renamed.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@39 be28352e-c001-0410-b1a7-c7978e42abec

diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
new file mode 100644 (file)
index 0000000..dd12108
--- /dev/null
+++ b/schemas/vamsas.xsd
@@ -0,0 +1,179 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- edited with XMLSPY v5 rel. 4 U (http://www.xmlspy.com) by MSD (EMBL OUTSTATION THE EBI WELLCOME TRUST GENOME CAMPUS) -->
+<!-- edited with XMLSpy v2005 rel. 3 U (http://www.altova.com) by lj (jl) -->
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="http://www.vamsas.org" targetNamespace="http://www.vamsas.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
+       <xs:element name="Version" type="xs:string"/>
+       <xs:complexType name="LockFile">
+               <xs:simpleContent>
+                       <xs:extension base="xs:string"/>
+               </xs:simpleContent>
+       </xs:complexType>
+       <xs:complexType name="VAMSAS">
+               <xs:sequence>
+                       <xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
+                       <xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
+               </xs:sequence>
+               <xs:attribute name="id" type="xs:ID"  minOccurs="0" maxOccurs="1"/>
+    </xs:complexType>
+    <xs:element name="Tree">
+               <xs:complexType>
+               <xs:sequence>
+                       <xs:element name="title" type="xs:string" minOccurs="0" maxOccurs="1"/>
+                       <xs:element name="newick" minOccurs="1" maxOccurs="unbounded">
+                         <xs:complexType>
+                         <xs:simpleContent>
+                         <xs:extension base="xs:string">
+                         <xs:attribute name="title" type="xs:string" minOccurs="0" maxOccurs="1"/>
+                         <xs:attribute name="id" type="xs:ID" minOccurs="0" maxOccurs="1"/>
+                         </xs:extension>
+                         </xs:simpleContent>
+                         </xs:complexType>
+                       </xs:element>
+                       <xs:element ref="vamsas:Provenance" minOccurs="1" maxOccurs="1"/>
+                   </xs:sequence>
+               <xs:attribute name="id" type="xs:ID" minOccurs="0" maxOccurs="1"/>
+       </xs:complexType>
+       </xs:element>
+       <xs:element name="Provenance">
+               <xs:complexType>
+                       <xs:sequence>
+                               <xs:element name="entry" minOccurs="0" maxOccurs="unbounded">
+                                       <xs:complexType>
+                                               <xs:sequence>
+                                                       <xs:element name="User" type="xs:string"/>
+                                                       <xs:element name="Action" type="xs:string"/>
+                                                       <xs:element name="Date" type="xs:date"/>
+                                               </xs:sequence>
+                                               <xs:attribute name="id" type="xs:ID"  minOccurs="0" maxOccurs="1"/>
+                                       </xs:complexType>
+                               </xs:element>
+                       </xs:sequence>
+               </xs:complexType>
+       </xs:element>
+
+       <xs:element name="SequenceSet">
+               <xs:complexType>
+                       <xs:sequence>
+                               <xs:element name="Sequence" maxOccurs="unbounded">
+                                       <xs:complexType>
+                                               <xs:complexContent>
+                                                       <xs:extension base="vamsas:SequenceType">
+                                                               <xs:sequence>
+                                                                   <xs:element name="dbRef" minOccurs="0" maxOccurs="unbounded">
+                                                                       <xs:complexType>
+                                                                               <xs:attribute name="source"/>
+                                                                               <xs:attribute name="version"/>
+                                                                               <xs:attribute name="accessionId"/>
+                                                                               <xs:attribute name="id" type="xs:ID" minOccurs="0" maxOccurs="1"/>
+                                                                       </xs:complexType>
+                                                                       </xs:element>
+                                                               </xs:sequence>
+                                                               <xs:attribute name="id" type="xs:ID" minOccurs="1" maxOccurs="1"/>
+                                                               <xs:attribute name="dictionary" type="xs:string"/>
+                                                       </xs:extension>
+                                               </xs:complexContent>
+                                       </xs:complexType>
+                               </xs:element>
+                               <xs:element name="SequenceSetAnnotations" minOccurs="0" maxOccurs="unbounded">
+                                       <xs:complexType>
+                                               <xs:sequence>
+                                                       <xs:element name="description" type="xs:string" minOccurs="0"/>
+                                                       <xs:element name="status" type="xs:string" minOccurs="0"/>
+                                                       <xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded"/>
+                                                       <xs:element ref="vamsas:Provenance" minOccurs="0" maxOccurs="unbounded"/>
+                                               </xs:sequence>
+                                               <xs:attribute name="type" type="xs:string" use="required"/>
+                                               <xs:attribute name="end" type="xs:string" use="required"/>
+                                               <xs:attribute name="begin" type="xs:string" use="required"/>
+                                               <xs:attribute name="seqRef" type="xs:IDREF" use="required"/>
