<?xml version="1.0" encoding="UTF-8"?>
+<!--
+ This file is part of the Vamsas Client version 0.1.
+ Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite,
+ Andrew Waterhouse and Dominik Lindner.
+
+ Earlier versions have also been incorporated into Jalview version 2.4
+ since 2008, and TOPALi version 2 since 2007.
+
+ The Vamsas Client is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ The Vamsas Client is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.
+ -->
<!-- edited with XMLSPY v5 rel. 4 U (http://www.xmlspy.com) by MSD (EMBL OUTSTATION THE EBI WELLCOME TRUST GENOME CAMPUS) -->
-<!-- edited with XMLSpy v2005 rel. 3 U (http://www.altova.com) by lj (jl) -->
-<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="http://www.vamsas.org" targetNamespace="http://www.vamsas.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
- <xs:element name="Version" type="xs:string"/>
+<!-- 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:annotation>
- <xs:documentation>Vamsas Document Version Number</xs:documentation>
+ <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
+ dataset sequence. Alignment sequence: documentRoot/datasetName/AlignmentId/SequenceUID
+ for an aligned form of a dataset sequence </xs:documentation>
</xs:annotation>
- <xs:element name="LockFile">
- <xs:complexType>
- <xs:simpleContent>
- <xs:extension base="xs:string"/>
- </xs:simpleContent>
- </xs:complexType>
- </xs:element>
<xs:element name="VAMSAS">
+ <xs:annotation>
+ <xs:documentation> contains unassociated trees and a number of analysis sets
+ </xs:documentation>
+ </xs:annotation>
<xs:complexType>
<xs:sequence>
<xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
- <xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="vamsas:DataSet" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:attribute name="id" type="xs:ID" use="optional">
+ <xs:annotation>
+ <xs:documentation> Primary Key for vamsas object referencing </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
</xs:complexType>
</xs:element>
+ <xs:annotation>
+ <xs:documentation> Properties. Generally, these are mutable so an application should check
+ them each time. This may change depending on the context of the property
+ </xs:documentation>
+ </xs:annotation>
<xs:element name="Tree">
<xs:complexType>
+ <xs:annotation>
+ <xs:documentation> Contains a named collection of trees </xs:documentation>
+ <xs:documentation> TODO: define way of referencing leaves of global tree for any
+ sequence/alignment object. SUggestion 1: Each named tree leafnode has a unique
+ id (which may be unique in combination with trees own vorba ID). Dataset
+ sequences can be tagged with a property "vamsas:tree_leaf" </xs:documentation>
+ </xs:annotation>
<xs:sequence>
- <xs:element name="title" type="xs:string" minOccurs="0" maxOccurs="1"/>
- <xs:element name="newick" minOccurs="1" maxOccurs="unbounded">
+ <xs:element name="title" type="xs:string" minOccurs="0"/>
+ <xs:element name="newick" maxOccurs="unbounded">
<xs:complexType>
<xs:simpleContent>
<xs:extension base="xs:string">
<xs:attribute name="title" type="xs:string" use="optional"/>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:attribute name="id" type="xs:ID" use="optional">
+ <xs:annotation>
+ <xs:documentation> Primary Key for vamsas object referencing
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType>
</xs:element>
- <xs:element ref="vamsas:Provenance" minOccurs="1" maxOccurs="1"/>
+ <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: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: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>
+ </xs:annotation>
+ </xs:attribute>
+
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="vamsas:Provenance"/>
</xs:sequence>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:attribute name="id" type="xs:ID" use="optional">
+ <xs:annotation>
+ <xs:documentation> Primary Key for vamsas object referencing </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:complexType name="referenceType">
+ <xs:annotation>
+ <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>
+ </xs:annotation>
+ <xs:attribute name="id" type="xs:ID" use="optional">
+ <xs:annotation>
+ <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:annotation>
+ </xs:attribute>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ <xs:complexType name="nodeType">
+ <xs:sequence>
+ <xs:element name="name" type="xs:string" minOccurs="0" maxOccurs="1">
+ <xs:annotation>
+ <xs:documentation>Short name for this node</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="description" type="xs:string" minOccurs="0" maxOccurs="1">
+ <xs:annotation>
+ <xs:documentation>Descriptive text for this node</xs:documentation>
+ </xs:annotation>
+ </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:annotation>
+ </xs:element>
+ <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:ID" use="optional">
+ <xs:annotation>
+ <xs:documentation> Primary Key for vamsas object referencing </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
+ </xs:complexType>
+ <xs:element name="property">
+ <xs:complexType>
+ <xs:simpleContent>
+ <xs:annotation>
+ <xs:documentation> Named and typed property string </xs:documentation>
+ </xs:annotation>
+ <xs:extension base="xs:string">
+ <xs:attribute name="name" type="xs:string" use="required"/>
+ <xs:attribute name="type" type="xs:string" use="required">
+ <xs:annotation>
+ <xs:documentation> The type specifies how the property will be parsed.
