X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fvamsas.xsd;h=abfabb117344c24de767cc45f02a54baec4ed13e;hb=refs%2Fheads%2Fnew_feature%2FJAL-4019_ambiguous_base_colourscheme;hp=5fd2bab696038e37a994518adeebfb9575b428b6;hpb=335e6b12c126bcb6825cd3f66422677db7cd91c7;p=jalview.git

diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
index 5fd2bab..abfabb1 100755
--- a/schemas/vamsas.xsd
+++ b/schemas/vamsas.xsd
@@ -219,12 +219,7 @@
 				<xs:element name="contactmatrix" type="vamsas:MatrixType"
 					maxOccurs="unbounded" minOccurs="0">
 				</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>
+				<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" />
@@ -312,13 +307,48 @@
 		<xs:attribute name="description" type="xs:string"/>
 	</xs:complexType>
 	<xs:complexType name="MatrixType">
-	<xs:simpleContent><xs:extension base="xs:string">
-	<xs:attribute name="id" type="xs:string"/>
-	<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:extension>
-	</xs:simpleContent>
+		<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 BigIntegers 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: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>