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Annotations
Attributes
Diagrams
Instances
Properties
Source
Used by
Imported schema vamsas.xsd
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
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
 
Properties. Generally, these are mutable so an application should check
them each time. This may change depending on the context of the property
Properties
attribute form default: unqualified
element form default: qualified
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:Provenance
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram vamsasDocument1.tmp#id6
Properties
content: complex
Used by
Model vamsas:entry+
Children vamsas:entry
Instance
 
<vamsas:Provenance>
  <vamsas:entry id="">{1,unbounded}</vamsas:entry>
</vamsas:Provenance>
Source
 
<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" maxOccurs="unbounded">
        <xs:complexType>
          <xs:sequence>
            <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: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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:Provenance/vamsas:entry
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram vamsasDocument1.tmp#id27 vamsasDocument1.tmp#id7 vamsasDocument1.tmp#id8 vamsasDocument1.tmp#id9 vamsasDocument1.tmp#id10 vamsasDocument1.tmp#id11 vamsasDocument1.tmp#id14 vamsasDocument1.tmp#id17
Properties
content: complex
maxOccurs: unbounded
Model vamsas:User , vamsas:App , vamsas:Action , vamsas:Date , vamsas:property* , vamsas:param* , vamsas:input*
Children vamsas:Action, vamsas:App, vamsas:Date, vamsas:User, vamsas:input, vamsas:param, vamsas:property
Instance
 
<vamsas:entry id="">
  <vamsas:User>{1,1}</vamsas:User>
  <vamsas:App>{1,1}</vamsas:App>
  <vamsas:Action>{1,1}</vamsas:Action>
  <vamsas:Date>{1,1}</vamsas:Date>
  <vamsas:property name="" type="">{0,unbounded}</vamsas:property>
  <vamsas:param name="" type="">{0,unbounded}</vamsas:param>
  <vamsas:input name="" objRef="">{0,unbounded}</vamsas:input>
</vamsas:entry>
Attributes
QName Type Fixed Default Use Annotation
id xs:ID optional 
Primary Key for vamsas object referencing
Source
 
<xs:element name="entry" maxOccurs="unbounded">
  <xs:complexType>
    <xs:sequence>
      <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:annotation>
        <xs:documentation>Primary Key for vamsas object referencing</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:entry/vamsas:Provenance/vamsas:User
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
Who
Diagram
Diagram
Type xs:string
Properties
content: simple
Source
 
<xs:element name="User" type="xs:string">
  <xs:annotation>
    <xs:documentation>Who</xs:documentation>
  </xs:annotation>
</xs:element>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:entry/vamsas:Provenance/vamsas:App
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
With which application
Diagram
Diagram
Type xs:string
Properties
content: simple
Source
 
<xs:element name="App" type="xs:string">
  <xs:annotation>
    <xs:documentation>With which application</xs:documentation>
  </xs:annotation>
</xs:element>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:entry/vamsas:Provenance/vamsas:Action
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
Did what
Diagram
Diagram
Type xs:string
Properties
content: simple
Source
 
<xs:element name="Action" type="xs:string">
  <xs:annotation>
    <xs:documentation>Did what</xs:documentation>
  </xs:annotation>
</xs:element>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:entry/vamsas:Provenance/vamsas:Date
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
When
Diagram
Diagram
Type xs:dateTime
Properties
content: simple
Source
 
<xs:element name="Date" type="xs:dateTime">
  <xs:annotation>
    <xs:documentation>When</xs:documentation>
  </xs:annotation>
</xs:element>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:property
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram vamsasDocument1.tmp#id12 vamsasDocument1.tmp#id13
Type extension of xs:string
Properties
content: complex
Used by
Attributes
QName Type Fixed Default Use Annotation
name xs:string required
type xs:string required 
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
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:param
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram vamsasDocument1.tmp#id15 vamsasDocument1.tmp#id16
Type extension of xs:string
Properties
content: complex
Used by
Attributes
QName Type Fixed Default Use Annotation
name xs:string required
type xs:string required 
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
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:input
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram vamsasDocument1.tmp#id19 vamsasDocument1.tmp#id21 vamsasDocument1.tmp#id18 vamsasDocument1.tmp#id25 vamsasDocument1.tmp#id26
Type extension of vamsas:rangeType
Type hierarchy
Properties
content: complex
Used by
Model vamsas:pos+ | vamsas:seg+
Children vamsas:pos, vamsas:seg
Instance
 
