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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 vamsasDocument1.tmp#id92 vamsasDocument1.tmp#id66 vamsasDocument1.tmp#id11 vamsasDocument1.tmp#id80 vamsasDocument1.tmp#id98 vamsasDocument1.tmp#id5
Type extension of vamsas:rangeAnnotation
Type hierarchy
Properties
content: complex
minOccurs: 0
maxOccurs: unbounded
Model (vamsas:pos+ | vamsas:seg+) , vamsas:label{0,1} , vamsas:description{0,1} , vamsas:status{0,1} , vamsas:annotationElement* , vamsas:score* , vamsas:link* , vamsas:property* , vamsas:Provenance
Children vamsas:Provenance, vamsas:annotationElement, vamsas:description, vamsas:label, vamsas:link, vamsas:pos, vamsas:property, vamsas:score, vamsas:seg, vamsas:status
Instance
 
<vamsas:DataSetAnnotations group="" id="" modifiable="" seqRef="" type="">
  <vamsas:pos i="">{1,unbounded}</vamsas:pos>
  <vamsas:seg end="" inclusive="" start="">{1,unbounded}</vamsas:seg>
</vamsas:DataSetAnnotations>
Attributes
QName Type Fixed Default Use Annotation
group xs:string optional 
Annotation with the same non-empty group name are grouped
together
id xs:ID optional 
Primary Key for vamsas object referencing
modifiable vamsas:locks optional
seqRef xs:IDREFS required 
annotation is associated with a
particular dataset sequence
type xs:string required 
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
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:rangeAnnotation/vamsas:label
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
Short, meaningful name for the annotation - if this
is absent, then the type string should be used in its place.
Diagram
Diagram
Type xs:string
Properties
content: simple
minOccurs: 0
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:rangeAnnotation/vamsas:description
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
Human readable description of the annotation
Diagram
Diagram
Type xs:string
Properties
content: simple
minOccurs: 0
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:rangeAnnotation/vamsas:status
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
TODO: specify this - we have considered taking the GO
evidence codes as a model for assessing a measure of quality to an
annotation.
Diagram
Diagram
Type xs:string
Properties
content: simple
minOccurs: 0
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:annotationElement
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram vamsasDocument1.tmp#id89 vamsasDocument1.tmp#id90 vamsasDocument1.tmp#id91 vamsasDocument1.tmp#id85 vamsasDocument1.tmp#id86 vamsasDocument1.tmp#id88
Properties
content: complex
Used by
Model vamsas:description{0,1} , vamsas:glyph* , vamsas:value*
Children vamsas:description, vamsas:glyph, vamsas:value
Instance
 
<vamsas:annotationElement after="false" id="" position="">
  <vamsas:description>{0,1}</vamsas:description>
  <vamsas:glyph dict="utf8">{0,unbounded}</vamsas:glyph>
  <vamsas:value>{0,unbounded}</vamsas:value>
</vamsas:annotationElement>
Attributes
QName Type Fixed Default Use Annotation
after xs:boolean false optional 
true means the annotation element appears between the
specified position and the next
id xs:ID optional 
Primary Key for vamsas object referencing
position xs:integer required 
position with respect to the coordinate frame defined by a
rangeType specification
Source
 
<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="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:sequence>
    <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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:annotationElement/vamsas:description
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
Free text at this position
Diagram
Diagram
Type xs:string
Properties
content: simple
minOccurs: 0
Source
 
<xs:element name="description" type="xs:string" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Free text at this position</xs:documentation>
  </xs:annotation>
</xs:element>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:annotationElement/vamsas:glyph
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
Discrete symbol - possibly graphically represented
Diagram
Diagram vamsasDocument1.tmp#id87
Type extension of xs:string
Properties
content: complex
minOccurs: 0
maxOccurs: unbounded
Attributes
QName Type Fixed Default Use Annotation
dict xs:string utf8 optional 
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
 
