X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fvamsas.xsd;h=4cc56b3f9321c97ff27906b8d405eafb33bf8ae3;hb=82483c09d45298e6f93a7d3d2b537598cc0451b5;hp=a7f731a664cdcb55c9844fbdd32af70d4896e0ae;hpb=4ac0fe29bbaaafc4d120c8369061391b9ae015f6;p=jalview.git

diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
index a7f731a..4cc56b3 100755
--- a/schemas/vamsas.xsd
+++ b/schemas/vamsas.xsd
@@ -3,24 +3,6 @@
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" targetNamespace="www.vamsas.ac.uk/jalview/version2" elementFormDefault="qualified" attributeFormDefault="unqualified">
 	<xs:complexType name="VAMSAS">
 		<xs:sequence>
-			<xs:element name="Alignment" minOccurs="0" maxOccurs="unbounded">
-				<xs:complexType>
-					<xs:sequence>
-						<xs:element name="Annotation" minOccurs="0">
-							<xs:complexType>
-								<xs:sequence>
-									<xs:element ref="vamsas:annotationElement" maxOccurs="unbounded"/>
-									<xs:element name="label" type="xs:string"/>
-									<xs:element name="description" type="xs:string"/>
-								</xs:sequence>
-								<xs:attribute name="graph" type="xs:boolean" use="required"/>
-								<xs:attribute name="graphType" type="xs:int" use="optional"/>
-							</xs:complexType>
-						</xs:element>
-						<xs:element ref="vamsas:SequenceSet"/>
-					</xs:sequence>
-				</xs:complexType>
-			</xs:element>
 			<xs:element name="Tree" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
 			<xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
 		</xs:sequence>
@@ -28,46 +10,71 @@
 	<xs:element name="SequenceSet">
 		<xs:complexType>
 			<xs:sequence>
-				<xs:element name="Sequence" type="vamsas:SequenceType" maxOccurs="unbounded"/>
+				<xs:element name="Sequence" minOccurs="0" maxOccurs="unbounded">
+					<xs:complexType>
+						<xs:complexContent>
+							<xs:extension base="vamsas:SequenceType">
+								<xs:sequence>
+									<xs:element name="DBRef" minOccurs="0" maxOccurs="unbounded">
+										<xs:complexType>
+											<xs:attribute name="source" type="xs:string"/>
+											<xs:attribute name="version" type="xs:string"/>
+											<xs:attribute name="accessionId" type="xs:string"/>
+										</xs:complexType>
+									</xs:element>
+								</xs:sequence>
+							</xs:extension>
+						</xs:complexContent>
+					</xs:complexType>
+				</xs:element>
 				<xs:element name="Annotation" minOccurs="0" maxOccurs="unbounded">
 					<xs:complexType>
 						<xs:sequence>
-							<xs:element name="description" type="xs:string" minOccurs="0"/>
-							<xs:element name="status" type="xs:string" minOccurs="0"/>
 							<xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded"/>
+							<xs:element name="label" type="xs:string"/>
+							<xs:element name="description" type="xs:string" minOccurs="0"/>
+							<xs:element name="thresholdLine" minOccurs="0">
+								<xs:complexType>
+									<xs:attribute name="label" type="xs:string"/>
+									<xs:attribute name="value" type="xs:float"/>
+									<xs:attribute name="colour" type="xs:int"/>
+								</xs:complexType>
+							</xs:element>
 						</xs:sequence>
-						<xs:attribute name="type" type="xs:string" use="required"/>
-						<xs:attribute name="end" type="xs:string" use="required"/>
-						<xs:attribute name="begin" type="xs:string" use="required"/>
-						<xs:attribute name="seqRef" type="xs:string" use="required"/>
+						<xs:attribute name="graph" type="xs:boolean" use="required"/>
+						<xs:attribute name="graphType" type="xs:int" use="optional"/>
+						<xs:attribute name="sequenceRef" type="xs:string" use="optional"/>
+						<xs:attribute name="graphColour" type="xs:int" use="optional"/>
+						<xs:attribute name="graphGroup" type="xs:int" use="optional"/>
+						<xs:attribute name="id" type="xs:string" use="optional"/>
 					</xs:complexType>
 				</xs:element>
 			</xs:sequence>
 			<xs:attribute name="gapChar" type="xs:string" use="required"/>
-			<xs:attribute name="aligned" type="xs:boolean" use="optional"/>
 		</xs:complexType>
 	</xs:element>
 	<xs:element name="annotationElement">
 		<xs:complexType>
 			<xs:sequence>
-				<xs:element name="displayCharacter" type="xs:string"/>
-				<xs:element name="description" type="xs:string"/>
-				<xs:element name="secondaryStructure">
+				<xs:element name="displayCharacter" type="xs:string" minOccurs="0"/>
+				<xs:element name="description" type="xs:string" minOccurs="0"/>
+				<xs:element name="secondaryStructure" minOccurs="0">
 					<xs:simpleType>
 						<xs:restriction base="xs:string">
 							<xs:length value="1"/>
 						</xs:restriction>
 					</xs:simpleType>
 				</xs:element>
-				<xs:element name="value" type="xs:float"/>
+				<xs:element name="value" type="xs:float" minOccurs="0"/>
 			</xs:sequence>
 			<xs:attribute name="position" type="xs:int" use="required"/>
+			<xs:attribute name="colour" type="xs:int" use="optional"/>
 		</xs:complexType>
 	</xs:element>
 	<xs:complexType name="SequenceType">
 		<xs:sequence>
-			<xs:element name="sequence" type="xs:string"/>
-			<xs:element name="name" type="xs:string"/>
+			<xs:element name="sequence" type="xs:string" minOccurs="0"/>
+			<xs:element name="name" type="xs:string" minOccurs="0"/>
 		</xs:sequence>
 		<xs:attribute name="id" type="xs:string"/>
 		<xs:attribute name="description" type="xs:string"/>