+ </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:MapOnAMatrixType" 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" />
+ <xs:element name="sequenceSetProperties" minOccurs="0"
+ maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:attribute name="key" type="xs:string" />
+ <xs:attribute name="value" type="xs:string" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element ref="vamsas:AlcodonFrame" minOccurs="0"
+ maxOccurs="unbounded" />
+ <xs:element name="Matrix" type="vamsas:MatrixType"
+ minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>Matrices referred to by this set of sequences.
+ </xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="gapChar" type="xs:string"
+ use="required" />
+ <xs:attribute name="datasetId" type="xs:string"
+ use="optional">
+ <xs:annotation>
+ <xs:documentation>
+ reference to set where jalview will gather the
+ dataset sequences for all sequences in the set.
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>