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
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:annotationElement/vamsas:value
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
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
Diagram
Diagram
Type xs:float
Properties
content: simple
minOccurs: 0
maxOccurs: unbounded
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:rangeAnnotation/vamsas:score
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
Ordered set of optionally named float values for the
whole annotation
Diagram
Diagram vamsasDocument1.tmp#id93
Type extension of xs:float
Properties
content: complex
minOccurs: 0
maxOccurs: unbounded
Attributes
QName Type Fixed Default Use Annotation
name xs:string score optional
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:DataSet/vamsas:Alignment
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram vamsasDocument1.tmp#id108 vamsasDocument1.tmp#id109 vamsasDocument1.tmp#id110 vamsasDocument1.tmp#id111 vamsasDocument1.tmp#id100 vamsasDocument1.tmp#id29 vamsasDocument1.tmp#id103 vamsasDocument1.tmp#id11 vamsasDocument1.tmp#id5
Properties
content: complex
minOccurs: 0
maxOccurs: unbounded
Model vamsas:AlignmentAnnotation* , vamsas:Tree* , vamsas:alignmentSequence+ , vamsas:property* , vamsas:Provenance
Children vamsas:AlignmentAnnotation, vamsas:Provenance, vamsas:Tree, vamsas:alignmentSequence, vamsas:property
Instance
 
<vamsas:Alignment aligned="" gapChar="" id="" modifiable="">
  <vamsas:AlignmentAnnotation graph="" group="" id="" modifiable="" seqrefs="" type="">{0,unbounded}</vamsas:AlignmentAnnotation>
  <vamsas:Tree id="" modifiable="">{0,unbounded}</vamsas:Tree>
  <vamsas:alignmentSequence end="" id="" refid="" start="">{1,unbounded}</vamsas:alignmentSequence>
  <vamsas:property name="" type="">{0,unbounded}</vamsas:property>
  <vamsas:Provenance>{1,1}</vamsas:Provenance>
</vamsas:Alignment>
Attributes
QName Type Fixed Default Use Annotation
aligned xs:boolean optional
gapChar xs:string required
id xs:ID optional 
Primary Key for vamsas object referencing
modifiable vamsas:locks optional
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:Alignment/vamsas:DataSet/vamsas:AlignmentAnnotation
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
This is annotation over the coordinate frame
defined by all the columns in the alignment.
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 vamsasDocument1.tmp#id92 vamsasDocument1.tmp#id66 vamsasDocument1.tmp#id11 vamsasDocument1.tmp#id80 vamsasDocument1.tmp#id101 vamsasDocument1.tmp#id102 vamsasDocument1.tmp#id5
Type extension of vamsas:rangeAnnotation
Type hierarchy
Properties
content: complex
minOccurs: 0
maxOccurs: unbounded
Model (vamsas:pos+ | vamsas:seg+) , vamsas:label{0,1} , vamsas:description{0,1} , vamsas:status{0,1} , vamsas:annotationElement* , vamsas:score* , vamsas:link* , vamsas:property* , vamsas:Provenance
Children vamsas:Provenance, vamsas:annotationElement, vamsas:description, vamsas:label, vamsas:link, vamsas:pos, vamsas:property, vamsas:score, vamsas:seg, vamsas:status
Instance
 
<vamsas:AlignmentAnnotation graph="" group="" id="" modifiable="" seqrefs="" type="">
  <vamsas:pos i="">{1,unbounded}</vamsas:pos>
  <vamsas:seg end="" inclusive="" start="">{1,unbounded}</vamsas:seg>
</vamsas:AlignmentAnnotation>
Attributes
QName Type Fixed Default Use Annotation
graph xs:boolean required 
TODO: decide if this flag is
redundant - when true it would suggest that
the annotationElement values together form a
graph
group xs:string optional 
Annotation with the same non-empty group name are grouped
together
id xs:ID optional 
Primary Key for vamsas object referencing
modifiable vamsas:locks optional
seqrefs xs:IDREFS optional 
annotation is associated with
a range on a particular group of alignment
sequences
type xs:string required 
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
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:Alignment/vamsas:DataSet/vamsas:alignmentSequence
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#id106 vamsasDocument1.tmp#id107 vamsasDocument1.tmp#id104
Type extension of vamsas:SequenceType
Type hierarchy
Properties
content: complex
maxOccurs: unbounded
Model vamsas:sequence , vamsas:name , vamsas:description{0,1} , vamsas:property* , vamsas:AlignmentSequenceAnnotation*
Children vamsas:AlignmentSequenceAnnotation, vamsas:description, vamsas:name, vamsas:property, vamsas:sequence
Instance
 
