<?xml version="1.0" encoding="UTF-8"?>
<!-- edited with XMLSPY v5 rel. 4 U (http://www.xmlspy.com) by MSD (EMBL OUTSTATION THE EBI WELLCOME TRUST GENOME CAMPUS) -->
<!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->
-<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes" targetNamespace="http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes" elementFormDefault="qualified" attributeFormDefault="unqualified">
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
+ xmlns:vamsas="http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes"
+ targetNamespace="http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes" elementFormDefault="qualified"
+ attributeFormDefault="unqualified">
<xs:annotation>
<xs:documentation> Vorba ID - Vamsas Object Request Broker Address ID (name needs to be
worked on): Suggest it could be of the form documentRoot/datasetName/SequenceUID for a
</xs:element>
<xs:element name="treenode" minOccurs="0" maxOccurs="unbounded">
<xs:annotation>
- <xs:documentation>
- node identity and mapping data between tree representations and vamsas document objects
- </xs:documentation>
+ <xs:documentation> node identity and mapping data between tree
+ representations and vamsas document objects </xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:complexContent>
<xs:extension base="vamsas:nodeType">
<xs:attribute name="treeId" type="xs:IDREFS">
<xs:annotation>
- <xs:documentation>
- reference to one or more trees containing the node being described.
- </xs:documentation>
+ <xs:documentation> reference to one or more trees containing
+ the node being described. </xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="nodespec" type="xs:string">
<xs:annotation>
- <xs:documentation>
- String uniquely identifying a particular node in the referenced tree according to the format of the tree representation that is referenced.
+ <xs:documentation> String uniquely identifying a particular
+ node in the referenced tree according to the format of
+ the tree representation that is referenced.
</xs:documentation>
</xs:annotation>
</xs:attribute>
-
+
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:complexType name="referenceType">
<xs:annotation>
- <xs:documentation>
- base type for citing arbitrary links between vamsas objects
+ <xs:documentation> base type for citing arbitrary links between vamsas objects
</xs:documentation>
</xs:annotation>
<xs:simpleContent>
<xs:extension base="xs:string">
<xs:annotation>
- <xs:documentation>
- Optional human readable description of the relationship
+ <xs:documentation> Optional human readable description of the relationship
</xs:documentation>
</xs:annotation>
<xs:attribute name="id" type="xs:ID" use="optional">
<xs:annotation>
- <xs:documentation> Primary Key for vamsas object referencing </xs:documentation>
+ <xs:documentation> Primary Key for vamsas object referencing
+ </xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="refs" type="xs:IDREFS">
<xs:annotation>
- <xs:documentation>List of one or more vamsas object references</xs:documentation>
+ <xs:documentation>List of one or more vamsas object
+ references</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:extension>
</xs:element>
<xs:element name="vref" type="vamsas:referenceType" minOccurs="0" maxOccurs="unbounded">
<xs:annotation>
- <xs:documentation>Direct associations between this node and any vamsas objects</xs:documentation>
+ <xs:documentation>Direct associations between this node and any vamsas
+ objects</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded"/>
<xs:complexType>
<xs:simpleContent>
<xs:extension base="xs:float">
- <xs:attribute name="name" type="xs:string" use="optional" default="score"/>
+ <xs:attribute name="name" type="xs:string" use="optional"
+ default="score"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType>
<xs:documentation> Did what </xs:documentation>
</xs:annotation>
</xs:element>
- <xs:element name="Date" type="xs:dateTime">
+ <xs:element name="Date" type="xs:dateTime">
<xs:annotation>
<xs:documentation> When</xs:documentation>
</xs:annotation>
<xs:element name="DataSet">
<xs:complexType>
<xs:annotation>
- <xs:documentation> A collection of sequences, alignments, trees and other things.
