From 3af890bd709e15615c0b98b2e23a090c21a8eccf Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Mon, 19 Sep 2005 23:26:31 +0000
Subject: [PATCH] tried to resolve some namespace clashes and add xs:ID
 attributes where necessary.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@30 be28352e-c001-0410-b1a7-c7978e42abec
---
 schemas/vamsas15_9.xsd |   52 ++++++++++++++++++++++++++----------------------
 1 file changed, 28 insertions(+), 24 deletions(-)

diff --git a/schemas/vamsas15_9.xsd b/schemas/vamsas15_9.xsd
index 1f1011f..787a929 100644
--- a/schemas/vamsas15_9.xsd
+++ b/schemas/vamsas15_9.xsd
@@ -10,10 +10,12 @@
 	</xs:complexType>
 	<xs:complexType name="VAMSAS">
 		<xs:sequence>
-			<xs:element name="Tree" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
+			<xs:element name="Dendro" type="vamsas:TreeType" minOccurs="0" maxOccurs="unbounded"/>
 			<xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
 		</xs:sequence>
-	</xs:complexType>
+		
+        <xs:attribute name="id" type="xs:ID"/>
+    </xs:complexType>
 	<xs:element name="Provenance">
 		<xs:complexType>
 			<xs:sequence maxOccurs="unbounded">
@@ -24,6 +26,7 @@
 							<xs:element name="Action" type="xs:string"/>
 							<xs:element name="Date" type="xs:date"/>
 						</xs:sequence>
+					<xs:attribute name="id" type="xs:ID"/>
 					</xs:complexType>
 				</xs:element>
 			</xs:sequence>
@@ -37,7 +40,6 @@
 						<xs:complexContent>
 							<xs:extension base="vamsas:SequenceType">
 								<xs:attribute name="dictionary" type="xs:string"/>
-								<xs:attribute name="id" type="xs:ID" use="required"/>
 							</xs:extension>
 						</xs:complexContent>
 					</xs:complexType>
@@ -54,6 +56,7 @@
 						<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"/>
 					</xs:complexType>
 				</xs:element>
 				<xs:element name="Alignment" minOccurs="0" maxOccurs="unbounded">
@@ -68,21 +71,15 @@
 										<xs:element ref="vamsas:Provenance"/>
 									</xs:sequence>
 									<xs:attribute name="graph" type="xs:boolean" use="required"/>
+									<xs:attribute name="id" type="xs:ID"/>
 								</xs:complexType>
 							</xs:element>
-							<xs:element name="tree" minOccurs="0" maxOccurs="unbounded">
-								<xs:complexType>
-									<xs:sequence>
-										<xs:element ref="vamsas:Provenance"/>
-										<xs:element name="newickFormat" type="xs:string"/>
-									</xs:sequence>
-								</xs:complexType>
-							</xs:element>
+							<xs:element name="tree" type="vamsas:TreeType" 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:IDREF" use="required"/>
+											<xs:attribute name="refid" type="xs:IDREF" use="required"/>
 										</xs:extension>
 									</xs:complexContent>
 								</xs:complexType>
@@ -91,18 +88,12 @@
 						</xs:sequence>
 					</xs:complexType>
 				</xs:element>
-				<xs:element name="tree">
-					<xs:complexType>
-						<xs:sequence>
-							<xs:element ref="vamsas:Provenance"/>
-							<xs:element name="newickFormat" type="xs:string"/>
-						</xs:sequence>
-					</xs:complexType>
-				</xs:element>
+				<xs:element name="tree" type="vamsas:TreeType"/>
 				<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"/>
 		</xs:complexType>
 	</xs:element>
 	<xs:element name="annotationElement">
@@ -120,9 +111,10 @@
 				<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"/>
 		</xs:complexType>
 	</xs:element>
-	<xs:complexType name="SequenceType">
+    <xs:complexType name="SequenceType">
 		<xs:sequence>
 			<xs:element name="sequence" type="xs:string"/>
 			<xs:element name="name" type="xs:string"/>
@@ -131,18 +123,30 @@
 					<xs:attribute name="source"/>
 					<xs:attribute name="version"/>
 					<xs:attribute name="accessionId"/>
+					<xs:attribute name="id" type="xs:ID"/>
 				</xs:complexType>
 			</xs:element>
 		</xs:sequence>
 		<xs:attribute name="start" type="xs:int" use="required"/>
 		<xs:attribute name="end" type="xs:int" use="required"/>
+		<xs:attribute name="id" type="xs:ID"/>
 	</xs:complexType>
-	<xs:complexType name="ApplicationData">
+	
+    <xs:complexType name="TreeType">
+        <xs:sequence>
+          <xs:element name="newickFormat" type="xs:string" minOccurs="1" maxOccurs="unbounded"/>
+          <xs:element ref="vamsas:Provenance" minOccurs="1" maxOccurs="1"/>
+        </xs:sequence>
+        <xs:attribute name="id" type="xs:ID"/>
+    </xs:complexType>
+    <xs:complexType name="ApplicationData">
 		<xs:sequence>
 			<xs:element name="Application">
 				<xs:complexType>
-					<xs:attribute name="version"/>
-					<xs:attribute name="name"/>
+					<xs:attribute name="version" type="xs:string"/>
+					<xs:attribute name="name" type="xs:string"/>
+					<xs:attribute name="session" type="xs:string"/>
+					<xs:attribute name="data" type="xs:string"/>
 				</xs:complexType>
 			</xs:element>
 		</xs:sequence>
-- 
1.7.10.2