+ Empty property strings are allowed, and can be used to prototype the
+ input to a document. TODO: specify allowed types </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="link">
+ <xs:complexType>
+ <xs:annotation>
+ <xs:documentation> Primitive labelled URI object </xs:documentation>
+ </xs:annotation>
+ <xs:simpleContent>
+ <xs:extension base="xs:string">
+ <xs:attribute name="href" type="xs:anyURI">
+ <xs:annotation>
+ <xs:documentation>The URI</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:complexType name="rangeType" abstract="true">
+ <xs:annotation>
+ <xs:documentation> Specify an ordered set of positions and/or regions on the principle
+ dimension of some associated vamsas object </xs:documentation>
+ <xs:documentation> Keeping to jaxb-1.0 specification for the moment - this choice should
+ become a substitution group when we use jaxb-2.0 capable bindings
+ </xs:documentation>
+ </xs:annotation>
+ <xs:choice>
+ <xs:element name="pos" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation> a position within the associated object's coordinate system
+ </xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:attribute name="i" type="xs:int" use="required"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="seg" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation> a region from start to end, with flag for inclusivity of
+ terminii </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="inclusive" type="xs:boolean" use="required">
+ <xs:annotation>
+ <xs:documentation> when false, a consecutive range like 'start=1, end=2'
+ means the region lying after position 1 and before position 2
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:complexType>
+ </xs:element>
+ </xs:choice>
+ <!-- Do we really need this - a position could be just a seg with start=end and inclusive=true -->
+ </xs:complexType>
+ <xs:complexType name="rangeAnnotation">
+ <xs:annotation>
+ <xs:documentation> Annotation for a rangeSpec - values can be attached for the whole
+ specification, and to each position within the spec. following the orientation
+ specified by the ordered set of rangeSpec (pos, seg) elements. </xs:documentation>
+ </xs:annotation>
+ <xs:complexContent>
+ <xs:extension base="vamsas:rangeType">
+ <xs:sequence>
+ <xs:element name="label" type="xs:string" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation> Short, meaningful name for the annotation - if this
+ is absent, then the type string should be used in its place.
+ </xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="description" type="xs:string" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation> Human readable description of the annotation
+ </xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="status" type="xs:string" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation> TODO: specify this - we have considered taking the GO
+ evidence codes as a model for assessing a measure of quality to an
+ annotation. </xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation> Annotation Element position maps to ordered positions
+ defined by the sequence of rangeType pos positions or concatenated
+ seg start/end segments. </xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="score" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation> Ordered set of optionally named float values for the
+ whole annotation </xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:simpleContent>
+ <xs:extension base="xs:float">
+ <xs:attribute name="name" type="xs:string" use="optional"
+ default="score"/>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element ref="vamsas:link" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation> Note:These are mutable so an application should check
+ them each time. </xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:ID" use="optional">
+ <xs:annotation>
+ <xs:documentation> Primary Key for vamsas object referencing
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
+ <xs:attribute name="group" type="xs:string" use="optional" default="">
+ <xs:annotation>
+ <xs:documentation> Annotation with the same non-empty group name are grouped
+ together </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="type" type="xs:string" use="required">
+ <xs:annotation>
+ <xs:documentation> A Das Feature has both a type and a Type ID. We go the
+ route of requiring the type string to be taken from a controlled
+ vocabulary if an application expects others to make sense of it. The
+ type may qualified - so uniprot:CHAIN is a valid type name, and
+ considered distinct from someotherDB:CHAIN </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ <xs:element name="param">
+ <xs:complexType>
+ <xs:annotation>
+ <xs:documentation> Specifies a named and typed value used to perform some data
+ transformation. </xs:documentation>
+ <xs:documentation> LATER: experiment with xml validation of property set prototypes
+ for services </xs:documentation>
+ </xs:annotation>
+ <xs:simpleContent>
+ <xs:annotation>
+ <xs:documentation> Named and typed property string </xs:documentation>
+ </xs:annotation>
+ <xs:extension base="xs:string">
+ <xs:attribute name="name" type="xs:string" use="required"/>
+ <xs:attribute name="type" type="xs:string" use="required">
+ <xs:annotation>
+ <xs:documentation> The type specifies how the property will be parsed.
