</xs:element>
</xs:choice>
</xs:sequence>
+ <xs:attribute name="mappingType" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>Biotype of the mapping e.g. CdsToPeptide</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
</xs:extension>
</xs:complexContent>
</xs:complexType>
<xs:attribute name="source" type="xs:string"/>
<xs:attribute name="version" type="xs:string"/>
<xs:attribute name="accessionId" type="xs:string"/>
+ <xs:attribute name="locus" type="xs:boolean" default="false">
+ <xs:annotation>
+ <xs:documentation>
+ true for gene locus mapping, source=species, version=assembly, accession=chromosome
+ </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>
</xs:documentation>
</xs:annotation>
</xs:attribute>
+ <xs:attribute name="biotype" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>
+ Biotype of the sequence (if known)
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
</xs:extension>
</xs:complexContent>
</xs:complexType>
<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" />
<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>