From: jprocter Date: Thu, 7 May 2009 15:32:01 +0000 (+0000) Subject: schema documentation autogenerated using Oxygen v10. 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Table of Contents

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Group by: +
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vamsasDocument.xsd

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Elements + +
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vamsas.xsd

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Elements + +
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Complex Types + +
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Simple Types + +
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XML Schema documentation generated by ® XML Editor. +
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+ \ No newline at end of file diff --git a/docs/schema/vamsasDocument.html b/docs/schema/vamsasDocument.html new file mode 100644 index 0000000..417997b --- /dev/null +++ b/docs/schema/vamsasDocument.html @@ -0,0 +1,4 @@ + + +Schema documentation for \ No newline at end of file diff --git a/docs/schema/vamsasDocument0.html b/docs/schema/vamsasDocument0.html new file mode 100644 index 0000000..3e66850 --- /dev/null +++ b/docs/schema/vamsasDocument0.html @@ -0,0 +1,800 @@ + + + + + Schema documentation for + + +
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Showing:

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Annotations
Diagrams
Instances
Properties
Source
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+
Main schema vamsasDocument.xsd
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Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasDocument
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Properties
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attribute form default: + + unqualified
element form default: + + qualified
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Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsasDocument.xsd
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Element vdoc:VamsasDocument
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Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasDocument
+
Diagram
+
+ 		+
Diagram + vamsasDocument0.tmp#id3 + vamsasDocument0.tmp#id4 + vamsasDocument1.tmp#id5 + vamsasDocument1.tmp#id28 + vamsasDocument1.tmp#id115 + vamsasDocument1.tmp#id127
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+
Properties
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+ 		+
+ + + + + + + + + +
content: + + complex
nillable: + + false
+
+
Modelvdoc:Version , vdoc:LockFile{0,1} , vamsas:Provenance{0,1} , vamsas:VAMSAS+ , vamsas:ApplicationData* , vamsas:Attachment*
Childrenvamsas:ApplicationData, vamsas:Attachment, vamsas:Provenance, vamsas:VAMSAS, vdoc:LockFile, vdoc:Version
+
Instance
+
+ 		+
+ + + + + 
<vdoc:VamsasDocument>
+  <vdoc:Version>{1,1}</vdoc:Version>
+  <vdoc:LockFile>{0,1}</vdoc:LockFile>
+  <vamsas:Provenance>{0,1}</vamsas:Provenance>
+  <vamsas:VAMSAS id="" modifiable="">{1,unbounded}</vamsas:VAMSAS>
+  <vamsas:ApplicationData name="" version="">{0,unbounded}</vamsas:ApplicationData>
+  <vamsas:Attachment compressed="false" id="" objectref="" type="">{0,unbounded}</vamsas:Attachment>
+</vdoc:VamsasDocument>
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:element name="VamsasDocument" nillable="false">
+  <xs:complexType>
+    <xs:sequence>
+      <xs:element name="Version" type="xs:string" minOccurs="1" maxOccurs="1">
+        <xs:annotation>
+          <xs:documentation>Vamsas Document Version Number</xs:documentation>
+        </xs:annotation>
+      </xs:element>
+      <xs:element name="LockFile" minOccurs="0" maxOccurs="1">
+        <xs:complexType>
+          <xs:simpleContent>
+            <xs:extension base="xs:string"/>
+          </xs:simpleContent>
+        </xs:complexType>
+      </xs:element>
+      <xs:element ref="vamsas:Provenance" minOccurs="0" maxOccurs="1"/>
+      <xs:element ref="vamsas:VAMSAS" minOccurs="1" maxOccurs="unbounded"/>
+      <xs:element ref="vamsas:ApplicationData" minOccurs="0" maxOccurs="unbounded"/>
+      <xs:element ref="vamsas:Attachment" minOccurs="0" maxOccurs="unbounded"/>
+    </xs:sequence>
+  </xs:complexType>
+</xs:element>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsasDocument.xsd
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Element vdoc:VamsasDocument/vdoc:Version
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Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasDocument
+
Annotations
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+ 		+
+
+ + + + + 
Vamsas Document Version Number
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+
+
+
Diagram
+
+ 		+
Diagram
+
Typexs:string
+
Properties
+
+ 		+
+ + + + + + + + + + + + + +
content: + + simple
minOccurs: + + 1
maxOccurs: + + 1
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+
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Source
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+ 		+
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<xs:element name="Version" type="xs:string" minOccurs="1" maxOccurs="1">
+  <xs:annotation>
+    <xs:documentation>Vamsas Document Version Number</xs:documentation>
+  </xs:annotation>
+</xs:element>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsasDocument.xsd
+
Element vdoc:VamsasDocument/vdoc:LockFile
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasDocument
+
Diagram
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+ 		+
Diagram
+
Typeextension of xs:string
+
Properties
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+ 		+
+ + + + + + + + + + + + + +
content: + + complex
minOccurs: + + 0
maxOccurs: + + 1
+
+
+
Source
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+ 		+
+ + + + + 
<xs:element name="LockFile" minOccurs="0" maxOccurs="1">
+  <xs:complexType>
+    <xs:simpleContent>
+      <xs:extension base="xs:string"/>
+    </xs:simpleContent>
+  </xs:complexType>
+</xs:element>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsasDocument.xsd
+
+
+
+
XML Schema documentation generated by ® XML Editor. +
+
+ \ No newline at end of file diff --git a/docs/schema/vamsasDocument1.html b/docs/schema/vamsasDocument1.html new file mode 100644 index 0000000..ed35e0c --- /dev/null +++ b/docs/schema/vamsasDocument1.html @@ -0,0 +1,20791 @@ + + + + + Schema documentation for + + +
+ + + + + + + + + + + + + + + + +
+

Showing:

+ + + + + + + + + + + + + + + + + + + + + + +
Annotations
Attributes
Diagrams
Instances
Properties
Source
Used by
+
+
+
Imported schema vamsas.xsd
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
Namespacehttp://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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:Provenance
