<?xml version="1.0" encoding="UTF-8"?>
+<!--
+ * This file is part of the Vamsas Client version 0.2.
+ * Copyright 2010 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 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.org"
- targetNamespace="http://www.vamsas.org" elementFormDefault="qualified"
+<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
<xs:documentation> Primary Key for vamsas object referencing </xs:documentation>
</xs:annotation>
</xs:attribute>
- <xs:attribute name="modifiable" type="xs:boolean" use="optional" default="true">
- <xs:annotation>
- <xs:documentation> objects with modifiable=false will not be modified by a
- vamsas client update </xs:documentation>
- </xs:annotation>
- </xs:attribute>
+ <xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
</xs:complexType>
</xs:element>
<xs:annotation>
</xs:documentation>
</xs:annotation>
</xs:attribute>
- <xs:attribute name="modifiable" type="xs:boolean" use="optional"
- default="true">
+ <xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ </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: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> objects with modifiable=false will not be
- modified by a vamsas client update </xs:documentation>
+ <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:simpleContent>
+ </xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded"/>
<xs:documentation> Primary Key for vamsas object referencing </xs:documentation>
</xs:annotation>
</xs:attribute>
- <xs:attribute name="modifiable" type="xs:boolean" use="optional" default="true">
- <xs:annotation>
- <xs:documentation> objects with modifiable=false will not be modified by a
- vamsas client update </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:documentation>
</xs:annotation>
</xs:attribute>
- <xs:attribute name="modifiable" type="xs:boolean" use="optional" default="true">
- <xs:annotation>
- <xs:documentation> objects with modifiable=false will not be modified by a
- vamsas client update </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
<xs:complexContent>
<xs:extension base="vamsas:rangeType">
<xs:attribute name="name" type="xs:string" use="required"/>
- <xs:attribute name="objRef" type="xs:IDREF" use="optional">
+ <xs:attribute name="objRef" type="xs:IDREFS" use="optional">
<xs:annotation>
<xs:documentation> Reference Frame for rangeType specfication
</xs:documentation>
<xs:documentation> Did what </xs:documentation>
</xs:annotation>
</xs:element>
- <xs:element name="Date" type="xs:date">
+ <xs:element name="Date" type="xs:dateTime">
<xs:annotation>
- <xs:documentation> When </xs:documentation>
+ <xs:documentation> When</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded">
<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:extension>
- </xs:complexContent>
- </xs:complexType>
+ <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: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="optional">
<xs:annotation>
</xs:complexContent>
</xs:complexType>
</xs:element>
+ <xs:element name="sequenceMapping" minOccurs="0" maxOccurs="unbounded">
+ <xs:complexType>
+ <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:sequence>
<xs:element ref="vamsas:Provenance"/>
</xs:sequence>
- <xs:attribute name="seqRef" type="xs:IDREF" use="required">
+ <xs:attribute name="seqRef" type="xs:IDREFS" use="required">
<xs:annotation>
<xs:documentation> annotation is associated with a
particular dataset sequence </xs:documentation>
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:documentation>
</xs:annotation>
</xs:attribute>
- <xs:attribute name="modifiable" type="xs:boolean" use="optional"
- default="true">
- <xs:annotation>
- <xs:documentation> objects with modifiable=false will not be
- modified by a vamsas client update </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:documentation> additional typed properties </xs:documentation>
</xs:annotation>
</xs:element>
- <xs:element name="mapping" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:complexContent>
- <xs:extension base="vamsas:mapList">
- <xs:attribute name="onto" type="xs:IDREF" use="required">
- <xs:annotation>
- <xs:documentation> object to which the mapping is being mapped
- </xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:extension>
- </xs:complexContent>
- </xs:complexType>
- </xs:element>
</xs:sequence>
<xs:attribute name="start" type="xs:integer" use="required"/>
<xs:attribute name="end" type="xs:integer" use="required"/>
<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:annotation>
+ <xs:restriction base="xs:string"/>
+ </xs:simpleType>
</xs:schema>
git://source.jalview.org / vamsas.git / blobdiff