<vamsas:alignmentSequence end="" id="" refid="" 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:alignmentSequence>
Attributes
QName Type Fixed Default Use Annotation
end xs:integer required
id xs:ID optional 
Primary Key for vamsas object
referencing
refid xs:IDREF required 
Dataset Sequence from which
this alignment sequence is taken from
start xs:integer required
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:alignmentSequence/vamsas:Alignment/vamsas:DataSet/vamsas:AlignmentSequenceAnnotation
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 vamsasDocument1.tmp#id92 vamsasDocument1.tmp#id66 vamsasDocument1.tmp#id11 vamsasDocument1.tmp#id80 vamsasDocument1.tmp#id105 vamsasDocument1.tmp#id5
Type extension of vamsas:rangeAnnotation
Type hierarchy
Properties
content: complex
minOccurs: 0
maxOccurs: unbounded
Model (vamsas:pos+ | vamsas:seg+) , vamsas:label{0,1} , vamsas:description{0,1} , vamsas:status{0,1} , vamsas:annotationElement* , vamsas:score* , vamsas:link* , vamsas:property* , vamsas:Provenance
Children vamsas:Provenance, vamsas:annotationElement, vamsas:description, vamsas:label, vamsas:link, vamsas:pos, vamsas:property, vamsas:score, vamsas:seg, vamsas:status
Instance
 
<vamsas:AlignmentSequenceAnnotation graph="" group="" id="" modifiable="" type="">
  <vamsas:pos i="">{1,unbounded}</vamsas:pos>
  <vamsas:seg end="" inclusive="" start="">{1,unbounded}</vamsas:seg>
</vamsas:AlignmentSequenceAnnotation>
Attributes
QName Type Fixed Default Use Annotation
graph xs:boolean required 
TODO:
decide if this flag is
redundant - when true it
would suggest that the
annotationElement values
together form a graph
group xs:string optional 
Annotation with the same non-empty group name are grouped
together
id xs:ID optional 
Primary Key for vamsas object referencing
modifiable vamsas:locks optional
type xs:string required 
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
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:ApplicationData
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram vamsasDocument1.tmp#id117 vamsasDocument1.tmp#id118 vamsasDocument1.tmp#id116 vamsasDocument1.tmp#id125 vamsasDocument1.tmp#id126 vamsasDocument1.tmp#id119 vamsasDocument1.tmp#id122 vamsasDocument1.tmp#id123
Type extension of vamsas:appData
Type hierarchy
Properties
content: complex
Used by
Model (vamsas:data | vamsas:dataReference) , vamsas:User* , vamsas:Common{0,1} , vamsas:Instance*
Children vamsas:Common, vamsas:Instance, vamsas:User, vamsas:data, vamsas:dataReference
Instance
 
<vamsas:ApplicationData name="" version="">
  <vamsas:data>{1,1}</vamsas:data>
  <vamsas:dataReference>{1,1}</vamsas:dataReference>
</vamsas:ApplicationData>
Attributes
QName Type Fixed Default Use Annotation
name xs:string required 
Canonical name of application
version xs:string required 
Version string describing the application specific
data storage version used
Source
 
<xs:element name="ApplicationData">
  <xs:complexType>
    <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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:appData/vamsas:data
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram
Type xs:base64Binary
Properties
content: simple
Source
 
<xs:element name="data" type="xs:base64Binary"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:appData/vamsas:dataReference
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram
Type xs:string
Properties
content: simple
Source
 
<xs:element name="dataReference" type="xs:string"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:ApplicationData/vamsas:User
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram vamsasDocument1.tmp#id117 vamsasDocument1.tmp#id118 vamsasDocument1.tmp#id116 vamsasDocument1.tmp#id120 vamsasDocument1.tmp#id121
Type extension of vamsas:appData
Type hierarchy
Properties
content: complex
minOccurs: 0
maxOccurs: unbounded
Model vamsas:data | vamsas:dataReference
Children vamsas:data, vamsas:dataReference
Instance
 