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+
Diagram
+
+ 		+
Diagram + vamsasDocument1.tmp#id6
+
+
Properties
+
+ 		+
+ + + + + +
content: + + complex
+
+
+
Used by
+
+ 		+ +
Modelvamsas:entry+
Childrenvamsas: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:Provenance/vamsas:entry
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
+
Modelvamsas:User , vamsas:App , vamsas:Action , vamsas:Date , vamsas:property* , vamsas:param* , vamsas:input*
Childrenvamsas: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
+
+ 		+
+ + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
idxs:IDoptional +
+ + + + + 
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:entry/vamsas:Provenance/vamsas:User
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+
Annotations
+
+ 		+
+
+ + + + + 
Who
+
+
+
+
Diagram
+
+ 		+
Diagram
+
Typexs:string
+
Properties
+
+ 		+
+ + + + + +
content: + + simple
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:element name="User" type="xs:string">
+  <xs:annotation>
+    <xs:documentation>Who</xs:documentation>
+  </xs:annotation>
+</xs:element>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:entry/vamsas:Provenance/vamsas:App
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+
Annotations
+
+ 		+
+
+ + + + + 
With which application
+
+
+
+
Diagram
+
+ 		+
Diagram
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:entry/vamsas:Provenance/vamsas:Action
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+
Annotations
+
+ 		+
+
+ + + + + 
Did what
+
+
+
+
Diagram
+
+ 		+
Diagram
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:entry/vamsas:Provenance/vamsas:Date
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+
Annotations
+
+ 		+
+
+ + + + + 
When
+
+
+
+
Diagram
+
+ 		+
Diagram
+
Typexs:dateTime
+
Properties
+
+ 		+
+ + + + + +
content: + + simple
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:element name="Date" type="xs:dateTime">
+  <xs:annotation>
+    <xs:documentation>When</xs:documentation>
+  </xs:annotation>
+</xs:element>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:property
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+
Diagram
+
+ 		+
Diagram + vamsasDocument1.tmp#id12 + vamsasDocument1.tmp#id13
+
Typeextension of xs:string
+
Properties
+
+ 		+
+ + + + + +
content: + + complex
+
+
+
Used by
+
+ 		+ +
+
Attributes
+
+ 		+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
namexs:stringrequired +
+
typexs:stringrequired +
+ + + + + 
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:param
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+
Diagram
+
+ 		+
Diagram + vamsasDocument1.tmp#id15 + vamsasDocument1.tmp#id16
+
Typeextension of xs:string
+
Properties
+
+ 		+
+ + + + + +
content: + + complex
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:Provenance/vamsas:entry
+
+
+
Attributes
+
+ 		+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
namexs:stringrequired +
+
typexs:stringrequired +
+ + + + + 
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:input
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
Typeextension of vamsas:rangeType
Type hierarchy + +
+
Properties
+
+ 		+
+ + + + + +
content: + + complex
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:Provenance/vamsas:entry
+
+
Modelvamsas:pos+ | vamsas:seg+
Childrenvamsas: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
+
+ 		+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
namexs:stringrequired +
+
objRefxs:IDREFSoptional +
+ + + + + 
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:rangeType/vamsas:pos
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
+ 		+
+ + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
ixs:intrequired +
+
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:rangeType/vamsas:seg
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
+ 		+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
endxs:intrequired +
+
inclusivexs:booleanrequired +
+ + + + + 
when false, a consecutive range like 'start=1, end=2'
+means the region lying after position 1 and before position 2
+
+
startxs:intrequired +
+
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:VAMSAS
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
+ 		+
+ + + + + +
Element vdoc:VamsasDocument
+
+
Modelvamsas:Tree* , vamsas:DataSet*
Childrenvamsas: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
+
+ 		+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
idxs:IDoptional +
+ + + + + 
Primary Key for vamsas object referencing
+
+
modifiablevamsas:locksoptional +
+
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:Tree
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
+ 		+ +
Modelvamsas:title{0,1} , vamsas:newick+ , vamsas:treenode* , vamsas:property* , vamsas:Provenance
Childrenvamsas: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
+
+ 		+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
idxs:IDoptional +
+ + + + + 
Primary Key for vamsas object referencing
+
+
modifiablevamsas:locksoptional +
+
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:Tree/vamsas:title
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+
Diagram
+
+ 		+
Diagram
+
Typexs:string
+
Properties
+
+ 		+
+ + + + + + + + + +
content: + + simple
minOccurs: + + 0
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:element name="title" type="xs:string" minOccurs="0"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:Tree/vamsas:newick
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+
Diagram
+
+ 		+
Diagram + vamsasDocument1.tmp#id32 + vamsasDocument1.tmp#id33 + vamsasDocument1.tmp#id34
+
Typeextension of xs:string
+
Properties
+
+ 		+
+ + + + + + + + + +
content: + + complex
maxOccurs: + + unbounded
+
+
+
Attributes
+
+ 		+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
idxs:IDoptional +
+ + + + + 
Primary Key for vamsas object referencing
+
+
modifiablevamsas:locksoptional +
+
titlexs:stringoptional +
+
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:Tree/vamsas:treenode
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
Typeextension of vamsas:nodeType
Type hierarchy + +
+
Properties
+
+ 		+
+ + + + + + + + + + + + + +
content: + + complex
minOccurs: + + 0
maxOccurs: + + unbounded
+
+
Modelvamsas:name{0,1} , vamsas:description{0,1} , vamsas:vref* , vamsas:property*
Childrenvamsas: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
+
+ 		+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
idxs:IDoptional +
+ + + + + 
Primary Key for vamsas object referencing
+
+
modifiablevamsas:locksoptional +
+
nodespecxs:stringoptional +
+ + + + + 
String uniquely identifying a particular
+node in the referenced tree according to the format of
+the tree representation that is referenced.
