Note this also generates code for included schemas
-->
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" targetNamespace="www.vamsas.ac.uk/jalview/version2" elementFormDefault="qualified" attributeFormDefault="unqualified">
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
+ xmlns:vamsas="www.vamsas.ac.uk/jalview/version2"
+ targetNamespace="www.vamsas.ac.uk/jalview/version2"
+ elementFormDefault="qualified" attributeFormDefault="unqualified">
<xs:complexType name="VAMSAS">
<xs:sequence>
- <xs:element name="Tree" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
- <xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="Tree" type="xs:string" minOccurs="0"
+ maxOccurs="unbounded" />
+ <xs:element ref="vamsas:SequenceSet" minOccurs="0"
+ maxOccurs="unbounded" />
</xs:sequence>
</xs:complexType>
<xs:complexType name="mapListType">
<xs:annotation>
- <xs:documentation>
- developed after mapRangeType from http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+ <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
+ This effectively represents a java.util.MapList
+ object
</xs:documentation>
</xs:annotation>
<xs:sequence>
- <xs:element name="mapListFrom" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="mapListFrom" minOccurs="0"
+ maxOccurs="unbounded">
<xs:annotation>
- <xs:documentation> a region from start to end inclusive</xs:documentation>
+ <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: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:element>
+ <xs:element name="mapListTo" minOccurs="0"
+ maxOccurs="unbounded">
<xs:annotation>
- <xs:documentation> a region from start to end inclusive</xs:documentation>
+ <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:attribute name="start" type="xs:int"
+ use="required" />
+ <xs:attribute name="end" type="xs:int" use="required" />
</xs:complexType>
- </xs:element>
+ </xs:element>
</xs:sequence>
- <xs:attribute name="mapFromUnit" type="xs:positiveInteger" use="required">
+ <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: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: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: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: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).
+ 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 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: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:attribute name="mappingType" type="xs:string" use="optional">
+ <xs:attribute name="mappingType" type="xs:string"
+ use="optional">
<xs:annotation>
- <xs:documentation>Biotype of the mapping e.g. CdsToPeptide</xs:documentation>
+ <xs:documentation>Biotype of the mapping e.g. CdsToPeptide
+ </xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:extension>
- </xs:complexContent>
+ </xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element name="AlcodonFrame">
<xs:complexType>
<xs:sequence>
- <xs:element name="alcodon" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="alcodon" minOccurs="0"
+ maxOccurs="unbounded">
<xs:complexType>
<xs:annotation>
<xs:documentation>
- specifies a series of aligned codons from an associated DNA sequence alignment that when translated correspond to columns of a peptide alignment.
- Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide).
+ specifies a series of aligned codons from an
+ associated DNA sequence alignment that when translated
+ correspond to columns of a peptide alignment.
+ Element may have
+ either all pos1,2,3 attributes specified, or none at all
+ (indicating a gapped column with no translated peptide).
</xs:documentation>
</xs:annotation>
- <xs:attribute name="pos1" type="xs:integer" use="optional"/>
- <xs:attribute name="pos2" type="xs:integer" use="optional"/>
- <xs:attribute name="pos3" type="xs:integer" use="optional"/>
+ <xs:attribute name="pos1" type="xs:integer"
+ use="optional" />
+ <xs:attribute name="pos2" type="xs:integer"
+ use="optional" />
+ <xs:attribute name="pos3" type="xs:integer"
+ use="optional" />
</xs:complexType>
</xs:element>
- <xs:element name="alcodMap" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="alcodMap" minOccurs="0"
+ maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
- <xs:element ref="vamsas:Mapping" maxOccurs="1" minOccurs="1">
+ <xs:element ref="vamsas:Mapping" maxOccurs="1"
+ minOccurs="1">
<xs:annotation>
<xs:documentation>
- a Mapping entry and an associated protein sequence
+ a Mapping entry and an associated protein
+ sequence
</xs:documentation>
</xs:annotation>
</xs:element>
</xs:sequence>
- <xs:attribute name="dnasq" type="xs:string" use="required">
+ <xs:attribute name="dnasq" type="xs:string"
+ use="required">
<xs:annotation>
<xs:documentation>
- internal jalview id for the dnasq for this mapping.
