X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fjalview.xsd;fp=schemas%2Fjalview.xsd;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=07dee982439467504808729fe51d4972477f7dd7;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
deleted file mode 100755
index 07dee98..0000000
--- a/schemas/jalview.xsd
+++ /dev/null
@@ -1,727 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- * 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: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" 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:complexType>
-									<xs:complexContent>
-										<xs:extension base="jv:pdbentry">
-											<xs:sequence>
-												<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: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: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>
-													</xs:complexType>
-												</xs:element>
-											</xs:sequence>
-										</xs:extension>
-									</xs:complexContent>
-								</xs:complexType>
-							</xs:element>
-							<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="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:complexType>
-						<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="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"
-					minOccurs="0">
-					<xs:complexType>
-						<xs:sequence>
-							<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="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: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="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="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>
-									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:complexType>
-						<xs:sequence>
-							<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:complexType>
-						<xs:sequence minOccurs="0">
-							<xs:element name="title" type="xs:string" />
-							<xs:element name="newick" type="xs:string" />
-						</xs:sequence>
-						<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: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:complexType>
-									<xs:sequence>
-									    <xs:element name="attributeName" type="xs:string" minOccurs="0" maxOccurs="2">
-										    	<xs:annotation>
-										    		<xs:documentation>name of feature attribute to colour by, or attribute and sub-attribute</xs:documentation>
-										    	</xs:annotation>
-									    </xs:element> 
-			    			  		   		<xs:element name="matcherSet" minOccurs="0" type="jalview:FeatureMatcherSet">
-										    	<xs:annotation>
-										    		<xs:documentation>optional filter(s) applied to the feature type</xs:documentation>
-										    	</xs:annotation>
-										</xs:element>
-								  	</xs:sequence>
-									<xs:attribute name="type" type="xs:string" use="required" />
-									<xs:attribute name="colour" type="xs:int" use="required" />
-									<xs:attribute name="display" type="xs:boolean"
-										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="noValueColour" use="optional" type="jalview:NoValueColour" default="Min" />
-									<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:complexType>
-									<xs:attribute name="name" type="xs:string" use="required" />
-									<xs:attribute name="display" type="xs:boolean"
-										use="required" />
-								</xs:complexType>
-							</xs:element>
-						</xs:sequence>
-					</xs:complexType>
-				</xs:element>
-			</xs:sequence>
-		</xs:sequence>
-	</xs:complexType>
-	<xs:complexType name="feature">
-		<xs:sequence>
-			<xs:element name="otherData" minOccurs="0" maxOccurs="unbounded">
-				<xs:complexType>
-					<xs:attribute name="key" type="xs:string" use="required" />
-					<xs:attribute name="key2" type="xs:string" use="optional">
-						<xs:annotation>
-							<xs:documentation>key2 may be used for a sub-attribute of key</xs:documentation>
-						</xs:annotation>
-					</xs:attribute>
-					<xs:attribute name="value" type="xs:string" use="required" />
-				</xs:complexType>
-			</xs:element>
-		</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: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: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: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: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:schema>