<vamsas:User fullname="" organization="">
  <vamsas:data>{1,1}</vamsas:data>
  <vamsas:dataReference>{1,1}</vamsas:dataReference>
</vamsas:User>
Attributes
QName Type Fixed Default Use Annotation
fullname xs:string required
organization xs:string required
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:ApplicationData/vamsas:Common
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram vamsasDocument1.tmp#id117 vamsasDocument1.tmp#id118 vamsasDocument1.tmp#id116
Type extension of vamsas:appData
Type hierarchy
Properties
content: complex
minOccurs: 0
Model vamsas:data | vamsas:dataReference
Children vamsas:data, vamsas:dataReference
Instance
 
<vamsas:Common>
  <vamsas:data>{1,1}</vamsas:data>
  <vamsas:dataReference>{1,1}</vamsas:dataReference>
</vamsas:Common>
Source
 
<xs:element name="Common" minOccurs="0">
  <xs:complexType>
    <xs:complexContent>
      <xs:extension base="vamsas:appData"/>
    </xs:complexContent>
  </xs:complexType>
</xs:element>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:ApplicationData/vamsas:Instance
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram vamsasDocument1.tmp#id117 vamsasDocument1.tmp#id118 vamsasDocument1.tmp#id116 vamsasDocument1.tmp#id124
Type extension of vamsas:appData
Type hierarchy
Properties
content: complex
minOccurs: 0
maxOccurs: unbounded
Model vamsas:data | vamsas:dataReference
Children vamsas:data, vamsas:dataReference
Instance
 
<vamsas:Instance urn="">
  <vamsas:data>{1,1}</vamsas:data>
  <vamsas:dataReference>{1,1}</vamsas:dataReference>
</vamsas:Instance>
Attributes
QName Type Fixed Default Use Annotation
urn xs:string required
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:Attachment
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram vamsasDocument1.tmp#id117 vamsasDocument1.tmp#id118 vamsasDocument1.tmp#id116 vamsasDocument1.tmp#id128 vamsasDocument1.tmp#id129 vamsasDocument1.tmp#id130 vamsasDocument1.tmp#id131
Type extension of vamsas:appData
Type hierarchy
Properties
content: complex
Used by
Model vamsas:data | vamsas:dataReference
Children vamsas:data, vamsas:dataReference
Instance
 
<vamsas:Attachment compressed="false" id="" objectref="" type="">
  <vamsas:data>{1,1}</vamsas:data>
  <vamsas:dataReference>{1,1}</vamsas:dataReference>
</vamsas:Attachment>
Attributes
QName Type Fixed Default Use Annotation
compressed xs:boolean false optional 
true implies data will be decompresses with Zip
before presenting to application
id xs:ID optional 
Primary Key for vamsas object referencing
objectref xs:IDREF required 
Object the arbitrary data is associated with
type xs:string required 
Type of arbitrary data - TODO: decide format - use
(extended) MIME types ?
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Complex Type vamsas:rangeType
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
Specify an ordered set of positions and/or regions on the principle
dimension of some associated vamsas object
 
Keeping to jaxb-1.0 specification for the moment - this choice should
become a substitution group when we use jaxb-2.0 capable bindings
Diagram
Diagram vamsasDocument1.tmp#id19 vamsasDocument1.tmp#id21
Properties
abstract: true
Used by
Model vamsas:pos+ | vamsas:seg+
Children vamsas:pos, vamsas:seg
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Simple Type vamsas:locks
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
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.
Diagram
Diagram
Type xs:string
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Complex Type vamsas:nodeType
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram vamsasDocument1.tmp#id44 vamsasDocument1.tmp#id45 vamsasDocument1.tmp#id38 vamsasDocument1.tmp#id39 vamsasDocument1.tmp#id40 vamsasDocument1.tmp#id11
Used by
Model vamsas:name{0,1} , vamsas:description{0,1} , vamsas:vref* , vamsas:property*
Children vamsas:description, vamsas:name, vamsas:property, vamsas:vref
Attributes
QName Type Fixed Default Use Annotation
id xs:ID optional 
Primary Key for vamsas object referencing
modifiable vamsas:locks optional
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Complex Type vamsas:referenceType
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
base type for citing arbitrary links between vamsas objects
Diagram
Diagram vamsasDocument1.tmp#id42 vamsasDocument1.tmp#id43
Type extension of xs:string
Used by
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: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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Complex Type vamsas:SequenceType
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
Used by
Model vamsas:sequence , vamsas:name , vamsas:description{0,1} , vamsas:property*
Children vamsas:description, vamsas:name, vamsas:property, vamsas:sequence
Attributes
QName Type Fixed Default Use Annotation
end xs:integer required
start xs:integer required
Source
 