<vamsas:input name="" objRef="">
  <vamsas:pos i="">{1,unbounded}</vamsas:pos>
  <vamsas:seg end="" inclusive="" start="">{1,unbounded}</vamsas:seg>
</vamsas:input>
Attributes
QName Type Fixed Default Use Annotation
name xs:string required
objRef xs:IDREFS optional 
Reference Frame for rangeType specfication
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:rangeType/vamsas:pos
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
a position within the associated object's coordinate system
Diagram
Diagram vamsasDocument1.tmp#id20
Properties
content: complex
maxOccurs: unbounded
Attributes
QName Type Fixed Default Use Annotation
i xs:int required
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:rangeType/vamsas:seg
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
a region from start to end, with flag for inclusivity of
terminii
Diagram
Diagram vamsasDocument1.tmp#id22 vamsasDocument1.tmp#id23 vamsasDocument1.tmp#id24
Properties
content: complex
maxOccurs: unbounded
Attributes
QName Type Fixed Default Use Annotation
end xs:int required
inclusive xs:boolean required 
when false, a consecutive range like 'start=1, end=2'
means the region lying after position 1 and before position 2
start xs:int required
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:VAMSAS
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
contains unassociated trees and a number of analysis sets
Diagram
Diagram vamsasDocument1.tmp#id113 vamsasDocument1.tmp#id114 vamsasDocument1.tmp#id29 vamsasDocument1.tmp#id50
Properties
content: complex
Used by
Model vamsas:Tree* , vamsas:DataSet*
Children vamsas:DataSet, vamsas:Tree
Instance
 
<vamsas:VAMSAS id="" modifiable="">
  <vamsas:Tree id="" modifiable="">{0,unbounded}</vamsas:Tree>
  <vamsas:DataSet id="">{0,unbounded}</vamsas:DataSet>
</vamsas:VAMSAS>
Attributes
QName Type Fixed Default Use Annotation
id xs:ID optional 
Primary Key for vamsas object referencing
modifiable vamsas:locks optional
Source
 
<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:DataSet" 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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:Tree
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram vamsasDocument1.tmp#id48 vamsasDocument1.tmp#id49 vamsasDocument1.tmp#id30 vamsasDocument1.tmp#id31 vamsasDocument1.tmp#id36 vamsasDocument1.tmp#id11 vamsasDocument1.tmp#id5
Properties
content: complex
Used by
Model vamsas:title{0,1} , vamsas:newick+ , vamsas:treenode* , vamsas:property* , vamsas:Provenance
Children vamsas:Provenance, vamsas:newick, vamsas:property, vamsas:title, vamsas:treenode
Instance
 
<vamsas:Tree id="" modifiable="">
  <vamsas:title>{0,1}</vamsas:title>
  <vamsas:newick id="" modifiable="" title="">{1,unbounded}</vamsas:newick>
  <vamsas:treenode id="" modifiable="" nodespec="" treeId="">{0,unbounded}</vamsas:treenode>
  <vamsas:property name="" type="">{0,unbounded}</vamsas:property>
  <vamsas:Provenance>{1,1}</vamsas:Provenance>
</vamsas:Tree>
Attributes
QName Type Fixed Default Use Annotation
id xs:ID optional 
Primary Key for vamsas object referencing
modifiable vamsas:locks optional
Source
 
<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"/>
      <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: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 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: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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:Tree/vamsas:title
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram
Type xs:string
Properties
content: simple
minOccurs: 0
Source
 
<xs:element name="title" type="xs:string" minOccurs="0"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:Tree/vamsas:newick
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram vamsasDocument1.tmp#id32 vamsasDocument1.tmp#id33 vamsasDocument1.tmp#id34
Type extension of xs:string
Properties
content: complex
maxOccurs: unbounded
Attributes
QName Type Fixed Default Use Annotation
id xs:ID optional 
Primary Key for vamsas object referencing
modifiable vamsas:locks optional
title xs:string optional
Source
 
