X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fvamsas.xsd;h=9ba791979f9f0c818436b36df7ec736741f6e680;hb=855f7a4bb3e8d5fcfa9059df64262fc73f0164be;hp=2143830f28302915ae2d6425595c396706758e08;hpb=74290f03cc870c13a983fb56c9c4c21c0662c28b;p=jalview.git

diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
index 2143830..9ba7919 100755
--- a/schemas/vamsas.xsd
+++ b/schemas/vamsas.xsd
@@ -1,75 +1,84 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->
-<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.org" targetNamespace="www.vamsas.org" 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>
-	</xs:complexType>
-	<xs:element name="SequenceSet">
-		<xs:complexType>
-			<xs:sequence>
-				<xs:element name="Sequence" type="vamsas:SequenceType" maxOccurs="unbounded"/>
-				<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: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: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:simpleType>
-						<xs:restriction base="xs:string">
-							<xs:length value="1"/>
-						</xs:restriction>
-					</xs:simpleType>
-				</xs:element>
-				<xs:element name="value" type="xs:float"/>
-			</xs:sequence>
-			<xs:attribute name="position" type="xs:int" use="required"/>
-		</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:sequence>
-		<xs:attribute name="id" type="xs:string"/>
-		<xs:attribute name="description" type="xs:string"/>
-	</xs:complexType>
-</xs:schema>
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->
+<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="Tree" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
+			<xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
+		</xs:sequence>
+	</xs:complexType>
+	<xs:element name="SequenceSet">
+		<xs:complexType>
+			<xs:sequence>
+				<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 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="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:attribute name="scoreOnly" type="xs:boolean" use="optional" default="false"/>
+						<xs:attribute name="score" type="xs:double" use="optional"/>
+					</xs:complexType>
+				</xs:element>
+			</xs:sequence>
+			<xs:attribute name="gapChar" type="xs:string" use="required"/>
+		</xs:complexType>
+	</xs:element>
+	<xs:element name="annotationElement">
+		<xs:complexType>
+			<xs:sequence>
+				<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" 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" 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"/>
+	</xs:complexType>
+</xs:schema>