<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:integer" use="required"/>
  <xs:attribute name="end" type="xs:integer" use="required"/>
</xs:complexType>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Complex Type vamsas:mapType
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
Two sets of ranges defined between objects - usually sequences, indicating which
regions on each are mapped.
Diagram
Diagram vamsasDocument1.tmp#id61 vamsasDocument1.tmp#id64
Used by
Model vamsas:local , vamsas:mapped
Children vamsas:local, vamsas:mapped
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Complex Type vamsas:mapRangeType
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram vamsasDocument1.tmp#id19 vamsasDocument1.tmp#id21 vamsasDocument1.tmp#id18 vamsasDocument1.tmp#id63
Type extension of vamsas:rangeType
Type hierarchy
Used by
Model vamsas:pos+ | vamsas:seg+
Children vamsas:pos, vamsas:seg
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: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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Complex Type vamsas:rangeAnnotation
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
 
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.
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 vamsasDocument1.tmp#id92 vamsasDocument1.tmp#id66 vamsasDocument1.tmp#id11
Type extension of vamsas:rangeType
Type hierarchy
Used by
Model (vamsas:pos+ | vamsas:seg+) , vamsas:label{0,1} , vamsas:description{0,1} , vamsas:status{0,1} , vamsas:annotationElement* , vamsas:score* , vamsas:link* , vamsas:property*
Children vamsas:annotationElement, vamsas:description, vamsas:label, vamsas:link, vamsas:pos, vamsas:property, vamsas:score, vamsas:seg, vamsas:status
Attributes
QName Type Fixed Default Use Annotation
group xs:string optional 
Annotation with the same non-empty group name are grouped
together
id xs:ID optional 
Primary Key for vamsas object referencing
modifiable vamsas:locks optional
type xs:string required 
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
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Complex Type vamsas:appData
Namespace http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Diagram
Diagram vamsasDocument1.tmp#id117 vamsasDocument1.tmp#id118
Used by
Model vamsas:data | vamsas:dataReference
Children vamsas:data, vamsas:dataReference
Source
 
<xs:complexType name="appData">
  <xs:choice>
    <xs:element name="data" type="xs:base64Binary"/>
    <xs:element name="dataReference" type="xs:string"/>
  </xs:choice>
</xs:complexType>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:property/@name
Namespace No namespace
Type xs:string
Properties
use: required
Used by
Element vamsas:property
Source
 
<xs:attribute name="name" type="xs:string" use="required"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:property/@type
Namespace No namespace
Annotations
 
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
Type xs:string
Properties
use: required
Used by
Element vamsas:property
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:param/@name
Namespace No namespace
Type xs:string
Properties
use: required
Used by
Element vamsas:param
Source
 
<xs:attribute name="name" type="xs:string" use="required"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:param/@type
Namespace No namespace
Annotations
 
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
Type xs:string
Properties
use: required
Used by
Element vamsas:param
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:pos/vamsas:rangeType/@i
Namespace No namespace
Type xs:int
Properties
use: required
Used by
Source
 
<xs:attribute name="i" type="xs:int" use="required"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:seg/vamsas:rangeType/@start
Namespace No namespace
Type xs:int
Properties
use: required
Used by
Source
 
<xs:attribute name="start" type="xs:int" use="required"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:seg/vamsas:rangeType/@end
Namespace No namespace
Type xs:int
Properties
use: required
Used by
Source
 