+                                               <xs:attribute name="id" type="xs:ID" minOccurs="0" maxOccurs="1"/>
+                                       </xs:complexType>
+                               </xs:element>
+                               <xs:element name="Alignment" minOccurs="0" maxOccurs="unbounded">
+                                       <xs:complexType>
+                                               <xs:sequence>
+                                                       <xs:element name="AlignmentAnnotations" minOccurs="0">
+                                                               <xs:complexType>
+                                                                       <xs:sequence>
+                                                                               <xs:element ref="vamsas:annotationElement" maxOccurs="unbounded"/>
+                                                                               <xs:element name="label" type="xs:string"/>
+                                                                               <xs:element name="description" type="xs:string"/>
+                                                                               <xs:element ref="vamsas:Provenance"/>
+                                                                       </xs:sequence>
+                                                                       <xs:attribute name="graph" type="xs:boolean" use="required"/>
+                                                                       <xs:attribute name="id" type="xs:ID" minOccurs="0" maxOccurs="1"/>
+                                                               </xs:complexType>
+                                                       </xs:element>
+                                                       <xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
+                                                       <xs:element name="alignmentSequence" minOccurs="2" maxOccurs="unbounded">
+                                                               <xs:complexType>
+                                                                       <xs:complexContent>
+                                                                               <xs:extension base="vamsas:SequenceType">
+                                                                                       <xs:attribute name="id" type="xs:ID" minOccurs="0" maxOccurs="1"/>
+                                                                                       <xs:attribute name="refid" type="xs:IDREF" use="required"/>
+                                                                               </xs:extension>
+                                                                       </xs:complexContent>
+                                                               </xs:complexType>
+                                                       </xs:element>
+                                                       <xs:element ref="vamsas:Provenance"/>
+                                               </xs:sequence>
+                                               <xs:attribute name="id" type="xs:ID" minOccurs="0" maxOccurs="1"/>
+                                       </xs:complexType>
+                               </xs:element>
+                               <xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
+                               <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"  minOccurs="0" maxOccurs="1"/>
+               </xs:complexType>
+       </xs:element>
+       <xs:element name="annotationElement">
+               <xs:complexType>
+                       <xs:sequence>
+                               <xs:element name="displayCharacter" type="xs:string"/>
+                               <xs:element name="description" type="xs:string"/>
+                               <xs:element name="secondaryStructure">
+                                       <xs:simpleType>
+                                               <xs:restriction base="xs:string">
+                                                       <xs:length value="1"/>
+                                               </xs:restriction>
+                                       </xs:simpleType>
+                               </xs:element>
+                               <xs:element name="value" type="xs:float"/>
+                       </xs:sequence>
+                       <xs:attribute name="position" type="xs:int" use="required"/>
+                       <xs:attribute name="id" type="xs:ID"  minOccurs="0" maxOccurs="1"/>
+               </xs:complexType>
+       </xs:element>
+    <xs:complexType name="SequenceType">
+               <xs:sequence>
+                       <xs:element name="sequence" type="xs:string"/>
+                       <xs:element name="name" type="xs:string"/>
+               </xs:sequence>
+               <xs:attribute name="start" type="xs:int" use="required"/>
+               <xs:attribute name="end" type="xs:int" use="required"/>
+       </xs:complexType>
+       
+    <xs:complexType name="ApplicationData">
+               <xs:sequence>
+                       <xs:element name="Application">
+                               <xs:complexType>
+                                       <xs:sequence>
+                                         <xs:element name="User">
+                                         <xs:complexType>
+                                               <xs:attribute name="fullname" type="xs:string"/>
+                                               <xs:attribute name="organization" type="xs:string"/>
+                                               <xs:attribute name="data" type="xs:string"/>
+                                         </xs:complexType>
+                                         </xs:element>
+                                       </xs:sequence>
+                                       <xs:attribute name="version" type="xs:string"/>
+                                       <xs:attribute name="name" type="xs:string"/>
+                                       <xs:attribute name="urn" type="xs:string"/>
+                                       <xs:attribute name="data" type="xs:string"/>
+                               </xs:complexType>
+                       </xs:element>
+               </xs:sequence>
+       </xs:complexType>
+</xs:schema>