X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fjalview.xsd;h=5631defca1e925a40164d5140151e742f773db49;hb=2f4f1d8fb6878271b64f327bc58c895f458137af;hp=b643d67285a4dbe5658c0e21df4346ab5583d853;hpb=94668ada1c2f3326264877969598cfa99e08d98e;p=jalview.git

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index b643d67..5631def 100755
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -1,31 +1,209 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<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">
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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" 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: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: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: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>
@@ -35,131 +213,305 @@
 									</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:element name="seq" type="xs:string"
+								maxOccurs="unbounded" />
 						</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="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:complexType>
 						<xs:sequence>
-							<xs:element name="AnnotationColours" minOccurs="0">
+							<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: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: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="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="showAnnotation" 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="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: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: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="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="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>
@@ -198,4 +550,27 @@
 		<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:schema>