<xs:attribute name="end" type="xs:int" use="required"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:seg/vamsas:rangeType/@inclusive
Namespace No namespace
Annotations
 
when false, a consecutive range like 'start=1, end=2'
means the region lying after position 1 and before position 2
Type xs:boolean
Properties
use: required
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:input/@name
Namespace No namespace
Type xs:string
Properties
use: required
Used by
Element vamsas:input
Source
 
<xs:attribute name="name" type="xs:string" use="required"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:input/@objRef
Namespace No namespace
Annotations
 
Reference Frame for rangeType specfication
Type xs:IDREFS
Properties
use: optional
Used by
Element vamsas:input
Source
 
<xs:attribute name="objRef" type="xs:IDREFS" use="optional">
  <xs:annotation>
    <xs:documentation>Reference Frame for rangeType specfication</xs:documentation>
  </xs:annotation>
</xs:attribute>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:entry/vamsas:Provenance/@id
Namespace No namespace
Annotations
 
Primary Key for vamsas object referencing
Type xs:ID
Properties
use: optional
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:newick/vamsas:Tree/@title
Namespace No namespace
Type xs:string
Properties
use: optional
Used by
Source
 
<xs:attribute name="title" type="xs:string" use="optional"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:newick/vamsas:Tree/@id
Namespace No namespace
Annotations
 
Primary Key for vamsas object referencing
Type xs:ID
Properties
use: optional
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:newick/vamsas:Tree/@modifiable
Namespace No namespace
Type vamsas:locks
Properties
use: optional
Used by
Source
 
<xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:referenceType/@id
Namespace No namespace
Annotations
 
Primary Key for vamsas object referencing
Type xs:ID
Properties
use: optional
Used by
Complex Type vamsas:referenceType
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:referenceType/@refs
Namespace No namespace
Annotations
 
List of one or more vamsas object
references
Type xs:IDREFS
Properties
content: simple
Used by
Complex Type vamsas:referenceType
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:nodeType/@id
Namespace No namespace
Annotations
 
Primary Key for vamsas object referencing
Type xs:ID
Properties
use: optional
Used by
Complex Type vamsas:nodeType
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:nodeType/@modifiable
Namespace No namespace
Type vamsas:locks
Properties
use: optional
Used by
Complex Type vamsas:nodeType
Source
 
<xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:treenode/vamsas:Tree/@treeId
Namespace No namespace
Annotations
 
reference to one or more trees containing
the node being described.
Type xs:IDREFS
Properties
content: simple
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:treenode/vamsas:Tree/@nodespec
Namespace No namespace
Annotations
 
String uniquely identifying a particular
node in the referenced tree according to the format of
the tree representation that is referenced.
Type xs:string
Properties
content: simple
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:Tree/@id
Namespace No namespace
Annotations
 
Primary Key for vamsas object referencing
Type xs:ID
Properties
use: optional
Used by
Element vamsas:Tree
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:Tree/@modifiable
Namespace No namespace
Type vamsas:locks
Properties
use: optional
Used by
Element vamsas:Tree
Source
 
<xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:SequenceType/@start
Namespace No namespace
Type xs:integer
Properties
use: required
Used by
Complex Type vamsas:SequenceType
Source
 
<xs:attribute name="start" type="xs:integer" use="required"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:SequenceType/@end
Namespace No namespace
Type xs:integer
Properties
use: required
Used by
Complex Type vamsas:SequenceType
Source
 
<xs:attribute name="end" type="xs:integer" use="required"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:mapRangeType/@unit
Namespace No namespace
Annotations
 
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.
Type xs:positiveInteger
Properties
use: optional
Used by
Complex Type vamsas:mapRangeType
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:map/vamsas:dbRef/vamsas:Sequence/vamsas:DataSet/@id
Namespace No namespace
Type xs:ID
Properties
content: simple
Used by
Source
 
<xs:attribute name="id" type="xs:ID"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:link/@href
Namespace No namespace
Annotations
 
The URI
Type xs:anyURI
Properties
content: simple
Used by
Element vamsas:link
Source
 
<xs:attribute name="href" type="xs:anyURI">
  <xs:annotation>
    <xs:documentation>The URI</xs:documentation>
  </xs:annotation>
</xs:attribute>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:dbRef/vamsas:Sequence/vamsas:DataSet/@source
Namespace No namespace
Annotations
 