+
+
treeIdxs:IDREFSoptional +
+ + + + + 
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:nodeType/vamsas:name
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+
Annotations
+
+ 		+
+
+ + + + + 
Short name for this node
+
+
+
+
Diagram
+
+ 		+
Diagram
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:nodeType/vamsas:description
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+
Annotations
+
+ 		+
+
+ + + + + 
Descriptive text for this node
+
+
+
+
Diagram
+
+ 		+
Diagram
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:nodeType/vamsas:vref
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
Typevamsas:referenceType
+
Properties
+
+ 		+
+ + + + + + + + + + + + + +
content: + + complex
minOccurs: + + 0
maxOccurs: + + unbounded
+
+
+
Attributes
+
+ 		+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
idxs:IDoptional +
+ + + + + 
Primary Key for vamsas object referencing
+
+
refsxs:IDREFSoptional +
+ + + + + 
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:DataSet
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
+
Modelvamsas:Sequence+ , vamsas:sequenceMapping* , vamsas:DataSetAnnotations* , vamsas:Alignment* , vamsas:Tree* , vamsas:Provenance
Childrenvamsas: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
+
+ 		+
+ + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
idxs:IDoptional +
+ + + + + 
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:DataSet/vamsas:Sequence
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
Typeextension of vamsas:SequenceType
Type hierarchy + +
+
Properties
+
+ 		+
+ + + + + + + + + +
content: + + complex
maxOccurs: + + unbounded
+
+
Modelvamsas:sequence , vamsas:name , vamsas:description{0,1} , vamsas:property* , vamsas:dbRef* , vamsas:vxref*
Childrenvamsas: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
+
+ 		+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
dictionaryxs:stringrequired +
+ + + + + 
symbol class for sequence
+
+
endxs:integerrequired +
+
idxs:IDoptional +
+ + + + + 
Primary Key for vamsas object referencing
+
+
startxs:integerrequired +
+
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:SequenceType/vamsas:sequence
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+
Diagram
+
+ 		+
Diagram
+
Typexs:string
+
Properties
+
+ 		+
+ + + + + +
content: + + simple
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:element name="sequence" type="xs:string"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:SequenceType/vamsas:name
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+
Diagram
+
+ 		+
Diagram
+
Typexs:string
+
Properties
+
+ 		+
+ + + + + +
content: + + simple
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:element name="name" type="xs:string"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:SequenceType/vamsas:description
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+
Diagram
+
+ 		+
Diagram
+
Typexs:string
+
Properties
+
+ 		+
+ + + + + + + + + +
content: + + simple
minOccurs: + + 0
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:element name="description" type="xs:string" minOccurs="0"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:Sequence/vamsas:DataSet/vamsas:dbRef
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
+
Modelvamsas:map* , vamsas:link* , vamsas:property*
Childrenvamsas: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
+
+ 		+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
accessionIdxs:stringrequired +
+ + + + + 
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 ?
+
+
idxs:IDoptional +
+ + + + + 
Primary Key for vamsas object
+referencing
+
+
sourcexs:stringrequired +
+ + + + + 
TODO Database Naming
+Convention: either start using LSID (so
+change type to URI) or leave this as an
+uncontrolled/unspecified string ID
+
+
versionxs:stringrequired +
+ + + + + 
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:dbRef/vamsas:Sequence/vamsas:DataSet/vamsas:map
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
Typeextension of vamsas:mapType
Type hierarchy + +
+
Properties
+
+ 		+
+ + + + + + + + + + + + + +
content: + + complex
minOccurs: + + 0
maxOccurs: + + unbounded
+
+
Modelvamsas:local , vamsas:mapped
Childrenvamsas:local, vamsas:mapped
+
Instance
+
+ 		+
+ + + + + 
<vamsas:map id="">
+  <vamsas:local unit="">{1,1}</vamsas:local>
+  <vamsas:mapped unit="">{1,1}</vamsas:mapped>
+</vamsas:map>
+
+
+
Attributes
+
+ 		+
+ + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
idxs:IDoptional +
+
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:mapType/vamsas:local
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
Typevamsas:mapRangeType
Type hierarchy + +
+
Properties
+
+ 		+
+ + + + + +
content: + + complex
+
+
Modelvamsas:pos+ | vamsas:seg+
Childrenvamsas: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
+
+ 		+
+ + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
unitxs:positiveIntegeroptional +
+ + + + + 
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:mapType/vamsas:mapped
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
Typevamsas:mapRangeType
Type hierarchy + +
+
Properties
+
+ 		+
+ + + + + +
content: + + complex
+
+
Modelvamsas:pos+ | vamsas:seg+
Childrenvamsas: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
+
+ 		+
+ + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
unitxs:positiveIntegeroptional +
+ + + + + 
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:link
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+
Diagram
+
+ 		+
Diagram + vamsasDocument1.tmp#id67
+
Typeextension of xs:string
+
Properties
+
+ 		+
+ + + + + +
content: + + complex
+
+
+
Used by
+
+ 		+ +
+
Attributes
+
+ 		+
+ + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
hrefxs:anyURIoptional +
+ + + + + 
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:Sequence/vamsas:DataSet/vamsas:vxref
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
Typevamsas:referenceType
+
Properties
+
+ 		+
+ + + + + + + + + + + + + +
content: + + complex
minOccurs: + + 0
maxOccurs: + + unbounded
+
+
+
Attributes
+
+ 		+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
idxs:IDoptional +
+ + + + + 
Primary Key for vamsas object referencing
+
+
refsxs:IDREFSoptional +
+ + + + + 
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:DataSet/vamsas:sequenceMapping
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
Typeextension of vamsas:mapType
Type hierarchy + +
+
Properties
+
+ 		+
+ + + + + + + + + + + + + +
content: + + complex
minOccurs: + + 0
maxOccurs: + + unbounded
+
+
Modelvamsas:local , vamsas:mapped , vamsas:Provenance
Childrenvamsas: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
+
+ 		+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
idxs:IDoptional +
+
locxs:IDREFrequired +
+ + + + + 
Object on which the local
+range is defined.
