xs:attribute name="ypos" type="xs:int"/>
-						<xs:attribute name="width" type="xs:int"/>
-						<xs:attribute name="height" type="xs:int"/>
-						<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="viewName" type="xs:string"/>
-						<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:attributeGroup ref="jv:swingwindow" />
+						<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="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="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="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="viewName" type="xs:string" />
+						<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:annotation>
+								<xs:documentation>
+									unique id used by jalview to
+									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>
-									unique id used by jalview to synchronize between stored and instantiated views
+									The viewport id of this viewport's (cdna/protein) coding complement, if any
 								</xs:documentation>
 							</xs:annotation>
 						</xs:attribute>
 					</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: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"/>
-							<xs:element name="newick" type="xs:string"/>
+							<xs:element name="title" type="xs:string" />
+							<xs:element name="newick" type="xs:string" />
 						</xs:sequence>
-						<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:attribute name="fontName" type="xs:string"/>
-						<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:annotation><xs:documentation>Tree ID added for binding tree visualization settings to vamsas document trees in jalview 2.4.1</xs:documentation></xs:annotation>
+						<xs:attribute name="fontName" type="xs:string" />
+						<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:annotation>
+								<xs:documentation>
+									Tree ID added for binding tree
+									visualization settings to vamsas
+									document trees in jalview 2.4.1
+								</xs:documentation>
+							</xs:annotation>
 						</xs:attribute>
+						<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:annotation><xs:documentation>Optional minimum colour for graduated feature colour</xs:documentation>
-									</xs:annotation></xs:attribute>
-									<xs:attribute name="threshold" type="xs:float" use="optional">
-									<xs:annotation><xs:documentation>threshold value for graduated feature colour</xs:documentation>
-									</xs:annotation></xs:attribute>
-									<xs:attribute name="threshstate" type="xs:int" use="optional">
-									<xs:annotation><xs:documentation>threshold type for graduated feature colour</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: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:annotation>
+											<xs:documentation>
+												Optional minimum colour
+												for graduated feature
+												colour
+											</xs:documentation>
+										</xs:annotation>
+									</xs:attribute>
+									<xs:attribute name="threshold"
+										type="xs:float" use="optional">
+										<xs:annotation>
+											<xs:documentation>
+												threshold value for
+												graduated feature colour
+											</xs:documentation>
+										</xs:annotation>
+									</xs:attribute>
+									<xs:attribute name="threshstate"
+										type="xs:int" use="optional">
+										<xs:annotation>
+											<xs:documentation>
+												threshold type for
+												graduated feature colour
+											</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: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>
@@ -270,4 +538,39 @@
 		<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>
+ -->
+    <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:schema>