X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=schemas%2Fjalview.xsd;h=c5d35fb945ecc0dbee157423c3af1540126ef299;hb=bb82beaac6ab97bcb2d38244dafdff7adee173a7;hp=7e995ddf151e7e9d8810a5dbae99693dd64bae21;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index 7e995dd..c5d35fb 100755
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<!-- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1) 
-	* Copyright (C) 2015 The Jalview Authors * * This file is part of 
+<!-- * 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) 
@@ -10,6 +10,11 @@
 	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"
@@ -21,6 +26,7 @@
 		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" />
@@ -30,22 +36,28 @@
 				<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
@@ -104,8 +116,9 @@
 																		</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
@@ -134,8 +147,9 @@
 																		</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
@@ -166,8 +180,9 @@
 																		</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
@@ -194,8 +209,8 @@
 																		</xs:documentation>
 																	</xs:annotation>
 																</xs:attribute>
-																<xs:attribute name="type" type="xs:string"
-																	use="optional">
+																<xs:attribute
+																	name="type" type="xs:string" use="optional">
 																	<xs:annotation>
 																		<xs:documentation>
 																			An
@@ -222,66 +237,109 @@
 									</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: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>
+										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"
+										<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: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>
+															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:attribute
+													name="gapped" type="xs:boolean">
 													<xs:annotation>
-														<xs:documentation>if true the RNA structure is shown with gaps, if false without
+														<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: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>
+															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: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>
+												An id unique to the RNA
+												viewer panel
 											</xs:documentation>
 										</xs:annotation>
 									</xs:attribute>
-									<xs:attribute name="dividerLocation" type="xs:int">
+									<xs:attribute name="dividerLocation"
+										type="xs:int">
 										<xs:annotation>
-											<xs:documentation>horizontal position of split pane divider
+											<xs:documentation>
+												horizontal position of
+												split pane divider
 											</xs:documentation>
 										</xs:annotation>
 									</xs:attribute>
-									<xs:attribute name="selectedRna" type="xs:int">
+									<xs:attribute name="selectedRna"
+										type="xs:int">
 										<xs:annotation>
-											<xs:documentation>Index of the selected structure in the
-												viewer panel
+											<xs:documentation>
+												Index of the selected
+												structure in the viewer
+												panel
 											</xs:documentation>
 										</xs:annotation>
 									</xs:attribute>
@@ -293,6 +351,7 @@
 						<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">
@@ -384,6 +443,16 @@
 									</xs:complexContent>
 								</xs:complexType>
 							</xs:element>
+							<xs:element name="overview" minOccurs="0">
+							  <xs:complexType>
+								<xs:attributeGroup ref="jv:swingwindow" />
+								<xs:attribute name="showHidden" type="xs:boolean" />
+								<xs:attribute name="residueColour" type="xs:int" />
+								<xs:attribute name="gapColour" type="xs:int" />
+								<xs:attribute name="hiddenColour" type="xs:int" />
+								<xs:attribute name="title" type="xs:string" />
+							  </xs:complexType>
+							</xs:element>
 						</xs:sequence>
 						<xs:attributeGroup ref="jv:swingwindow" />
 						<xs:attribute name="conservationSelected" type="xs:boolean" />
@@ -427,9 +496,13 @@
 							use="optional" default="true" />
 						<xs:attribute name="startRes" type="xs:int" />
 						<xs:attribute name="startSeq" type="xs:int" />
+						<xs:attribute name="charWidth" type="xs:int" />
+						<xs:attribute name="charHeight" 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="idWidth" type="xs:int" />
+						<xs:attribute name="idWidthManuallyAdjusted" type="xs:boolean" />
 						<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" />
@@ -456,6 +529,8 @@
 								</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">
@@ -481,6 +556,8 @@
 						<xs:attribute name="markUnlinked" type="xs:boolean" />
 						<xs:attribute name="fitToWindow" type="xs:boolean" />
 						<xs:attribute name="currentTree" type="xs:boolean" />
+						<xs:attribute name="columnWise" type="xs:boolean" use="optional" default="false"><xs:annotation><xs:documentation>Set for trees associated with columns of an alignment, sequence or annotation row</xs:documentation></xs:annotation></xs:attribute>
+						<xs:attribute name="columnReference" type="xs:string" use="optional"><xs:annotation><xs:documentation>Refers to annotation row the tree is provided by</xs:documentation></xs:annotation></xs:attribute>
 						<xs:attribute name="id" type="xs:ID" use="optional">
 							<xs:annotation>
 								<xs:documentation>
@@ -492,6 +569,51 @@
 							</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">
@@ -499,6 +621,18 @@
 						<xs:sequence>
 							<xs:element name="setting" minOccurs="0" maxOccurs="unbounded">
 								<xs:complexType>
+									<xs:sequence>
+									    <xs:element name="attributeName" type="xs:string" minOccurs="0" maxOccurs="2">
+										    	<xs:annotation>
+										    		<xs:documentation>name of feature attribute to colour by, or attribute and sub-attribute</xs:documentation>
+										    	</xs:annotation>
+									    </xs:element> 
+			    			  		   		<xs:element name="matcherSet" minOccurs="0" type="jalview:FeatureMatcherSet">
+										    	<xs:annotation>
+										    		<xs:documentation>optional filter(s) applied to the feature type</xs:documentation>
+										    	</xs:annotation>
+										</xs:element>
+								  	</xs:sequence>
 									<xs:attribute name="type" type="xs:string" use="required" />
 									<xs:attribute name="colour" type="xs:int" use="required" />
 									<xs:attribute name="display" type="xs:boolean"
@@ -514,6 +648,7 @@
 											</xs:documentation>
 										</xs:annotation>
 									</xs:attribute>
+									<xs:attribute name="noValueColour" use="optional" type="jalview:NoValueColour" default="Min" />
 									<xs:attribute name="threshold" type="xs:float"
 										use="optional">
 										<xs:annotation>
@@ -558,6 +693,11 @@
 			<xs:element name="otherData" minOccurs="0" maxOccurs="unbounded">
 				<xs:complexType>
 					<xs:attribute name="key" type="xs:string" use="required" />
+					<xs:attribute name="key2" type="xs:string" use="optional">
+						<xs:annotation>
+							<xs:documentation>key2 may be used for a sub-attribute of key</xs:documentation>
+						</xs:annotation>
+					</xs:attribute>
 					<xs:attribute name="value" type="xs:string" use="required" />
 				</xs:complexType>
 			</xs:element>
@@ -612,5 +752,46 @@
 		<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>