+ Empty property strings are allowed, and can be used to prototype the
+ input to a document. TODO: specify allowed types </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="input">
+ <xs:complexType>
+ <xs:annotation>
+ <xs:documentation> Selects all or part of a collection of vamsas objects as a named
+ input to some transformation process. Many inputs with the same name imply a
+ group input (such as a collection of sequences) </xs:documentation>
+ </xs:annotation>
+ <xs:complexContent>
+ <xs:extension base="vamsas:rangeType">
+ <xs:attribute name="name" type="xs:string" use="required"/>
+ <xs:attribute name="objRef" type="xs:IDREFS" use="optional">
+ <xs:annotation>
+ <xs:documentation> Reference Frame for rangeType specfication
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:extension>
+ </xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element name="Provenance">
<xs:complexType>
+ <xs:annotation>
+ <xs:documentation> Defines the origin and series of operations applied directly to
+ the object that references it. </xs:documentation>
+ </xs:annotation>
<xs:sequence>
- <xs:element name="entry" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="entry" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
- <xs:element name="User" type="xs:string"/>
- <xs:element name="Action" type="xs:string"/>
- <xs:element name="Date" type="xs:date"/>
+ <xs:element name="User" type="xs:string">
+ <xs:annotation>
+ <xs:documentation> Who </xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="App" type="xs:string">
+ <xs:annotation>
+ <xs:documentation> With which application </xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="Action" type="xs:string">
+ <xs:annotation>
+ <xs:documentation> Did what </xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="Date" type="xs:dateTime">
+ <xs:annotation>
+ <xs:documentation> When</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation> additional information </xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element ref="vamsas:param" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation> parameter for the action </xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element ref="vamsas:input" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation> bioinformatic objects input to action
+ </xs:documentation>
+ </xs:annotation>
+ </xs:element>
</xs:sequence>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:attribute name="id" type="xs:ID" use="optional">
+ <xs:annotation>
+ <xs:documentation> Primary Key for vamsas object referencing
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
- <xs:element name="SequenceSet">
+ <xs:element name="DataSet">
<xs:complexType>
+ <xs:annotation>
+ <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:element name="Sequence" maxOccurs="unbounded">
<xs:complexType>
+ <xs:annotation>
+ <xs:documentation> a primary or secondary sequence record from which all
+ other sequences may be derived </xs:documentation>
+ </xs:annotation>
<xs:complexContent>
<xs:extension base="vamsas:SequenceType">
<xs:sequence>
<xs:element name="dbRef" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation> Store a list of database references
+ for this sequence record - with optional mapping
+ from database sequence to the given sequence record </xs:documentation>
+ <xs:documentation/>
+ <xs:documentation/>
+ </xs:annotation>
<xs:complexType>
- <xs:attribute name="source"/>
- <xs:attribute name="version"/>
- <xs:attribute name="accessionId"/>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:sequence>
+ <xs:element name="map" minOccurs="0"
+ maxOccurs="unbounded">
+ <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:sequence>
+ <xs:attribute name="source" type="xs:string"
+ use="required">
+ <xs:annotation>
+ <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:annotation>
+ <xs:documentation> Version must be specified -
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="accessionId" type="xs:string"
+ use="required">
+ <xs:annotation>
+ <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:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="id" type="xs:ID" use="optional">
+ <xs:annotation>
+ <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:annotation>
+ <xs:documentation> explicitly named cross reference to
+ other objects in the document. </xs:documentation>
+ </xs:annotation>
+ </xs:element>
</xs:sequence>
- <xs:attribute name="id" type="xs:ID" use="required"/>
- <xs:attribute name="dictionary" type="xs:string"/>
+ <xs:attribute name="id" type="xs:ID" use="optional">
+ <xs:annotation>
+ <xs:documentation> Primary Key for vamsas object referencing
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="dictionary" type="xs:string" use="required">
+ <xs:annotation>
+ <xs:documentation> symbol class for sequence
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
- <xs:element name="SequenceSetAnnotations" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="sequenceMapping" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
- <xs:sequence>
- <xs:element name="description" type="xs:string" minOccurs="0"/>
- <xs:element name="status" type="xs:string" minOccurs="0"/>
- <xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded"/>
- <xs:element ref="vamsas:Provenance" minOccurs="0" maxOccurs="unbounded"/>
- </xs:sequence>
- <xs:attribute name="type" type="xs:string" use="required"/>
- <xs:attribute name="end" type="xs:string" use="required"/>
