From 87565aa7a2b8ed181ecf5cf234baf8e9448dc2b6 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Tue, 20 Sep 2005 16:37:09 +0000
Subject: [PATCH] renamed.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@39 be28352e-c001-0410-b1a7-c7978e42abec
---
 schemas/vamsas.xsd |  179 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 179 insertions(+)
 create mode 100644 schemas/vamsas.xsd

diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
new file mode 100644
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>
-- 
1.7.10.2