+
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="Sequence">
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="vamsas:SequenceType">
+ <xs:sequence>
+ <xs:element name="DBRef" minOccurs="0" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="vamsas:Mapping" minOccurs="0" maxOccurs="1"/>
+ </xs:sequence>
+ <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:attribute name="dsseqid" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>
+ dataset sequence id for this sequence. Will be created as union of sequences.
+ </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:element>
+ <xs:element name="Annotation">
+ <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: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="sequenceRef" type="xs:string"
+ use="optional" />
+ <xs:attribute name="groupRef" 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="graphHeight" type="xs:int" use="optional">
+ <xs:annotation><xs:documentation>height in pixels for the graph if this is a graph-type annotation.</xs:documentation></xs:annotation></xs:attribute>
+ <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:attribute name="visible" type="xs:boolean"
+ use="optional" />
+ <xs:attribute name="centreColLabels" type="xs:boolean"
+ use="optional" />
+ <xs:attribute name="scaleColLabels" type="xs:boolean"
+ use="optional" />
+ <xs:attribute name="showAllColLabels" type="xs:boolean"
+ use="optional" />
+
+
+ <xs:attribute name="autoCalculated" type="xs:boolean" use="optional" default="false">
+ <xs:annotation><xs:documentation>is an autocalculated annotation row</xs:documentation>
+ </xs:annotation></xs:attribute>
+ <xs:attribute name="belowAlignment" type="xs:boolean" use="optional" default="true">
+ <xs:annotation><xs:documentation>is to be shown below the alignment - introduced in Jalview 2.8 for visualizing T-COFFEE alignment scores</xs:documentation></xs:annotation></xs:attribute>
+ <xs:attribute name="calcId" type="xs:string" use="optional">
+ <xs:annotation><xs:documentation>Optional string identifier used to group sets of annotation produced by a particular calculation. Values are opaque strings but have semantic meaning to Jalview's renderer, data importer and calculation system.</xs:documentation></xs:annotation>
+ </xs:attribute>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="SequenceSet">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="vamsas:Sequence" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="vamsas:Annotation" minOccurs="0" maxOccurs="unbounded"/>