TODO Database Naming
Convention: either start using LSID (so
change type to URI) or leave this as an
uncontrolled/unspecified string ID
Type xs:string
Properties
use: required
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:dbRef/vamsas:Sequence/vamsas:DataSet/@version
Namespace No namespace
Annotations
 
Version must be specified -
Type xs:string
Properties
use: required
Used by
Source
 
<xs:attribute name="version" type="xs:string" use="required">
  <xs:annotation>
    <xs:documentation>Version must be specified -</xs:documentation>
  </xs:annotation>
</xs:attribute>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:dbRef/vamsas:Sequence/vamsas:DataSet/@accessionId
Namespace No namespace
Annotations
 
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 ?
Type xs:string
Properties
use: required
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:dbRef/vamsas:Sequence/vamsas:DataSet/@id
Namespace No namespace
Annotations
 
Primary Key for vamsas object
referencing
Type xs:ID
Properties
use: optional
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:Sequence/vamsas:DataSet/@id
Namespace No namespace
Annotations
 
Primary Key for vamsas object referencing
Type xs:ID
Properties
use: optional
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:Sequence/vamsas:DataSet/@dictionary
Namespace No namespace
Annotations
 
symbol class for sequence
Type xs:string
Properties
use: required
Used by
Source
 
<xs:attribute name="dictionary" type="xs:string" use="required">
  <xs:annotation>
    <xs:documentation>symbol class for sequence</xs:documentation>
  </xs:annotation>
</xs:attribute>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:sequenceMapping/vamsas:DataSet/@loc
Namespace No namespace
Annotations
 
Object on which the local
range is defined.
Type xs:IDREF
Properties
use: required
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:sequenceMapping/vamsas:DataSet/@map
Namespace No namespace
Annotations
 
Object on which the mapped
range is defined.
Type xs:IDREF
Properties
use: required
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:sequenceMapping/vamsas:DataSet/@id
Namespace No namespace
Type xs:ID
Properties
use: optional
Used by
Source
 
<xs:attribute name="id" type="xs:ID" use="optional"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:glyph/vamsas:annotationElement/@dict
Namespace No namespace
Annotations
 
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
 
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
Type xs:string
Properties
use: optional
default: utf8
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:annotationElement/@position
Namespace No namespace
Annotations
 
position with respect to the coordinate frame defined by a
rangeType specification
Type xs:integer
Properties
use: required
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:annotationElement/@after
Namespace No namespace
Annotations
 
true means the annotation element appears between the
specified position and the next
Type xs:boolean
Properties
use: optional
default: false
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:annotationElement/@id
Namespace No namespace
Annotations
 
Primary Key for vamsas object referencing
Type xs:ID
Properties
use: optional
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:score/vamsas:rangeAnnotation/@name
Namespace No namespace
Type xs:string
Properties
use: optional
default: score
Used by
Source
 
<xs:attribute name="name" type="xs:string" use="optional" default="score"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:rangeAnnotation/@id
Namespace No namespace
Annotations
 
Primary Key for vamsas object referencing
Type xs:ID
Properties
use: optional
Used by
Complex Type vamsas:rangeAnnotation
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:rangeAnnotation/@modifiable
Namespace No namespace
Type vamsas:locks
Properties
use: optional
Used by
Complex Type vamsas:rangeAnnotation
Source
 
<xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:rangeAnnotation/@group
Namespace No namespace
Annotations
 
Annotation with the same non-empty group name are grouped
together
Type xs:string
Properties
use: optional
default:
Used by
Complex Type vamsas:rangeAnnotation
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:rangeAnnotation/@type
Namespace No namespace
Annotations
 
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
Type xs:string
Properties
use: required
Used by
Complex Type vamsas:rangeAnnotation
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:DataSetAnnotations/vamsas:DataSet/@seqRef
Namespace No namespace
Annotations
 
annotation is associated with a
particular dataset sequence
Type xs:IDREFS
Properties
use: required
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:AlignmentAnnotation/vamsas:Alignment/vamsas:DataSet/@graph
Namespace No namespace
Annotations
 