- <xs:attribute name="begin" type="xs:string" use="required"/>
- <xs:attribute name="seqRef" 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:complexType>
+ <xs:annotation>
+ <xs:documentation> Annotate over positions and regions of a dataset
+ sequence </xs:documentation>
+ </xs:annotation>
+ <xs:complexContent>
+ <xs:extension base="vamsas:rangeAnnotation">
+ <xs:sequence>
+ <xs:element ref="vamsas:Provenance"/>
+ </xs:sequence>
+ <xs:attribute name="seqRef" type="xs:IDREFS" use="required">
+ <xs:annotation>
+ <xs:documentation> annotation is associated with a
+ particular dataset sequence </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:extension>
+ </xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element name="Alignment" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
- <xs:element name="AlignmentAnnotations" minOccurs="0">
+ <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:documentation>
+ </xs:annotation>
<xs:complexType>
- <xs:sequence>
- <xs:element ref="vamsas:annotationElement" maxOccurs="unbounded"/>
- <xs:element name="label" type="xs:string"/>
- <xs:element name="description" type="xs:string"/>
- <xs:element ref="vamsas:Provenance"/>
- </xs:sequence>
- <xs:attribute name="graph" type="xs:boolean" use="required"/>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <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: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:annotation>
+ </xs:attribute>
+
+ </xs:extension>
+ </xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
- <xs:element name="alignmentSequence" minOccurs="2" maxOccurs="unbounded">
+ <xs:element name="alignmentSequence" maxOccurs="unbounded">
<xs:complexType>
<xs:complexContent>
<xs:extension base="vamsas:SequenceType">
- <xs:attribute name="id" type="xs:ID" use="optional"/>
- <xs:attribute name="refid" type="xs:IDREF" use="required"/>
+ <xs:sequence>
+ <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:
+ 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>
+ <!--
+ 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:annotation><xs:complexContent>
+ <xs:extension base="vamsas:rangeFeature">
+ <xs:attribute name="seqRef" type="xs:IDREF" use="optional">
+ <xs:annotation><xs:documentation>annotation may be associated with a particular sequence lying within the same reference frame as the rangeType's objRef</xs:documentation></xs:annotation>
+ </xs:attribute>
+ </xs:extension>
+ </xs:complexContent></xs:complexType></xs:element> -->
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="id" type="xs:ID" use="optional">
+ <xs:annotation>
+ <xs:documentation> Primary Key for vamsas object
+ referencing </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="refid" type="xs:IDREF"
+ use="required">
+ <xs:annotation>
+ <xs:documentation> Dataset Sequence from which
+ this alignment sequence is taken from
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
+ <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation> typical properties may be additional
+ alignment score objects </xs:documentation>
+ </xs:annotation>
+ </xs:element>
<xs:element ref="vamsas:Provenance"/>
</xs:sequence>
<xs:attribute name="gapChar" type="xs:string" use="required"/>
<xs:attribute name="aligned" type="xs:boolean" use="optional"/>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:attribute name="id" type="xs:ID" use="optional">
+ <xs:annotation>
+ <xs:documentation> Primary Key for vamsas object referencing
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
</xs:complexType>
</xs:element>
<xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
<xs:element ref="vamsas:Provenance"/>
</xs:sequence>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:attribute name="id" type="xs:ID" use="optional">
+ <xs:annotation>
+ <xs:documentation> Primary Key for vamsas object referencing </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
</xs:complexType>
</xs:element>
<xs:element name="annotationElement">
<xs:complexType>
+ <xs:annotation>
+ <xs:documentation> per-site symbolic and/or quantitative annotation </xs:documentation>
+ <xs:documentation> SecondaryStructure and display character (from Jalview) have been
+ subsumed into the glyph element </xs:documentation>
+ </xs:annotation>
<xs:sequence>
- <xs:element name="displayCharacter" type="xs:string"/>
- <xs:element name="description" type="xs:string"/>
- <xs:element name="secondaryStructure">
- <xs:simpleType>
- <xs:restriction base="xs:string">
- <xs:length value="1"/>
- </xs:restriction>
- </xs:simpleType>
+ <xs:element name="description" type="xs:string" minOccurs="0">
+ <xs:annotation>
+ <xs:documentation> Free text at this position </xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="glyph" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation> Discrete symbol - possibly graphically represented
+ </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:annotation>
+ <xs:documentation> specifies the symbol dictionary for this
+ glyph - eg utf8 (the default), aasecstr_3 or
+ kd_hydrophobicity - the content is not validated so
+ applications must ensure they gracefully deal with
+ invalid entries here </xs:documentation>
+ <xs:documentation> TODO: specify a minimum list of glyph
+ dictionaries to get us started and provide a way for the
+ vamsasClient to validate their content if regexes are
+ specified </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="value" type="xs:float" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation> Ordered set of float values - an application may treat