+ <xs:documentation> A collection of sequences, alignments, trees and other things. </xs:documentation>
+ <xs:documentation> TODO: Add a title field and properties for programs that can
+ present the user with different distinct datasets For the moment, the program
+ just presents them as a list and perhaps lets the user work out which dataset it
+ wants based on the alignments that it contains. (Dominik and Jim 7th June 2007)
</xs:documentation>
</xs:annotation>
<xs:sequence>
</xs:annotation>
<xs:complexType>
<xs:sequence>
- <xs:element name="map" minOccurs="0" maxOccurs="unbounded">
- <xs:annotation>
- <xs:documentation> From: Offset to first
- position in dataset sequence record that
- this database entry maps to To: Offset
- to last position in dataset sequence
- record that this database entry maps to
- Start: Offset to first last position in
- database entry that first (or offset)
- position in sequence maps to End: Offset
- to last position in database entry that
- last (offset) position in sequence maps
- to </xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:complexContent>
- <xs:extension base="vamsas:mapList"/>
- </xs:complexContent>
- </xs:complexType>
+ <xs:element name="map" minOccurs="0"
+ maxOccurs="1">
+ <xs:annotation>
+ <xs:documentation>
+ the local mapType maps from the parent
+ sequence coordinate frame to the reference
+ frame defined by the dbRef element.
+ The mapped mapType is the mapped range defined
+ on the dbRef element's reference frame.
+ Conventionally, the unit attribute defaults to 1, or
+ will be inferred from the local sequence's
+ dictionary type and any dictionary type associated
+ with the database being mapped to.
+ However, it may be used to avoid ambiguity.
+ </xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="vamsas:mapType">
+ <xs:attribute name="id" type="xs:ID"/>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
</xs:element>
- <xs:element ref="vamsas:link" minOccurs="0" maxOccurs="unbounded"/>
- <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="vamsas:link" minOccurs="0"
+ maxOccurs="unbounded"/>
+ <xs:element ref="vamsas:property" minOccurs="0"
+ maxOccurs="unbounded"/>
</xs:sequence>
- <xs:attribute name="source" type="xs:string" use="required">
+ <xs:attribute name="source" type="xs:string"
+ use="required">
<xs:annotation>
- <xs:documentation> TODO Database Naming
+ <xs:documentation> TODO Database Naming
Convention: either start using LSID (so
change type to URI) or leave this as an
uncontrolled/unspecified string ID
</xs:documentation>
</xs:annotation>
</xs:attribute>
- <xs:attribute name="version" type="xs:string" use="required">
+ <xs:attribute name="version" type="xs:string"
+ use="required">
<xs:annotation>
- <xs:documentation> Version must be specified -
+ <xs:documentation> Version must be specified -
</xs:documentation>
</xs:annotation>
</xs:attribute>
- <xs:attribute name="accessionId" type="xs:string" use="required">
+ <xs:attribute name="accessionId" type="xs:string"
+ use="required">
<xs:annotation>
- <xs:documentation> TODO: make some specification
+ <xs:documentation> TODO: make some specification
of the database field from which this
accessionId is taken from - should that be a
special property of the dbRef object ?
</xs:attribute>
<xs:attribute name="id" type="xs:ID" use="optional">
<xs:annotation>
- <xs:documentation> Primary Key for vamsas object
+ <xs:documentation> Primary Key for vamsas object
referencing </xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:complexType>
</xs:element>
- <xs:element name="vxref" type="vamsas:referenceType" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="vxref" type="vamsas:referenceType"
+ minOccurs="0" maxOccurs="unbounded">
<xs:annotation>
- <xs:documentation>
- explicitly named cross reference to other objects in the document.
- </xs:documentation>
+ <xs:documentation> explicitly named cross reference to
+ other objects in the document. </xs:documentation>
</xs:annotation>
</xs:element>
</xs:sequence>
</xs:element>
<xs:element name="sequenceMapping" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
- <xs:sequence>
- <xs:element name="range" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="seqAStart" type="xs:int"/>
- <xs:attribute name="seqAEnd" type="xs:int"/>
- <xs:attribute name="seqBStart" type="xs:int"/>
- <xs:attribute name="seqBEnd" type="xs:int"/>
- </xs:complexType>
- </xs:element>
- <xs:element ref="vamsas:Provenance"/>
- </xs:sequence>
- <xs:attribute name="sequenceA" type="xs:IDREF" use="required"/>
- <xs:attribute name="sequenceB" type="xs:IDREF" use="required"/>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:annotation>
+ <xs:documentation>
+ A mapping between the specified 'local' and 'mapped' sequence coordinate frames.