<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: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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:Tree/vamsas:treenode
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
node identity and mapping data between tree
representations and vamsas document objects
Diagram
Diagram vamsasDocument1.tmp#id44 vamsasDocument1.tmp#id45 vamsasDocument1.tmp#id38 vamsasDocument1.tmp#id39 vamsasDocument1.tmp#id40 vamsasDocument1.tmp#id11 vamsasDocument1.tmp#id37 vamsasDocument1.tmp#id46 vamsasDocument1.tmp#id47
Type extension of vamsas:nodeType
Type hierarchy
Properties
content: complex
minOccurs: 0
maxOccurs: unbounded
Model vamsas:name{0,1} , vamsas:description{0,1} , vamsas:vref* , vamsas:property*
Children vamsas:description, vamsas:name, vamsas:property, vamsas:vref
Instance
 
<vamsas:treenode id="" modifiable="" nodespec="" treeId="">
  <vamsas:name>{0,1}</vamsas:name>
  <vamsas:description>{0,1}</vamsas:description>
  <vamsas:vref id="" refs="">{0,unbounded}</vamsas:vref>
  <vamsas:property name="" type="">{0,unbounded}</vamsas:property>
</vamsas:treenode>
Attributes
QName Type Fixed Default Use Annotation
id xs:ID optional 
Primary Key for vamsas object referencing
modifiable vamsas:locks optional
nodespec xs:string optional 
String uniquely identifying a particular
node in the referenced tree according to the format of
the tree representation that is referenced.
treeId xs:IDREFS optional 
reference to one or more trees containing
the node being described.
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:nodeType/vamsas:name
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
Short name for this node
Diagram
Diagram
Type xs:string
Properties
content: simple
minOccurs: 0
maxOccurs: 1
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:nodeType/vamsas:description
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
Descriptive text for this node
Diagram
Diagram
Type xs:string
Properties
content: simple
minOccurs: 0
maxOccurs: 1
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:nodeType/vamsas:vref
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
Direct associations between this node and any vamsas
objects
Diagram
Diagram vamsasDocument1.tmp#id42 vamsasDocument1.tmp#id43 vamsasDocument1.tmp#id41
Type vamsas:referenceType
Properties
content: complex
minOccurs: 0
maxOccurs: unbounded
Attributes
QName Type Fixed Default Use Annotation
id xs:ID optional 
Primary Key for vamsas object referencing
refs xs:IDREFS optional 
List of one or more vamsas object
references
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:DataSet
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram vamsasDocument1.tmp#id112 vamsasDocument1.tmp#id51 vamsasDocument1.tmp#id75 vamsasDocument1.tmp#id79 vamsasDocument1.tmp#id99 vamsasDocument1.tmp#id29 vamsasDocument1.tmp#id5
Properties
content: complex
Used by
Element vamsas:VAMSAS
Model vamsas:Sequence+ , vamsas:sequenceMapping* , vamsas:DataSetAnnotations* , vamsas:Alignment* , vamsas:Tree* , vamsas:Provenance
Children vamsas:Alignment, vamsas:DataSetAnnotations, vamsas:Provenance, vamsas:Sequence, vamsas:Tree, vamsas:sequenceMapping
Instance
 
<vamsas:DataSet id="">
  <vamsas:Sequence dictionary="" end="" id="" start="">{1,unbounded}</vamsas:Sequence>
  <vamsas:sequenceMapping id="" loc="" map="">{0,unbounded}</vamsas:sequenceMapping>
  <vamsas:DataSetAnnotations group="" id="" modifiable="" seqRef="" type="">{0,unbounded}</vamsas:DataSetAnnotations>
  <vamsas:Alignment aligned="" gapChar="" id="" modifiable="">{0,unbounded}</vamsas:Alignment>
  <vamsas:Tree id="" modifiable="">{0,unbounded}</vamsas:Tree>
  <vamsas:Provenance>{1,1}</vamsas:Provenance>
</vamsas:DataSet>
Attributes
QName Type Fixed Default Use Annotation
id xs:ID optional 
Primary Key for vamsas object referencing
Source
 
