X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fjalview.xsd;h=6c1e65fc633feb739077f68c9d822a2ecddf72ca;hb=fb4c54617dd9c5ac605853551478596902f34541;hp=d5c140b4fdff258f69b56dcd505d58b39aeee4d9;hpb=61f5dddd508a7f036cc8b60c33f227754063c0ed;p=jalview.git

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index d5c140b..6c1e65f 100755
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -1,12 +1,7 @@
 <?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"
-				 xmlns:jv="www.jalview.org" 
-				 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: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"/>
@@ -16,20 +11,21 @@
 				<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: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:complexType>
+							<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 minOccurs="1">
-							<xs:element name="seq" maxOccurs="unbounded" type="xs:int"/>
+						<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"/>
@@ -45,6 +41,24 @@
 				</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"/>
@@ -75,7 +89,7 @@
 				</xs:element>
 				<xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">
 					<xs:complexType>
-						<xs:sequence minOccurs="1">
+						<xs:sequence>
 							<xs:element name="UserColourScheme" type="jalview:JalviewUserColours"/>
 						</xs:sequence>
 						<xs:attribute name="id" type="xs:string"/>
@@ -83,7 +97,7 @@
 				</xs:element>
 				<xs:element name="tree" minOccurs="0" maxOccurs="unbounded">
 					<xs:complexType>
-						<xs:sequence minOccurs="0" maxOccurs="1">
+						<xs:sequence minOccurs="0">
 							<xs:element name="title" type="xs:string"/>
 							<xs:element name="newick" type="xs:string"/>
 						</xs:sequence>
@@ -102,33 +116,30 @@
 						<xs:attribute name="currentTree" type="xs:boolean"/>
 					</xs:complexType>
 				</xs:element>
-				
-				<xs:element name="FeatureSettings" minOccurs="0" maxOccurs="1">
-						<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 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: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:complexType>
-		
 	<xs:complexType name="pdbentry">
 		<xs:sequence minOccurs="0" maxOccurs="unbounded">
 			<xs:element name="property" minOccurs="0" maxOccurs="unbounded">
@@ -140,6 +151,6 @@
 		</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>