X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fjalview.xsd;h=3df295114475d1a83d1739be99c358015d248a38;hb=84c69c8b17a65ea0fc0bc4a475773e23612f1c18;hp=65c74223d73cf00ea097e2a34d82fb2ad238cbb8;hpb=7b16db738774068ff6df6d65acbbd046ecfa446a;p=jalview.git

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index 65c7422..3df2951 100755
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -1,146 +1,165 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" 
-			xmlns:vamsas="www.vamsas.org" 
-			xmlns:jalview="www.jalview.org/colours" 
-			targetNamespace="www.jalview.org" 
-			elementFormDefault="qualified" 
-			attributeFormDefault="unqualified">
-
-<xs:import schemaLocation="vamsas.xsd" namespace="www.vamsas.org" />
-<xs:import schemaLocation="jalviewUserColours.xsd" namespace="www.jalview.org/colours"/>
-
-<xs:complexType name="JalviewModel">
-
-    <xs:sequence>
-
-	    <xs:element name="creationDate" type="xs:dateTime"/>
-
-        <xs:element name="vamsasModel" type="vamsas:VAMSAS"/>
-
-        <xs:sequence>
-
-            <xs:element name="JSeq" maxOccurs="unbounded">
-
-                <xs:complexType>
-                    
-					<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:int" use="required"/>
-
-                </xs:complexType>
-
-            </xs:element>
-
-            <xs:element name="JGroup" maxOccurs="unbounded">
-
-                <xs:complexType>
-
-                    <xs:sequence minOccurs="1">
-
-                        <xs:element name="seq" maxOccurs="unbounded" type="xs:int"/>
-					
-                    </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: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:import namespace="www.vamsas.ac.uk/jalview/version2" schemaLocation="vamsas.xsd"/>
+	<xs:import namespace="www.jalview.org/colours" schemaLocation="JalviewUserColours.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: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" type="jv:pdbentry" 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:int" use="required"/>
+						<xs:attribute name="hidden" type="xs:boolean"/>
+					</xs:complexType>
+				</xs:element>
+				<xs:element name="JGroup" minOccurs="0" maxOccurs="unbounded">
+					<xs:complexType>
+						<xs:sequence>
+							<xs:element name="seq" type="xs:int" 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:complexType>
-
-            </xs:element>
-
-            <xs:element name="Viewport" maxOccurs="unbounded">
-
-                <xs:complexType>
-				     	<xs:attribute name="conservationSelected" type="xs:boolean"/>
-
+						<xs:attribute name="outlineColour" type="xs:int"/>
+						<xs:attribute name="displayBoxes" type="xs:boolean"/>
+						<xs:attribute name="displayText" type="xs:boolean"/>
+						<xs:attribute name="colourText" type="xs:boolean"/>
+					</xs:complexType>
+				</xs:element>
+				<xs:element name="Viewport" maxOccurs="unbounded">
+					<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>
+							<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: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="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="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="title" type="xs:string"/>
+						<xs:attribute name="showFullId" 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="showConservation" type="xs:boolean"/>
-
-                        <xs:attribute name="showQuality" type="xs:boolean"/>
-
-						<xs:attribute name="showIdentity" 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:complexType>
-
-            </xs:element>    
-
-			<xs:element name="UserColours" maxOccurs="unbounded">
-                <xs:complexType>  
-					 <xs:sequence minOccurs="1">
-					 	<xs:element name="UserColourScheme" type="jalview:JalviewUserColours"/>
-					 </xs:sequence>
-					 <xs:attribute name="id" type="xs:string"/>
-                 </xs:complexType>
-            </xs:element>
-
-	</xs:sequence>
-
-    </xs:sequence>
-
-</xs:complexType>
-
-
-
-
+						<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: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="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:complexType>
+				</xs:element>
+				<xs:element name="FeatureSettings" minOccurs="0">
+					<xs:complexType>
+						<xs:sequence>
+							<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: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="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:schema>