+
+
mapxs:IDREFrequired +
+ + + + + 
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:DataSet/vamsas:DataSetAnnotations
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
Typeextension 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
Childrenvamsas: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
+
+ 		+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
groupxs:stringoptional +
+ + + + + 
Annotation with the same non-empty group name are grouped
+together
+
+
idxs:IDoptional +
+ + + + + 
Primary Key for vamsas object referencing
+
+
modifiablevamsas:locksoptional +
+
seqRefxs:IDREFSrequired +
+ + + + + 
annotation is associated with a
+particular dataset sequence
+
+
typexs:stringrequired +
+ + + + + 
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:rangeAnnotation/vamsas:label
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:rangeAnnotation/vamsas:description
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+
Annotations
+
+ 		+
+
+ + + + + 
Human readable description of the annotation
+
+
+
+
Diagram
+
+ 		+
Diagram
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:rangeAnnotation/vamsas:status
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:annotationElement
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
+ 		+ +
Modelvamsas:description{0,1} , vamsas:glyph* , vamsas:value*
Childrenvamsas: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
+
+ 		+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
afterxs:booleanfalseoptional +
+ + + + + 
true means the annotation element appears between the
+specified position and the next
+
+
idxs:IDoptional +
+ + + + + 
Primary Key for vamsas object referencing
+
+
positionxs:integerrequired +
+ + + + + 
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:annotationElement/vamsas:description
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+
Annotations
+
+ 		+
+
+ + + + + 
Free text at this position
+
+
+
+
Diagram
+
+ 		+
Diagram
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:annotationElement/vamsas:glyph
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+
Annotations
+
+ 		+
+
+ + + + + 
Discrete symbol - possibly graphically represented
+
+
+
+
Diagram
+
+ 		+
Diagram + vamsasDocument1.tmp#id87
+
Typeextension of xs:string
+
Properties
+
+ 		+
+ + + + + + + + + + + + + +
content: + + complex
minOccurs: + + 0
maxOccurs: + + unbounded
+
+
+
Attributes
+
+ 		+
+ + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
dictxs:stringutf8optional +
+ + + + + 
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:annotationElement/vamsas:value
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:rangeAnnotation/vamsas:score
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
Typeextension of xs:float
+
Properties
+
+ 		+
+ + + + + + + + + + + + + +
content: + + complex
minOccurs: + + 0
maxOccurs: + + unbounded
+
+
+
Attributes
+
+ 		+
+ + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
namexs:stringscoreoptional +
+
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:DataSet/vamsas:Alignment
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
+
Modelvamsas:AlignmentAnnotation* , vamsas:Tree* , vamsas:alignmentSequence+ , vamsas:property* , vamsas:Provenance
Childrenvamsas: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
+
+ 		+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
alignedxs:booleanoptional +
+
gapCharxs:stringrequired +
+
idxs:IDoptional +
+ + + + + 
Primary Key for vamsas object referencing
+
+
modifiablevamsas:locksoptional +
+
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:Alignment/vamsas:DataSet/vamsas:AlignmentAnnotation
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
Typeextension 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
Childrenvamsas: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
+
+ 		+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
graphxs:booleanrequired +
+ + + + + 
TODO: decide if this flag is
+redundant - when true it would suggest that
+the annotationElement values together form a
+graph
+
+
groupxs:stringoptional +
+ + + + + 
Annotation with the same non-empty group name are grouped
+together
+
+
idxs:IDoptional +
+ + + + + 
Primary Key for vamsas object referencing
+
+
modifiablevamsas:locksoptional +
+
seqrefsxs:IDREFSoptional +
+ + + + + 
annotation is associated with
+a range on a particular group of alignment
+sequences
+
+
typexs:stringrequired +
+ + + + + 
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:Alignment/vamsas:DataSet/vamsas:alignmentSequence
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
Typeextension of vamsas:SequenceType
Type hierarchy + +
+
Properties
+
+ 		+
+ + + + + + + + + +
content: + + complex
maxOccurs: + + unbounded
+
+
Modelvamsas:sequence , vamsas:name , vamsas:description{0,1} , vamsas:property* , vamsas:AlignmentSequenceAnnotation*
Childrenvamsas: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
+
+ 		+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
endxs:integerrequired +
+
idxs:IDoptional +
+ + + + + 
Primary Key for vamsas object
+referencing
+
+
refidxs:IDREFrequired +
+ + + + + 
Dataset Sequence from which
+this alignment sequence is taken from
+
+
startxs:integerrequired +
+
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:alignmentSequence/vamsas:Alignment/vamsas:DataSet/vamsas:AlignmentSequenceAnnotation
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
Typeextension 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
Childrenvamsas: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
+
+ 		+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
graphxs:booleanrequired +
+ + + + + 
TODO:
+decide if this flag is
+redundant - when true it
+would suggest that the
+annotationElement values
+together form a graph
+
+
groupxs:stringoptional +
+ + + + + 
Annotation with the same non-empty group name are grouped
+together
+
+
idxs:IDoptional +
+ + + + + 
Primary Key for vamsas object referencing
+
+
modifiablevamsas:locksoptional +
+
typexs:stringrequired +
+ + + + + 
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:ApplicationData
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
Typeextension of vamsas:appData
Type hierarchy + +
+
Properties
+
+ 		+
+ + + + + +
content: + + complex
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vdoc:VamsasDocument
+
+
Model(vamsas:data | vamsas:dataReference) , vamsas:User* , vamsas:Common{0,1} , vamsas:Instance*
Childrenvamsas: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
+
+ 		+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
namexs:stringrequired +
+ + + + + 
Canonical name of application
+
+
versionxs:stringrequired +
+ + + + + 
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:appData/vamsas:data
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+
Diagram
+
+ 		+
Diagram
+
Typexs:base64Binary
+
Properties
+
+ 		+
+ + + + + +
content: + + simple
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:element name="data" type="xs:base64Binary"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:appData/vamsas:dataReference
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+
Diagram
+
+ 		+
Diagram
+
Typexs:string
+
Properties
+
+ 		+
+ + + + + +
content: + + simple
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:element name="dataReference" type="xs:string"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:ApplicationData/vamsas:User
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
Typeextension of vamsas:appData
Type hierarchy + +
+
Properties
+
+ 		+
+ + + + + + + + + + + + + +
content: + + complex
minOccurs: + + 0
maxOccurs: + + unbounded
+
+
Modelvamsas:data | vamsas:dataReference
Childrenvamsas:data, vamsas:dataReference
+
Instance
+
+ 		+
+ + + + + 
<vamsas:User fullname="" organization="">
+  <vamsas:data>{1,1}</vamsas:data>
+  <vamsas:dataReference>{1,1}</vamsas:dataReference>
+</vamsas:User>
+
+
+
Attributes
+
+ 		+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
fullnamexs:stringrequired +
+
organizationxs:stringrequired +
+
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:ApplicationData/vamsas:Common
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+
Diagram
+
+ 		+
Diagram + vamsasDocument1.tmp#id117 + vamsasDocument1.tmp#id118 + vamsasDocument1.tmp#id116
+
Typeextension of vamsas:appData
Type hierarchy + +
+
Properties
+
+ 		+
+ + + + + + + + + +
content: + + complex
minOccurs: + + 0
+
+
Modelvamsas:data | vamsas:dataReference
Childrenvamsas: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:ApplicationData/vamsas:Instance
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+
Diagram
+
+ 		+
Diagram + vamsasDocument1.tmp#id117 + vamsasDocument1.tmp#id118 + vamsasDocument1.tmp#id116 + vamsasDocument1.tmp#id124
+
Typeextension of vamsas:appData
Type hierarchy + +
+
Properties
+
+ 		+
+ + + + + + + + + + + + + +
content: + + complex
minOccurs: + + 0
maxOccurs: + + unbounded
+
+
Modelvamsas:data | vamsas:dataReference
Childrenvamsas:data, vamsas:dataReference
+
Instance
+
+ 		+
+ + + + + 
<vamsas:Instance urn="">
+  <vamsas:data>{1,1}</vamsas:data>
+  <vamsas:dataReference>{1,1}</vamsas:dataReference>
+</vamsas:Instance>
+
+
+
Attributes
+
+ 		+
+ + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
urnxs:stringrequired +
+
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Element vamsas:Attachment
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
Typeextension of vamsas:appData
Type hierarchy + +
+