+ the values together as a vector with common support for a set of
+ annotation elements - but this is, again, not validated so applications
+ should deal gracefully with varying numbers of dimensions
+ </xs:documentation>
+ </xs:annotation>
</xs:element>
- <xs:element name="value" type="xs:float"/>
</xs:sequence>
- <xs:attribute name="position" type="xs:int" use="required"/>
- <xs:attribute name="id" type="xs:ID" use="optional"/>
+ <xs:attribute name="position" type="xs:integer" use="required">
+ <xs:annotation>
+ <xs:documentation> position with respect to the coordinate frame defined by a
+ rangeType specification </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="after" type="xs:boolean" use="optional" default="false">
+ <xs:annotation>
+ <xs:documentation> true means the annotation element appears between the
+ specified position and the next </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="id" type="xs:ID" use="optional">
+ <xs:annotation>
+ <xs:documentation> Primary Key for vamsas object referencing </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
</xs:complexType>
</xs:element>
<xs:complexType name="SequenceType">
<xs:sequence>
<xs:element name="sequence" type="xs:string"/>
<xs:element name="name" type="xs:string"/>
+ <xs:element name="description" type="xs:string" minOccurs="0"/>
+ <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation> additional typed properties </xs:documentation>
+ </xs:annotation>
+ </xs:element>
</xs:sequence>
- <xs:attribute name="start" type="xs:int" use="required"/>
- <xs:attribute name="end" type="xs:int" use="required"/>
+ <xs:attribute name="start" type="xs:integer" use="required"/>
+ <xs:attribute name="end" type="xs:integer" use="required"/>
</xs:complexType>
<xs:element name="ApplicationData">
<xs:complexType>
- <xs:sequence>
- <xs:element name="Application">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="User">
- <xs:complexType>
- <xs:attribute name="fullname" type="xs:string"/>
- <xs:attribute name="organization" type="xs:string"/>
- <xs:attribute name="data" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="version" type="xs:string"/>
- <xs:attribute name="name" type="xs:string"/>
- <xs:attribute name="urn" type="xs:string"/>
- <xs:attribute name="data" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
+ <xs:annotation>
+ <xs:documentation> Data specific to a particular type and version of vamsas
+ application </xs:documentation>
+ </xs:annotation>
+ <xs:complexContent>
+ <xs:extension base="vamsas:appData">
+ <xs:sequence>
+ <xs:element name="User" minOccurs="0" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="vamsas:appData">
+ <xs:annotation>
+ <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:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="Common" minOccurs="0">
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="vamsas:appData"/>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="Instance" minOccurs="0" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="vamsas:appData">
+ <xs:annotation>
+ <xs:documentation> Data available to just a specific
+ instance of the application </xs:documentation>
+ <xs:documentation> VAMSAS/Pierre: Is this data volatile
+ ? Application instances may not be accessible after
+ the session has closed - the user may have to be
+ presented with the option of picking up the data in
+ that instance </xs:documentation>
+ </xs:annotation>
+ <xs:attribute name="urn" type="xs:string" use="required"/>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="version" type="xs:string" use="required">
+ <xs:annotation>
+ <xs:documentation> Version string describing the application specific
+ data storage version used</xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="name" type="xs:string" use="required">
+ <xs:annotation>
+ <xs:documentation> Canonical name of application </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="Attachment">
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="vamsas:appData">
+ <xs:annotation>
+ <xs:documentation> General data container to attach a typed data object to
+ any vamsas object </xs:documentation>
+ </xs:annotation>
+ <xs:attribute name="compressed" type="xs:boolean" use="optional" default="false">
+ <xs:annotation>
+ <xs:documentation> true implies data will be decompresses with Zip
+ before presenting to application </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="type" type="xs:string" use="required">
+ <xs:annotation>
+ <xs:documentation> Type of arbitrary data - TODO: decide format - use
+ (extended) MIME types ? </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="objectref" type="xs:IDREF" use="required">
+ <xs:annotation>
+ <xs:documentation> Object the arbitrary data is associated with
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="id" type="xs:ID" use="optional">
+ <xs:annotation>
+ <xs:documentation> Primary Key for vamsas object referencing
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:extension>
+ </xs:complexContent>
</xs:complexType>
</xs:element>
+ <xs:complexType name="appData">
+ <xs:choice>
+ <xs:element name="data" type="xs:base64Binary"/>
+ <xs:element name="dataReference" type="xs:string"/>
+ </xs:choice>
+ </xs:complexType>
+ <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:annotation>
+ <xs:restriction base="xs:string"/>
+ </xs:simpleType>
</xs:schema>
git://source.jalview.org / vamsas.git / blobdiff