+ The step size between each coordinate frame depends on the sequence
+ dictionary types, or alternatively specified in the optional unit
+ attribute on each range element. </xs:documentation>
+ </xs:annotation>
+ <xs:complexContent>
+ <xs:extension base="vamsas:mapType">
+ <xs:sequence>
+ <xs:element ref="vamsas:Provenance"/>
+ </xs:sequence>
+ <xs:attribute name="loc" type="xs:IDREF" use="required">
+ <xs:annotation>
+ <xs:documentation> Object on which the local
+ range is defined. </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="map" type="xs:IDREF" use="required">
+ <xs:annotation>
+ <xs:documentation>Object on which the mapped
+ range is defined. </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="id" type="xs:ID" use="optional"/>
+ </xs:extension>
+ </xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element name="DataSetAnnotations" minOccurs="0" maxOccurs="unbounded">
<xs:element name="Alignment" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
- <xs:element name="AlignmentAnnotation" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="AlignmentAnnotation" minOccurs="0"
+ maxOccurs="unbounded">
<xs:annotation>
<xs:documentation> This is annotation over the coordinate frame
defined by all the columns in the alignment.
<xs:sequence>
<xs:element ref="vamsas:Provenance"/>
</xs:sequence>
- <xs:attribute name="graph" type="xs:boolean" use="required">
+ <xs:attribute name="graph" type="xs:boolean"
+ use="required">
<xs:annotation>
- <xs:documentation> TODO: decide if this flag is
+ <xs:documentation> TODO: decide if this flag is
redundant - when true it would suggest that
the annotationElement values together form a
graph </xs:documentation>
</xs:annotation>
</xs:attribute>
- <xs:attribute name="seqrefs" type="xs:IDREFS" use="optional">
+ <xs:attribute name="seqrefs" type="xs:IDREFS"
+ use="optional">
<xs:annotation>
- <xs:documentation> annotation is associated with a
- range on a particular group of alignment sequences</xs:documentation>
+ <xs:documentation> annotation is associated with
+ a range on a particular group of alignment
+ sequences</xs:documentation>
</xs:annotation>
</xs:attribute>
-
+
</xs:extension>
</xs:complexContent>
</xs:complexType>
<xs:complexContent>
<xs:extension base="vamsas:SequenceType">
<xs:sequence>
- <xs:element name="AlignmentSequenceAnnotation" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:annotation>
- <xs:documentation> Annotate over
+ <xs:element name="AlignmentSequenceAnnotation"
+ minOccurs="0" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:annotation>
+ <xs:documentation> Annotate over
positions and regions of the
ungapped sequence in the context of
the alignment </xs:documentation>
- <xs:documentation/>
- </xs:annotation>
- <xs:complexContent>
- <xs:extension base="vamsas:rangeAnnotation">
- <xs:sequence>
- <xs:element ref="vamsas:Provenance"/>
- </xs:sequence>
- <xs:attribute name="graph" type="xs:boolean" use="required">
- <xs:annotation>
- <xs:documentation> TODO:
+ <xs:documentation/>
+ </xs:annotation>
+ <xs:complexContent>
+ <xs:extension
+ base="vamsas:rangeAnnotation">
+ <xs:sequence>
+ <xs:element
+ ref="vamsas:Provenance"/>
+ </xs:sequence>
+ <xs:attribute name="graph"
+ type="xs:boolean" use="required">
+ <xs:annotation>
+ <xs:documentation> TODO:
decide if this flag is
redundant - when true it
would suggest that the
annotationElement values
together form a graph
</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:extension>
- </xs:complexContent>
- <!--
+ </xs:annotation>
+ </xs:attribute>
+ </xs:extension>
+ </xs:complexContent>
+ <!--
This replaces the flat list of sequenceFeatures.