Properties
+
+ 		+
+ + + + + +
content: + + complex
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vdoc:VamsasDocument
+
+
Modelvamsas:data | vamsas:dataReference
Childrenvamsas: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
+
+ 		+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
compressedxs:booleanfalseoptional +
+ + + + + 
true implies data will be decompresses with Zip
+before presenting to application
+
+
idxs:IDoptional +
+ + + + + 
Primary Key for vamsas object referencing
+
+
objectrefxs:IDREFrequired +
+ + + + + 
Object the arbitrary data is associated with
+
+
typexs:stringrequired +
+ + + + + 
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Complex Type vamsas:rangeType
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
+ 		+
+ + + + + + + + + +
Element vamsas:input
Complex Types vamsas:mapRangeType, vamsas:rangeAnnotation
+
+
Modelvamsas:pos+ | vamsas:seg+
Childrenvamsas: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Simple Type vamsas:locks
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Complex Type vamsas:nodeType
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
+ 		+
+ + + + + +
Element vamsas:Tree/vamsas:treenode
+
+
Modelvamsas:name{0,1} , vamsas:description{0,1} , vamsas:vref* , vamsas:property*
Childrenvamsas:description, vamsas:name, vamsas:property, vamsas:vref
+
Attributes
+
+ 		+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
idxs:IDoptional +
+ + + + + 
Primary Key for vamsas object referencing
+
+
modifiablevamsas:locksoptional +
+
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Complex Type vamsas:referenceType
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
Typeextension of xs:string
+
Used by
+
+ 		+ +
+
Attributes
+
+ 		+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
idxs:IDoptional +
+ + + + + 
Primary Key for vamsas object referencing
+
+
refsxs:IDREFSoptional +
+ + + + + 
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Complex Type vamsas:SequenceType
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
+ 		+ +
Modelvamsas:sequence , vamsas:name , vamsas:description{0,1} , vamsas:property*
Childrenvamsas:description, vamsas:name, vamsas:property, vamsas:sequence
+
Attributes
+
+ 		+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
endxs:integerrequired +
+
startxs:integerrequired +
+
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Complex Type vamsas:mapType
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
+ 		+ +
Modelvamsas:local , vamsas:mapped
Childrenvamsas: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Complex Type vamsas:mapRangeType
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+
Diagram
+
+ 		+
Diagram + vamsasDocument1.tmp#id19 + vamsasDocument1.tmp#id21 + vamsasDocument1.tmp#id18 + vamsasDocument1.tmp#id63
+
Typeextension of vamsas:rangeType
Type hierarchy + +
+
Used by
+
+ 		+ +
Modelvamsas:pos+ | vamsas:seg+
Childrenvamsas:pos, vamsas:seg
+
Attributes
+
+ 		+
+ + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
unitxs:positiveIntegeroptional +
+ + + + + 
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Complex Type vamsas:rangeAnnotation
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://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
+
Typeextension 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*
Childrenvamsas:annotationElement, vamsas:description, vamsas:label, vamsas:link, vamsas:pos, vamsas:property, vamsas:score, vamsas:seg, vamsas:status
+
Attributes
+
+ 		+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeFixedDefaultUseAnnotation
groupxs:stringoptional +
+ + + + + 
Annotation with the same non-empty group name are grouped
+together
+
+
idxs:IDoptional +
+ + + + + 
Primary Key for vamsas object referencing
+
+
modifiablevamsas:locksoptional +
+
typexs:stringrequired +
+ + + + + 
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Complex Type vamsas:appData
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+
Diagram
+
+ 		+
Diagram + vamsasDocument1.tmp#id117 + vamsasDocument1.tmp#id118
+
+
Used by
+
+ 		+ +
Modelvamsas:data | vamsas:dataReference
Childrenvamsas: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:property/@name
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:string
+
Properties
+
+ 		+
+ + + + + +
use: + + required
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:property
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:attribute name="name" type="xs:string" use="required"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:property/@type
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo 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
+
+
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:param/@name
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:string
+
Properties
+
+ 		+
+ + + + + +
use: + + required
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:param
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:attribute name="name" type="xs:string" use="required"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:param/@type
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo 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
+
+
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:pos/vamsas:rangeType/@i
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:int
+
Properties
+
+ 		+
+ + + + + +
use: + + required
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:rangeType/vamsas:pos
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:attribute name="i" type="xs:int" use="required"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:seg/vamsas:rangeType/@start
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:int
+
Properties
+
+ 		+
+ + + + + +
use: + + required
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:rangeType/vamsas:seg
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:attribute name="start" type="xs:int" use="required"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:seg/vamsas:rangeType/@end
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:int
+
Properties
+
+ 		+
+ + + + + +
use: + + required
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:rangeType/vamsas:seg
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:attribute name="end" type="xs:int" use="required"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:seg/vamsas:rangeType/@inclusive
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
when false, a consecutive range like 'start=1, end=2'
+means the region lying after position 1 and before position 2
+
+
+
Typexs:boolean
+
Properties
+
+ 		+
+ + + + + +
use: + + required
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:rangeType/vamsas:seg
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:input/@name
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:string
+
Properties
+
+ 		+
+ + + + + +
use: + + required
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:input
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:attribute name="name" type="xs:string" use="required"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:input/@objRef
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
Reference Frame for rangeType specfication
+
+
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:entry/vamsas:Provenance/@id
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
Primary Key for vamsas object referencing
+
+
+
Typexs:ID
+
Properties
+
+ 		+
+ + + + + +
use: + + optional
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:Provenance/vamsas:entry
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:newick/vamsas:Tree/@title
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:string
+
Properties
+
+ 		+
+ + + + + +
use: + + optional
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:Tree/vamsas:newick
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:attribute name="title" type="xs:string" use="optional"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:newick/vamsas:Tree/@id
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
Primary Key for vamsas object referencing
+
+
+
Typexs:ID
+
Properties
+
+ 		+
+ + + + + +
use: + + optional
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:Tree/vamsas:newick
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:newick/vamsas:Tree/@modifiable
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typevamsas:locks
+
Properties
+
+ 		+
+ + + + + +
use: + + optional
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:Tree/vamsas:newick
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:referenceType/@id
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
Primary Key for vamsas object referencing
+
+
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:referenceType/@refs
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
List of one or more vamsas object
+references
+
+
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:nodeType/@id
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
Primary Key for vamsas object referencing
+
+
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:nodeType/@modifiable
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typevamsas:locks
+
Properties
+
+ 		+
+ + + + + +
use: + + optional
+
+
+
Used by
+
+ 		+
+ + + + + +
Complex Type vamsas:nodeType
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:treenode/vamsas:Tree/@treeId
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
reference to one or more trees containing
+the node being described.
