X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fvamsas.xsd;h=fedbae3fc4c2819fce08013443252d9cfcab9c33;hb=a2d271cc24be4411224b296c9130b372fc8086c7;hp=20c19dd259aefd34d470b84da08f4b4e1238bdb6;hpb=17625a5cfc226dc98fe65fedaa8678a6bdfdbaf1;p=jalview.git

diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
index 20c19dd..fedbae3 100755
--- a/schemas/vamsas.xsd
+++ b/schemas/vamsas.xsd
@@ -173,6 +173,13 @@
 										</xs:documentation>
 									</xs:annotation>
 								</xs:attribute>
+								<xs:attribute name="canonical" type="xs:boolean" default="false">
+									<xs:annotation>
+										<xs:documentation>
+											true for the representative accession for databases where multiple accessions map to the same entry (eg. Uniprot)
+										</xs:documentation>
+									</xs:annotation>
+								</xs:attribute>
 							</xs:complexType>
 						</xs:element>
 					</xs:sequence>
@@ -209,12 +216,10 @@
 						<xs:attribute name="colour" type="xs:int" />
 					</xs:complexType>
 				</xs:element>
-				<xs:element name="property" minOccurs="0" maxOccurs="unbounded">
-					<xs:complexType>
-						<xs:attribute name="name" type="xs:string" />
-						<xs:attribute name="value" type="xs:string" />
-					</xs:complexType>
+				<xs:element name="contactmatrix" type="vamsas:MatrixType"
+					maxOccurs="unbounded" minOccurs="0">
 				</xs:element>
+				<xs:element name="property" type="vamsas:property" minOccurs="0" maxOccurs="unbounded"/>
 			</xs:sequence>
 			<xs:attribute name="graph" type="xs:boolean" use="required" />
 			<xs:attribute name="graphType" type="xs:int" use="optional" />
@@ -301,4 +306,56 @@
 		<xs:attribute name="id" type="xs:string"/>
 		<xs:attribute name="description" type="xs:string"/>
 	</xs:complexType>
+	<xs:complexType name="MatrixType">
+		<xs:sequence>
+			<xs:element name="elements" type="xs:string" minOccurs="1"
+				maxOccurs="1">
+				<xs:annotation>
+					<xs:documentation>serialised representation of matrix as one or
+						more sets of comma separated values</xs:documentation>
+				</xs:annotation>
+			</xs:element>
+			<xs:element name="groups" type="xs:string" minOccurs="0"
+				maxOccurs="unbounded">
+				<xs:annotation>
+					<xs:documentation>Comma separated series of longs formed from
+						bitsets defining partitions on the rows/columns of the matrix
+					</xs:documentation>
+				</xs:annotation>
+			</xs:element>
+			<xs:element name="newick" type="xs:string" minOccurs="0"
+				maxOccurs="unbounded">
+				<xs:annotation>
+					<xs:documentation>tree computed for this</xs:documentation>
+				</xs:annotation>
+			</xs:element>
+			<xs:element name="property" type="vamsas:property"
+				minOccurs="0" maxOccurs="unbounded" />
+			<xs:element name="mapping" type="vamsas:mapListType"
+				minOccurs="0" maxOccurs="1">
+			<xs:annotation>
+				<xs:documentation>mapping from the matrix row and column positions to
+					associated reference frame</xs:documentation>
+				</xs:annotation>
+			</xs:element>
+		</xs:sequence>
+
+		<xs:attribute name="type" type="xs:string" use="required" />
+		<xs:attribute name="rows" type="xs:integer"
+			use="required" />
+		<xs:attribute name="cols" type="xs:integer"
+			use="required" />
+		<xs:attribute name="treeMethod" type="xs:string"
+			use="optional" />
+		<xs:attribute name="cutHeight" type="xs:double"
+			use="optional" />
+		<xs:attribute name="id" type="xs:string" use="optional" />
+
+	</xs:complexType>
+	<xs:complexType name="property">
+		<xs:attribute name="name" type="xs:string" />
+		<xs:attribute name="value" type="xs:string" />
+	</xs:complexType>
+				
+	
 </xs:schema>