TODO: decide if this flag is
redundant - when true it would suggest that
the annotationElement values together form a
graph
Type xs:boolean
Properties
use: required
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:AlignmentAnnotation/vamsas:Alignment/vamsas:DataSet/@seqrefs
Namespace No namespace
Annotations
 
annotation is associated with
a range on a particular group of alignment
sequences
Type xs:IDREFS
Properties
use: optional
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:AlignmentSequenceAnnotation/vamsas:alignmentSequence/vamsas:Alignment/vamsas:DataSet/@graph
Namespace No namespace
Annotations
 
TODO:
decide if this flag is
redundant - when true it
would suggest that the
annotationElement values
together form a graph
Type xs:boolean
Properties
use: required
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:alignmentSequence/vamsas:Alignment/vamsas:DataSet/@id
Namespace No namespace
Annotations
 
Primary Key for vamsas object
referencing
Type xs:ID
Properties
use: optional
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:alignmentSequence/vamsas:Alignment/vamsas:DataSet/@refid
Namespace No namespace
Annotations
 
Dataset Sequence from which
this alignment sequence is taken from
Type xs:IDREF
Properties
use: required
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:Alignment/vamsas:DataSet/@gapChar
Namespace No namespace
Type xs:string
Properties
use: required
Used by
Source
 
<xs:attribute name="gapChar" type="xs:string" use="required"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:Alignment/vamsas:DataSet/@aligned
Namespace No namespace
Type xs:boolean
Properties
use: optional
Used by
Source
 
<xs:attribute name="aligned" type="xs:boolean" use="optional"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:Alignment/vamsas:DataSet/@id
Namespace No namespace
Annotations
 
Primary Key for vamsas object referencing
Type xs:ID
Properties
use: optional
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:Alignment/vamsas:DataSet/@modifiable
Namespace No namespace
Type vamsas:locks
Properties
use: optional
Used by
Source
 
<xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:DataSet/@id
Namespace No namespace
Annotations
 
Primary Key for vamsas object referencing
Type xs:ID
Properties
use: optional
Used by
Element vamsas:DataSet
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:VAMSAS/@id
Namespace No namespace
Annotations
 
Primary Key for vamsas object referencing
Type xs:ID
Properties
use: optional
Used by
Element vamsas:VAMSAS
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:VAMSAS/@modifiable
Namespace No namespace
Type vamsas:locks
Properties
use: optional
Used by
Element vamsas:VAMSAS
Source
 
<xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:User/vamsas:ApplicationData/@fullname
Namespace No namespace
Type xs:string
Properties
use: required
Used by
Source
 
<xs:attribute name="fullname" type="xs:string" use="required"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:User/vamsas:ApplicationData/@organization
Namespace No namespace
Type xs:string
Properties
use: required
Used by
Source
 
<xs:attribute name="organization" type="xs:string" use="required"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:Instance/vamsas:ApplicationData/@urn
Namespace No namespace
Type xs:string
Properties
use: required
Used by
Source
 
<xs:attribute name="urn" type="xs:string" use="required"/>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:ApplicationData/@version
Namespace No namespace
Annotations
 
Version string describing the application specific
data storage version used
Type xs:string
Properties
use: required
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:ApplicationData/@name
Namespace No namespace
Annotations
 
Canonical name of application
Type xs:string
Properties
use: required
Used by
Source
 
<xs:attribute name="name" type="xs:string" use="required">
  <xs:annotation>
    <xs:documentation>Canonical name of application</xs:documentation>
  </xs:annotation>
</xs:attribute>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:Attachment/@compressed
Namespace No namespace
Annotations
 
true implies data will be decompresses with Zip
before presenting to application
Type xs:boolean
Properties
use: optional
default: false
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:Attachment/@type
Namespace No namespace
Annotations
 
Type of arbitrary data - TODO: decide format - use
(extended) MIME types ?
Type xs:string
Properties
use: required
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:Attachment/@objectref
Namespace No namespace
Annotations
 
Object the arbitrary data is associated with
Type xs:IDREF
Properties
use: required
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Attribute vamsas:Attachment/@id
Namespace No namespace
Annotations
 
Primary Key for vamsas object referencing
Type xs:ID
Properties
use: optional
Used by
Source
 
<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>
Schema location file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
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