<xs:element name="AlignmentFeatures" minOccurs="0" maxOccurs="unbounded"><xs:complexType><xs:annotation>
<xs:documentation>Annotate over positions and regions of the alignment</xs:documentation>
</xs:attribute>
</xs:extension>
</xs:complexContent></xs:complexType></xs:element> -->
- </xs:complexType>
+ </xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="id" type="xs:ID" use="optional">
<xs:annotation>
- <xs:documentation> Primary Key for vamsas object
+ <xs:documentation> Primary Key for vamsas object
referencing </xs:documentation>
</xs:annotation>
</xs:attribute>
- <xs:attribute name="refid" type="xs:IDREF" use="required">
+ <xs:attribute name="refid" type="xs:IDREF"
+ use="required">
<xs:annotation>
- <xs:documentation> Dataset Sequence from which
+ <xs:documentation> Dataset Sequence from which
this alignment sequence is taken from
</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:simpleContent>
<xs:extension base="xs:string">
- <xs:attribute name="dict" type="xs:string" use="optional" default="utf8">
+ <xs:attribute name="dict" type="xs:string" use="optional"
+ default="utf8">
<xs:annotation>
<xs:documentation> specifies the symbol dictionary for this
glyph - eg utf8 (the default), aasecstr_3 or
<xs:documentation> Data available to just a particular
user </xs:documentation>
</xs:annotation>
- <xs:attribute name="fullname" type="xs:string" use="required"/>
- <xs:attribute name="organization" type="xs:string" use="required"/>
+ <xs:attribute name="fullname" type="xs:string"
+ use="required"/>
+ <xs:attribute name="organization" type="xs:string"
+ use="required"/>
</xs:extension>
</xs:complexContent>
</xs:complexType>
<xs:element name="dataReference" type="xs:string"/>
</xs:choice>
</xs:complexType>
- <xs:complexType name="mapList">
- <xs:attribute name="from" type="xs:integer" use="optional" default="0">
- <xs:annotation>
- <xs:documentation> Offset to first position in dataset sequence record that start
- position on 'onto' maps to </xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="to" type="xs:integer" use="optional" default="0">
- <xs:annotation>
- <xs:documentation> Offset to last position in dataset sequence record that end
- position on 'onto' maps to </xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="start" type="xs:integer" use="required">
- <xs:annotation>
- <xs:documentation> Offset to first position in database entry that first (or offset)
- position in sequence maps to </xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="end" type="xs:integer" use="required">
- <xs:annotation>
- <xs:documentation> Offset to last position in database entry that last (offset)
- position in sequence maps to </xs:documentation>
- </xs:annotation>
- </xs:attribute>
+ <xs:complexType name="mapType">
+ <xs:annotation>
+ <xs:documentation> Two sets of ranges defined between objects - usually sequences, indicating which
+ regions on each are mapped. </xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="local" type="vamsas:mapRangeType">
+ <xs:annotation>
+ <xs:documentation>
+
+ </xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="mapped" type="vamsas:mapRangeType">
+ <xs:annotation>
+ <xs:documentation>
+
+ </xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="mapRangeType">
+ <xs:complexContent>
+ <xs:extension base="vamsas:rangeType">
+ <xs:attribute name="unit" type="xs:positiveInteger" use="optional">
+ <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:extension>
+ </xs:complexContent>
</xs:complexType>
+
<xs:simpleType name="locks">
<xs:annotation>
- <xs:documentation>
- Contains lock information:
- locktype:ApplicationHandle
- locktype is 'local' or 'full'
- A lock is only valid if the ApplicationHandle resolves to a living application in the vamsas session.
- A local lock means that the application has locked changes to all local properties on the object.
- A full lock means that the application has locked changes to all properties on the object, and any objects that it holds references to.
- </xs:documentation>
+ <xs:documentation> Contains lock information: locktype:ApplicationHandle locktype is
+ 'local' or 'full' A lock is only valid if the ApplicationHandle resolves to a living
+ application in the vamsas session. A local lock means that the application has
+ locked changes to all local properties on the object. A full lock means that the
+ application has locked changes to all properties on the object, and any objects that
+ it holds references to. </xs:documentation>
</xs:annotation>
<xs:restriction base="xs:string"/>
</xs:simpleType>
git://source.jalview.org / vamsas.git / blobdiff