+
+
+
Typexs:IDREFS
+
Properties
+
+ 		+
+ + + + + +
content: + + simple
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:Tree/vamsas:treenode
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:treenode/vamsas:Tree/@nodespec
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
String uniquely identifying a particular
+node in the referenced tree according to the format of
+the tree representation that is referenced.
+
+
+
Typexs:string
+
Properties
+
+ 		+
+ + + + + +
content: + + simple
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:Tree/vamsas:treenode
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:Tree/@id
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
Primary Key for vamsas object referencing
+
+
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:Tree/@modifiable
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typevamsas:locks
+
Properties
+
+ 		+
+ + + + + +
use: + + optional
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:Tree
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:SequenceType/@start
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:integer
+
Properties
+
+ 		+
+ + + + + +
use: + + required
+
+
+
Used by
+
+ 		+
+ + + + + +
Complex Type vamsas:SequenceType
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:attribute name="start" type="xs:integer" use="required"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:SequenceType/@end
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:integer
+
Properties
+
+ 		+
+ + + + + +
use: + + required
+
+
+
Used by
+
+ 		+
+ + + + + +
Complex Type vamsas:SequenceType
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:attribute name="end" type="xs:integer" use="required"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:mapRangeType/@unit
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo 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.
+
+
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:map/vamsas:dbRef/vamsas:Sequence/vamsas:DataSet/@id
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:ID
+
Properties
+
+ 		+
+ + + + + +
content: + + simple
+
+
+
Used by
+
+ 		+ +
+
Source
+
+ 		+
+ + + + + 
<xs:attribute name="id" type="xs:ID"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:link/@href
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
The URI
+
+
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:dbRef/vamsas:Sequence/vamsas:DataSet/@source
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
TODO Database Naming
+Convention: either start using LSID (so
+change type to URI) or leave this as an
+uncontrolled/unspecified string ID
+
+
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:dbRef/vamsas:Sequence/vamsas:DataSet/@version
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
Version must be specified -
+
+
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:dbRef/vamsas:Sequence/vamsas:DataSet/@accessionId
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo 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 ?
+
+
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:dbRef/vamsas:Sequence/vamsas:DataSet/@id
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
Primary Key for vamsas object
+referencing
+
+
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:Sequence/vamsas:DataSet/@id
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
Primary Key for vamsas object referencing
+
+
+
Typexs:ID
+
Properties
+
+ 		+
+ + + + + +
use: + + optional
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:DataSet/vamsas:Sequence
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:Sequence/vamsas:DataSet/@dictionary
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
symbol class for sequence
+
+
+
Typexs:string
+
Properties
+
+ 		+
+ + + + + +
use: + + required
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:DataSet/vamsas:Sequence
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:sequenceMapping/vamsas:DataSet/@loc
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
Object on which the local
+range is defined.
+
+
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:sequenceMapping/vamsas:DataSet/@map
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
Object on which the mapped
+range is defined.
+
+
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:sequenceMapping/vamsas:DataSet/@id
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:ID
+
Properties
+
+ 		+
+ + + + + +
use: + + optional
+
+
+
Used by
+
+ 		+ +
+
Source
+
+ 		+
+ + + + + 
<xs:attribute name="id" type="xs:ID" use="optional"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:glyph/vamsas:annotationElement/@dict
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo 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
+
+
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:annotationElement/@position
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
position with respect to the coordinate frame defined by a
+rangeType specification
+
+
+
Typexs:integer
+
Properties
+
+ 		+
+ + + + + +
use: + + required
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:annotationElement
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:annotationElement/@after
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
true means the annotation element appears between the
+specified position and the next
+
+
+
Typexs:boolean
+
Properties
+
+ 		+
+ + + + + + + + + +
use: + + optional
default: + + false
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:annotationElement
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:annotationElement/@id
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
Primary Key for vamsas object referencing
+
+
+
Typexs:ID
+
Properties
+
+ 		+
+ + + + + +
use: + + optional
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:annotationElement
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:score/vamsas:rangeAnnotation/@name
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:string
+
Properties
+
+ 		+
+ + + + + + + + + +
use: + + optional
default: + + score
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:rangeAnnotation/vamsas:score
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:attribute name="name" type="xs:string" use="optional" default="score"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:rangeAnnotation/@id
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
Primary Key for vamsas object referencing
+
+
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:rangeAnnotation/@modifiable
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typevamsas:locks
+
Properties
+
+ 		+
+ + + + + +
use: + + optional
+
+
+
Used by
+
+ 		+
+ + + + + +
Complex Type vamsas:rangeAnnotation
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:rangeAnnotation/@group
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
Annotation with the same non-empty group name are grouped
+together
+
+
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:rangeAnnotation/@type
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo 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
+
+
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:DataSetAnnotations/vamsas:DataSet/@seqRef
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
annotation is associated with a
+particular dataset sequence
+
+
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:AlignmentAnnotation/vamsas:Alignment/vamsas:DataSet/@graph
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
TODO: decide if this flag is
+redundant - when true it would suggest that
+the annotationElement values together form a
+graph
+
+
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:AlignmentAnnotation/vamsas:Alignment/vamsas:DataSet/@seqrefs