<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: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="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="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: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="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: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" maxOccurs="unbounded">
              <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 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: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:annotation>
        <xs:documentation>Primary Key for vamsas object referencing</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:DataSet/vamsas:Sequence
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram vamsasDocument1.tmp#id56 vamsasDocument1.tmp#id57 vamsasDocument1.tmp#id53 vamsasDocument1.tmp#id54 vamsasDocument1.tmp#id55 vamsasDocument1.tmp#id11 vamsasDocument1.tmp#id52 vamsasDocument1.tmp#id73 vamsasDocument1.tmp#id74 vamsasDocument1.tmp#id58 vamsasDocument1.tmp#id72
Type extension of vamsas:SequenceType
Type hierarchy
Properties
content: complex
maxOccurs: unbounded
Model vamsas:sequence , vamsas:name , vamsas:description{0,1} , vamsas:property* , vamsas:dbRef* , vamsas:vxref*
Children vamsas:dbRef, vamsas:description, vamsas:name, vamsas:property, vamsas:sequence, vamsas:vxref
Instance
 
<vamsas:Sequence dictionary="" end="" id="" start="">
  <vamsas:sequence>{1,1}</vamsas:sequence>
  <vamsas:name>{1,1}</vamsas:name>
  <vamsas:description>{0,1}</vamsas:description>
  <vamsas:property name="" type="">{0,unbounded}</vamsas:property>
</vamsas:Sequence>
Attributes
QName Type Fixed Default Use Annotation
dictionary xs:string required 
symbol class for sequence
end xs:integer required
id xs:ID optional 
Primary Key for vamsas object referencing
start xs:integer required
Source
 
<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: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="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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:SequenceType/vamsas:sequence
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram
Type xs:string
Properties
content: simple
Source
 
<xs:element name="sequence" type="xs:string"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:SequenceType/vamsas:name
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram
Type xs:string
Properties
content: simple
Source
 
<xs:element name="name" type="xs:string"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:SequenceType/vamsas:description
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram
Type xs:string
Properties
content: simple
minOccurs: 0
Source
 
<xs:element name="description" type="xs:string" minOccurs="0"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:Sequence/vamsas:DataSet/vamsas:dbRef
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
Store a list of database references
for this sequence record - with optional mapping
from database sequence to the given sequence record
Diagram
Diagram vamsasDocument1.tmp#id68 vamsasDocument1.tmp#id69 vamsasDocument1.tmp#id70 vamsasDocument1.tmp#id71 vamsasDocument1.tmp#id59 vamsasDocument1.tmp#id66 vamsasDocument1.tmp#id11
Properties
content: complex
minOccurs: 0
maxOccurs: unbounded
Model vamsas:map* , vamsas:link* , vamsas:property*
Children vamsas:link, vamsas:map, vamsas:property
Instance
 
<vamsas:dbRef accessionId="" id="" source="" version="">
  <vamsas:map id="">{0,unbounded}</vamsas:map>
  <vamsas:link href="">{0,unbounded}</vamsas:link>
  <vamsas:property name="" type="">{0,unbounded}</vamsas:property>
</vamsas:dbRef>
Attributes
QName Type Fixed Default Use Annotation
accessionId xs:string required 
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 ?
id xs:ID optional 
Primary Key for vamsas object
referencing
source xs:string required 
TODO Database Naming
Convention: either start using LSID (so
change type to URI) or leave this as an
uncontrolled/unspecified string ID
version xs:string required 
Version must be specified -
Source
 
<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: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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:dbRef/vamsas:Sequence/vamsas:DataSet/vamsas:map
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
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.
Diagram
Diagram vamsasDocument1.tmp#id61 vamsasDocument1.tmp#id64 vamsasDocument1.tmp#id60 vamsasDocument1.tmp#id65
Type extension of vamsas:mapType
Type hierarchy
Properties
content: complex
minOccurs: 0
maxOccurs: unbounded
Model vamsas:local , vamsas:mapped
Children vamsas:local, vamsas:mapped
Instance
 
