<xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
- <xs:element name="SequenceSet">
+ <xs:complexType name="mapListType">
+ <xs:annotation>
+ <xs:documentation>
+ developed after mapRangeType from http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+ </xs:documentation>
+ <xs:documentation>
+ This effectively represents a java.util.MapList object
+ </xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="mapListFrom" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation> a region from start to end inclusive</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:attribute name="start" type="xs:int" use="required"/>
+ <xs:attribute name="end" type="xs:int" use="required"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="mapListTo" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation> a region from start to end inclusive</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:attribute name="start" type="xs:int" use="required"/>
+ <xs:attribute name="end" type="xs:int" use="required"/>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="mapFromUnit" type="xs:positiveInteger" use="required">
+ <xs:annotation>
+ <xs:documentation>number of dictionary symbol widths involved in each
+ mapped position on this sequence (for example, 3 for a dna sequence exon
+ region that is being mapped to a protein sequence). This is optional,
+ since the unit can be usually be inferred from the dictionary type of
+ each sequence involved in the mapping. </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="mapToUnit" type="xs:positiveInteger" use="required">
+ <xs:annotation>
+ <xs:documentation>number of dictionary symbol widths involved in each
+ mapped position on this sequence (for example, 3 for a dna sequence exon
+ region that is being mapped to a protein sequence). This is optional,
+ since the unit can be usually be inferred from the dictionary type of
+ each sequence involved in the mapping. </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:complexType>
+ <xs:element name="Mapping">
+ <xs:complexType>
+ <xs:annotation>
+ <xs:documentation>
+ Represent the jalview.datamodel.Mapping object - it also provides
+ a way of storing sequences that are mapped 'to' without adding them
+ to the sequence set (which will mean they are then added to the alignment too).
+ </xs:documentation>
+ </xs:annotation>
+ <xs:complexContent>
+ <xs:extension base="vamsas:mapListType">
+ <xs:sequence>
+ <xs:choice minOccurs="0" maxOccurs="1">
+ <xs:element ref="vamsas:Sequence"/>
+ <xs:element name="dseqFor">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:annotation>
+ <xs:documentation>The sequence whose dataset sequence is to be referenced here</xs:documentation>
+ </xs:annotation>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:element>
+ </xs:choice>
+ </xs:sequence>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="AlcodonFrame">
<xs:complexType>
<xs:sequence>
- <xs:element name="Sequence" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="alcodon" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
- <xs:complexContent>
- <xs:extension base="vamsas:SequenceType">
- <xs:sequence>
- <xs:element name="DBRef" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="source" type="xs:string"/>
- <xs:attribute name="version" type="xs:string"/>
- <xs:attribute name="accessionId" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- </xs:extension>
- </xs:complexContent>
+ <xs:attribute name="pos1" type="xs:integer"/>
+ <xs:attribute name="pos2" type="xs:integer"/>
+ <xs:attribute name="pos3" type="xs:integer"/>
</xs:complexType>
</xs:element>
- <xs:element name="Annotation" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="alcodMap" minOccurs="0" maxOccurs="unbounded">
<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 ref="vamsas:Mapping" maxOccurs="1" minOccurs="1">
+ <xs:annotation>
+ <xs:documentation>
+ a Mapping entry and an associated protein sequence
+ </xs:documentation>
+ </xs:annotation>
</xs:element>
</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="graphColour" type="xs:int" use="optional"/>
- <xs:attribute name="graphGroup" type="xs:int" use="optional"/>
- <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="dnasq" type="xs:string" use="required">
+ <xs:annotation>
+ <xs:documentation>
+ internal jalview id for the dnasq for this mapping.
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
</xs:complexType>
+
</xs:element>
+
+ </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: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: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: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="graphColour" type="xs:int" use="optional"/>
+ <xs:attribute name="graphGroup" type="xs:int" use="optional"/>
+ <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: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: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>
</xs:complexType>
</xs:element>
<xs:element name="annotationElement">