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

diff --git a/schemas/vamsas15_9.xsd b/schemas/vamsas15_9.xsd
index 1f1011f..787a929 100644 (file)
--- 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>