+ 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:complexContent>
<xs:extension base="vamsas:SequenceType">
<xs:sequence>
- <xs:element name="DBRef" minOccurs="0" maxOccurs="unbounded">
+ <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: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
+ 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: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)
+ 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: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.
+ 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:attribute name="biotype" type="xs:string"
+ use="optional">
<xs:annotation>
<xs:documentation>
Biotype of the sequence (if known)
<xs:attribute name="colour" type="xs:int" />
</xs:complexType>
</xs:element>
- <xs:element name="contactmatrix" type="vamsas:MatrixType"
- maxOccurs="unbounded" minOccurs="0">
+ <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: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="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="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="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="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="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 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>
<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: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: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="Matrices" type="vamsas:MatrixType" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="vamsas:AlcodonFrame" minOccurs="0"
+ maxOccurs="unbounded" />
+ <xs:element name="Matrices" 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: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.
+ reference to set where jalview will gather the
+ dataset sequences for all sequences in the set.
</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:element name="annotationElement">
<xs:complexType>
<xs:sequence>
- <xs:element name="displayCharacter" type="xs:string" minOccurs="0"/>
- <xs:element name="description" type="xs:string" minOccurs="0"/>
+ <xs:element name="displayCharacter" type="xs:string"
+ minOccurs="0" />
+ <xs:element name="description" type="xs:string"
+ minOccurs="0" />
<xs:element name="secondaryStructure" minOccurs="0">
<xs:simpleType>
<xs:restriction base="xs:string">
- <xs:length value="1"/>
+ <xs:length value="1" />
</xs:restriction>
</xs:simpleType>
</xs:element>
- <xs:element name="value" type="xs:float" minOccurs="0"/>
+ <xs:element name="value" type="xs:float" minOccurs="0" />
</xs:sequence>
- <xs:attribute name="position" type="xs:int" use="required"/>
- <xs:attribute name="colour" type="xs:int" use="optional"/>
+ <xs:attribute name="position" type="xs:int"
+ use="required" />
+ <xs:attribute name="colour" type="xs:int" use="optional" />
</xs:complexType>
</xs:element>
<xs:complexType name="SequenceType">
<xs:sequence>
- <xs:element name="sequence" type="xs:string" minOccurs="0"/>
- <xs:element name="name" type="xs:string" minOccurs="0"/>
+ <xs:element name="sequence" type="xs:string" minOccurs="0" />
+ <xs:element name="name" type="xs:string" minOccurs="0" />
</xs:sequence>
- <xs:attribute name="id" type="xs:string"/>
- <xs:attribute name="description" type="xs:string"/>
+ <xs:attribute name="id" type="xs:string" />
+ <xs:attribute name="description" type="xs:string" />
</xs:complexType>
<xs:complexType name="MatrixType">
+ <xs:annotation>
+ <xs:documentation>Represents matrix data imported to Jalview, and the
+ results of any derived calculations (independent of a particular
+ view
+ on the matrix).
+ </xs:documentation>
+ </xs:annotation>
<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>
+ more sets of comma separated values
+ </xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="groups" type="xs:string" minOccurs="0"
</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:complexType>
<xs:complexType name="MapOnAMatrixType">
+ <xs:annotation>
+ <xs:documentation>Defines a mapping from the local frame to a matrix
+ and its associated data specified by MatrixType
+ </xs:documentation>
+ </xs:annotation>
<xs:sequence>
<xs:element name="property" type="vamsas:property"
minOccurs="0" maxOccurs="unbounded" />
</xs:annotation>
</xs:element>
</xs:sequence>
-
+
<xs:attribute name="matrix" type="xs:string"
use="required">
-
+
<xs:annotation>
<xs:documentation>reference to the matrix type this Map refers to
</xs:documentation>
<xs:attribute name="name" type="xs:string" />
<xs:attribute name="value" type="xs:string" />
</xs:complexType>
-
-
+
+
</xs:schema>
git://source.jalview.org / jalview.git / blobdiff