<vamsas:map id="">
  <vamsas:local unit="">{1,1}</vamsas:local>
  <vamsas:mapped unit="">{1,1}</vamsas:mapped>
</vamsas:map>
Attributes
QName Type Fixed Default Use Annotation
id xs:ID optional
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:mapType/vamsas:local
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
Diagram
Diagram vamsasDocument1.tmp#id19 vamsasDocument1.tmp#id21 vamsasDocument1.tmp#id18 vamsasDocument1.tmp#id63 vamsasDocument1.tmp#id62
Type vamsas:mapRangeType
Type hierarchy
Properties
content: complex
Model vamsas:pos+ | vamsas:seg+
Children vamsas:pos, vamsas:seg
Instance
 
<vamsas:local unit="">
  <vamsas:pos i="">{1,unbounded}</vamsas:pos>
  <vamsas:seg end="" inclusive="" start="">{1,unbounded}</vamsas:seg>
</vamsas:local>
Attributes
QName Type Fixed Default Use Annotation
unit xs:positiveInteger optional 
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.
Source
 
<xs:element name="local" type="vamsas:mapRangeType">
  <xs:annotation>
    <xs:documentation>
    </xs:documentation>
  </xs:annotation>
</xs:element>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:mapType/vamsas:mapped
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
Diagram
Diagram vamsasDocument1.tmp#id19 vamsasDocument1.tmp#id21 vamsasDocument1.tmp#id18 vamsasDocument1.tmp#id63 vamsasDocument1.tmp#id62
Type vamsas:mapRangeType
Type hierarchy
Properties
content: complex
Model vamsas:pos+ | vamsas:seg+
Children vamsas:pos, vamsas:seg
Instance
 
<vamsas:mapped unit="">
  <vamsas:pos i="">{1,unbounded}</vamsas:pos>
  <vamsas:seg end="" inclusive="" start="">{1,unbounded}</vamsas:seg>
</vamsas:mapped>
Attributes
QName Type Fixed Default Use Annotation
unit xs:positiveInteger optional 
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.
Source
 
<xs:element name="mapped" type="vamsas:mapRangeType">
  <xs:annotation>
    <xs:documentation>
    </xs:documentation>
  </xs:annotation>
</xs:element>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:link
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram vamsasDocument1.tmp#id67
Type extension of xs:string
Properties
content: complex
Used by
Attributes
QName Type Fixed Default Use Annotation
href xs:anyURI optional 
The URI
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:Sequence/vamsas:DataSet/vamsas:vxref
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
explicitly named cross reference to
other objects in the document.
Diagram
Diagram vamsasDocument1.tmp#id42 vamsasDocument1.tmp#id43 vamsasDocument1.tmp#id41
Type vamsas:referenceType
Properties
content: complex
minOccurs: 0
maxOccurs: unbounded
Attributes
QName Type Fixed Default Use Annotation
id xs:ID optional 
Primary Key for vamsas object referencing
refs xs:IDREFS optional 
List of one or more vamsas object
references
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:DataSet/vamsas:sequenceMapping
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram vamsasDocument1.tmp#id61 vamsasDocument1.tmp#id64 vamsasDocument1.tmp#id60 vamsasDocument1.tmp#id76 vamsasDocument1.tmp#id77 vamsasDocument1.tmp#id78 vamsasDocument1.tmp#id5
Type extension of vamsas:mapType
Type hierarchy
Properties
content: complex
minOccurs: 0
maxOccurs: unbounded
Model vamsas:local , vamsas:mapped , vamsas:Provenance
Children vamsas:Provenance, vamsas:local, vamsas:mapped
Instance
 
<vamsas:sequenceMapping id="" loc="" map="">
  <vamsas:local unit="">{1,1}</vamsas:local>
  <vamsas:mapped unit="">{1,1}</vamsas:mapped>
</vamsas:sequenceMapping>
Attributes
QName Type Fixed Default Use Annotation
id xs:ID optional
loc xs:IDREF required 
Object on which the local
range is defined.
map xs:IDREF required 
Object on which the mapped
range is defined.
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:DataSet/vamsas:DataSetAnnotations
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram vamsasDocument1.tmp#id19 vamsasDocument1.tmp#id21 vamsasDocument1.tmp#id18 vamsasDocument1.tmp#id94 vamsasDocument1.tmp#id95 vamsasDocument1.tmp#id96 vamsasDocument1.tmp#id97 vamsasDocument1.tmp#id81 vamsasDocument1.tmp#id82 vamsasDocument1.tmp#id83 vamsasDocument1.tmp#id84