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
annotation is associated with
+a range on a particular group of alignment
+sequences
+
+
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:AlignmentSequenceAnnotation/vamsas:alignmentSequence/vamsas:Alignment/vamsas:DataSet/@graph
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
TODO:
+decide if this flag is
+redundant - when true it
+would suggest that the
+annotationElement values
+together form a graph
+
+
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:alignmentSequence/vamsas:Alignment/vamsas:DataSet/@id
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
Primary Key for vamsas object
+referencing
+
+
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:alignmentSequence/vamsas:Alignment/vamsas:DataSet/@refid
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
Dataset Sequence from which
+this alignment sequence is taken from
+
+
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:Alignment/vamsas:DataSet/@gapChar
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:string
+
Properties
+
+ 		+
+ + + + + +
use: + + required
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:DataSet/vamsas:Alignment
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:attribute name="gapChar" type="xs:string" use="required"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:Alignment/vamsas:DataSet/@aligned
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:boolean
+
Properties
+
+ 		+
+ + + + + +
use: + + optional
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:DataSet/vamsas:Alignment
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:attribute name="aligned" type="xs:boolean" use="optional"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:Alignment/vamsas:DataSet/@id
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
Primary Key for vamsas object referencing
+
+
+
Typexs:ID
+
Properties
+
+ 		+
+ + + + + +
use: + + optional
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:DataSet/vamsas:Alignment
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:Alignment/vamsas:DataSet/@modifiable
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typevamsas:locks
+
Properties
+
+ 		+
+ + + + + +
use: + + optional
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:DataSet/vamsas:Alignment
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:DataSet/@id
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
Primary Key for vamsas object referencing
+
+
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:VAMSAS/@id
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
Primary Key for vamsas object referencing
+
+
+
Typexs: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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:VAMSAS/@modifiable
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typevamsas:locks
+
Properties
+
+ 		+
+ + + + + +
use: + + optional
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:VAMSAS
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:User/vamsas:ApplicationData/@fullname
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:string
+
Properties
+
+ 		+
+ + + + + +
use: + + required
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:ApplicationData/vamsas:User
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:attribute name="fullname" type="xs:string" use="required"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:User/vamsas:ApplicationData/@organization
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:string
+
Properties
+
+ 		+
+ + + + + +
use: + + required
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:ApplicationData/vamsas:User
+
+
+
Source
+
+ 		+
+ + + + + 
<xs:attribute name="organization" type="xs:string" use="required"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:Instance/vamsas:ApplicationData/@urn
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:string
+
Properties
+
+ 		+
+ + + + + +
use: + + required
+
+
+
Used by
+
+ 		+ +
+
Source
+
+ 		+
+ + + + + 
<xs:attribute name="urn" type="xs:string" use="required"/>
+
+
Schema locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:ApplicationData/@version
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
Version string describing the application specific
+data storage version used
+
+
+
Typexs:string
+
Properties
+
+ 		+
+ + + + + +
use: + + required
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:ApplicationData
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:ApplicationData/@name
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
Canonical name of application
+
+
+
Typexs:string
+
Properties
+
+ 		+
+ + + + + +
use: + + required
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:ApplicationData
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:Attachment/@compressed
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
true implies data will be decompresses with Zip
+before presenting to application
+
+
+
Typexs:boolean
+
Properties
+
+ 		+
+ + + + + + + + + +
use: + + optional
default: + + false
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:Attachment
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:Attachment/@type
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
Type of arbitrary data - TODO: decide format - use
+(extended) MIME types ?
+
+
+
Typexs:string
+
Properties
+
+ 		+
+ + + + + +
use: + + required
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:Attachment
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:Attachment/@objectref
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
Object the arbitrary data is associated with
+
+
+
Typexs:IDREF
+
Properties
+
+ 		+
+ + + + + +
use: + + required
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:Attachment
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
Attribute vamsas:Attachment/@id
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
+
Annotations
+
+ 		+
+
+ + + + + 
Primary Key for vamsas object referencing
+
+
+
Typexs:ID
+
Properties
+
+ 		+
+ + + + + +
use: + + optional
+
+
+
Used by
+
+ 		+
+ + + + + +
Element vamsas:Attachment
+
+
+
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 locationfile:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
+
+
+
+
XML Schema documentation generated by ® XML Editor. +
+
+ \ No newline at end of file diff --git a/docs/schema/xsdDocHtml.css b/docs/schema/xsdDocHtml.css new file mode 100644 index 0000000..da6c217 --- /dev/null +++ b/docs/schema/xsdDocHtml.css @@ -0,0 +1,555 @@ +/*---------------------------------------- + Global +-----------------------------------------*/ + +body{ +} +body, table { + font-family:arial, helvetica, sans-serif; + font-size:12px; +} + +@media print{ + body, table { + font-size:10px; + } +} + +/*-------------------------------------------- + Source code in the instance, source or + annotations. +--------------------------------------------*/ +span.tokenElement { + color: #000096; + background-color:inherit; +} +span.tokenAttrName { + color: #F5844C; + background-color:inherit; +} +span.tokenAttrValue { + color: #993300; + background-color:inherit; +} +span.tokenIndent { + color: #000000; + background-color:inherit; +} +span.tokenText { + white-space:normal; + color: #000000; + background-color:inherit; +} +span.tokenComment { + color: #006400; + background-color:inherit; +} +span.tokenCDATA { + color: #008C00; + background-color:inherit; +} +span.tokenPI { + color: #8B26C9; + background-color:inherit; +} +span.tokenEntity { + color: #969600; + background-color:inherit; +} +span.qname{ + color:#000096; + background-color:inherit; +} + +/*----------------------------------------- + Documentation sections. +------------------------------------------*/ + +div.componentTitle { + font-size:1.4em; + font-weight:bold; + text-align:left; + margin-top:1.4em; + margin-bottom:0.7em; +} +div.componentTitle{ +/* color:rgb(255, 160, 100);*/ + color:#333333; + background-color:inherit; +} + + +/* Tables. */ + +td, th { + padding:2px 2px 2px 5px; + text-align:left; + vertical-align:top; +} + +tr > th { + background-color:#C4DAF4; + color:inherit; +} + +/* Contrast for the titles*/ +table.component { + width:100%; + border-spacing:1px; +} + +@media print{ + table.component{ + border:1px solid gray; + border-collapse:collapse; + } + + table.component td{ + border:1px solid gray; + } +} + + + +table.component td.firstColumn{ +/* pink */ + /*background-color:#FFC0C0;*/ +/*green */ + /* background-color:#C0F0A0;*/ +/*bleu*/ + /*background-color:#89C6E2;*/ +/*orange*/ + /*background-color:#FFD697;*/ +/*brown*/ + /*background-color:#D5BC8E;*/ +/*lilla*/ + /*background-color:#DDDDFF;*/ +/*gray-bleu*/ + /*background-color:#CAD0DD;*/ +/*brown-light*/ + /*background-color:#DECFB8;*/ +/*gray-green*/ + /*background-color:#C6D0CD;*/ +/*bleu-2*/ + /*background-color:#B5D5FF;*/ +/*gray*/ + /*background-color:#CCCCCC;*/ + + +/*bleu */ +background-color:#C4DAF4; + + + + color:black; + width:12%; +} + +table.component table td.firstColumn{ + border:none; + background-color:#EAF1FB; + color: inherit; +} + +td.firstColumn b{ + font-weight:normal; +} + + +/* The Name and Expand/Collapse control are on the same line + but at different ends.*/ +td.firstColumn div.floatLeft{ + float:left; +} +td.firstColumn div.floatRight{ + float:right; +} + +/* Subtables */ +table.component table{ + width:100%; +} +table.component table, +table.component table td, +table.component table th{ + border:0; +} + + +/* Properties table */ +table.propertiesTable { + border-spacing:1px; +} +table.propertiesTable td.firstColumn{ + width:140px; + text-transform:capitalize; +} +/* Used by table */ +table.usedByTable { + border-spacing:1px; +} +table.usedByTable td.firstColumn{ + width:140px; + text-transform:capitalize; +} + +/* Facets table*/ +table.facetsTable { + border-spacing:1px; +} +table.facetsTable td.firstColumn{ + width:140px; + text-transform:capitalize; +} + +/* Attributes table */ +table.attributesTable { + border-spacing:1px; +} +table.attributesTable th{ + font-weight:normal; +} +table.attributesTable tr:hover{ + color:inherit; + background-color:#EAF1FB; +} + + +/* Identity constraints table */ +table.identityConstraintsTable { + border-spacing:1px; +} +table.identityConstraintsTable th{ + font-weight:normal; +} +table.identityConstraintsTable tr:hover{ + color:inherit; + background-color:#EAF1FB; +} + + + +/*--------------------------------------- + The diagram. +----------------------------------------*/ + +table.component td.diagram { + background-color:white; + color:inherit; +} + + +/* This table is a workaround for an IE bug regarding pre-wrap */ +table.preWrapContainer, +table.preWrapContainer td{ + border:0; + margin:0; + padding:0; +} + + +/* Annotations. */ +div.annotation{ +} +div.annotation pre{ + font-family:arial, helvetica, sans-serif; + margin:0; +} +div.annotation, +div.annotation table, +div.annotation table td{ + margin:0; + padding:0; +} + +/* Hierarchy */ +ul > li{ + list-style:none; +} + +ul { + margin:2px; + padding:0; +} + +ul ul li { + padding-left:10px; + + list-style-image:url('images/hierarchy_arrow.gif'); + list-style-position:inside; +} + +/*------------------------------------- + Rounded tables. +---------------------------------------*/ + +table.rt, +table.rt_with_bg{ + border-collapse:collapse; + border-spacing:0; + width:100%; +} +table.rt_with_bg{ + /*background-color:#C0F0A0;*/ + background-color:white; + color:inherit; +} + + +.rt_cornerTopLeft{ + background-color:transparent; + background-repeat:no-repeat; + background-position:right; + width:8px; + height:8px; + margin:0; + padding:0; +} +.rt_cornerTopLeft{ + background-image:url('images/corner_top_left.gif'); +} + + +.rt_cornerBottomLeft{ + background-color:transparent; + background-repeat:no-repeat; + background-position:right; + width:8px; + height:8px; + margin:0; + padding:0; +} +.rt_cornerBottomLeft{ + background-image:url('images/corner_bottom_left.gif'); +} + + +.rt_cornerTopRight{ + background-color:transparent; + background-repeat:no-repeat; + width:8px; + height:8px; + margin:0; + padding:0; + +} +.rt_cornerTopRight{ + background-image:url('images/corner_top_right.gif'); +} + + +.rt_cornerBottomRight{ + background-color:transparent; + background-repeat:no-repeat; + width:8px; + height:8px; + margin:0; + padding:0; + +} +.rt_cornerBottomRight{ + background-image:url('images/corner_bottom_right.gif'); +} + + +.rt_content{ + background-color:white; + color:inherit; + width:auto; + margin:0; + padding:0; +} + + +.rt_lineLeft{ + background-color:transparent; + background-repeat:repeat-y; + background-position:right; + width:8px; + margin:0; + padding:0; + +} +.rt_lineLeft{ + background-image:url('images/line_left.gif'); +} + + +.rt_lineRight{ + background-repeat:repeat-y; + width:8px; + margin:0; + padding:0; +} +.rt_lineRight{ + background-image:url('images/line_right.gif'); +} + + +.rt_lineTop{ + background-color:transparent; + background-repeat:repeat-x; + height:8px; + width:auto; + margin:0; + padding:0; +} +.rt_lineTop{ + background-image:url('images/line_top.gif'); +} + +.rt_lineBottom{ + background-color:transparent; + background-repeat:repeat-x; + height:8px; + width:auto; + margin:0; + padding:0; +} +.rt_lineBottom{ + background-image:url('images/line_bottom.gif'); +} + + +/* -------------------------------------- + Controls for bulk showing/hidding sections + from the documentation. +----------------------------------------*/ + +.globalControls h3{ + margin:0.1em; + font-size:1.2em; +} + +.globalControls table td{ + padding:0; + margin:0; +} + +.globalControls{ + position:fixed; + right:0; + background-color:transparent; + padding-left:0.5em; + padding-right:0.5em; + padding-bottom:0.5em; + width:190px; +} + +@media print{ + .globalControls{ + display:none; + } +} + +/* Expand/collapse of a single section. */ +input.control { + text-align:center; + vertical-align:middle; + padding:0; + padding-right:3px; + padding-bottom:2px; + +} + + +/* close button */ +td.rt_content div span input{ + font-size:0.8em; +} + +@media print{ + input.control{ + display:none; + } +} + + + + +/*----------------------------------------- + Navigation. +------------------------------------------*/ +a, a:visited { + color:rgb(0, 0, 150); + background-color:inherit; +} + +a:link, a:visited { + text-decoration:none; +} +a:hover { + text-decoration:underline; +} + +div.toTop{ + text-align:right; +} +div.toTop a{ + font-weight:normal; +} + + + + +/*------------------------------------------ + The second level of index. Floating DIVs +-------------------------------------------*/ +.toc { +} +.toc div.verticalLayout, div.horizontalLayout{ + float:left; + display:block; + + background-color:white; + color:inherit; + + min-width:130px; + min-height:50px; + + padding:0.5em; +} +/* This is not used. */ +.toc div.verticalLayout { + clear:left; +} + +/* Hack for the IE - acts like a minimum height.*/ +* html .toc div.horizontalLayout, +* html .toc div.verticalLayout { + width:120px; + height:60px; +} + +.toc div.componentGroupTitle{ + font-weight:bold; + margin-bottom:0.5em; + color:black; + background-color:inherit; +} + +/* Namespacces or system ids in the TOC. */ +.toc .indexGroupTitle { + font-weight:bold; + margin-bottom:0.5em; +} + +/*---------------- + The footer. +-----------------*/ +.footer{ + margin-top:3em; +} +.redX{ + color:red; + background-color:inherit; + font-size:1.2em; +} +.oXygenLogo{ + color:#1166DD; + background-color:inherit; + font-weight:bold; + font-size:1.2em; +} + +