X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fvamsas.xsd;h=1a0409512f1cd00098ed8dd6ed2400d3f6ce4b49;hb=80acdc052f616d400c7435d26b29162bc0fbb98f;hp=dd12108aafb8dd39b46ea40736a5709f74d3d33c;hpb=87565aa7a2b8ed181ecf5cf234baf8e9448dc2b6;p=vamsas.git

diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
index dd12108..1a04095 100644
--- a/schemas/vamsas.xsd
+++ b/schemas/vamsas.xsd
@@ -2,56 +2,51 @@
 <!-- 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 name="VAMSAS">
+		<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:complexType>
+	</xs:element>
+	<xs:element name="Tree">
+		<xs:complexType>
+			<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:extension>
+						</xs:simpleContent>
+					</xs:complexType>
+				</xs:element>
+				<xs:element ref="vamsas:Provenance"/>
+			</xs:sequence>
+			<xs:attribute name="id" type="xs:ID" use="optional"/>
+		</xs:complexType>
 	</xs:element>
 	<xs:element name="Provenance">
 		<xs:complexType>
 			<xs:sequence>
-				<xs:element name="entry" minOccurs="0" maxOccurs="unbounded">
+				<xs:element name="entry" 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:attribute name="id" type="xs:ID" use="optional"/>
 					</xs:complexType>
 				</xs:element>
 			</xs:sequence>
 		</xs:complexType>
 	</xs:element>
-
-	<xs:element name="SequenceSet">
+	<xs:element name="DataSet">
 		<xs:complexType>
 			<xs:sequence>
 				<xs:element name="Sequence" maxOccurs="unbounded">
@@ -59,40 +54,40 @@
 						<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 name="dbRef" minOccurs="0" maxOccurs="unbounded">
+										<xs:complexType>
+											<xs:attribute name="source" type="xs:string"/>
+											<xs:attribute name="version" type="xs:string"/>
+											<xs:attribute name="accessionId" type="xs:string"/>
+											<xs:attribute name="id" type="xs:ID" use="optional"/>
+										</xs:complexType>
 									</xs:element>
 								</xs:sequence>
-								<xs:attribute name="id" type="xs:ID" minOccurs="1" maxOccurs="1"/>
+								<xs:attribute name="id" type="xs:ID" use="required"/>
 								<xs:attribute name="dictionary" type="xs:string"/>
 							</xs:extension>
 						</xs:complexContent>
 					</xs:complexType>
 				</xs:element>
-				<xs:element name="SequenceSetAnnotations" minOccurs="0" maxOccurs="unbounded">
+				<xs:element name="DataSetAnnotations" 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:element ref="vamsas:Provenance" 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="end" type="xs:integer" use="required"/>
+						<xs:attribute name="begin" type="xs:integer" use="required"/>
 						<xs:attribute name="seqRef" type="xs:IDREF" use="required"/>
-						<xs:attribute name="id" type="xs:ID" minOccurs="0" maxOccurs="1"/>
+						<xs:attribute name="id" type="xs:ID" use="optional"/>
 					</xs:complexType>
 				</xs:element>
 				<xs:element name="Alignment" minOccurs="0" maxOccurs="unbounded">
 					<xs:complexType>
 						<xs:sequence>
-							<xs:element name="AlignmentAnnotations" minOccurs="0">
+							<xs:element name="AlignmentAnnotations" minOccurs="0" maxOccurs="unbounded">
 								<xs:complexType>
 									<xs:sequence>
 										<xs:element ref="vamsas:annotationElement" maxOccurs="unbounded"/>
@@ -101,15 +96,15 @@
 										<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:attribute name="id" type="xs:ID" use="optional"/>
 								</xs:complexType>
 							</xs:element>
 							<xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
-							<xs:element name="alignmentSequence" minOccurs="2" maxOccurs="unbounded">
+							<xs:element name="alignmentSequence" 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="id" type="xs:ID" use="optional"/>
 											<xs:attribute name="refid" type="xs:IDREF" use="required"/>
 										</xs:extension>
 									</xs:complexContent>
@@ -117,61 +112,68 @@
 							</xs:element>
 							<xs:element ref="vamsas:Provenance"/>
 						</xs:sequence>
-						<xs:attribute name="id" type="xs:ID" minOccurs="0" maxOccurs="1"/>
+						<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: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:attribute name="id" type="xs:ID" use="optional"/>
 		</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:element name="displayCharacter" type="xs:string" minOccurs="0"/>
+				<xs:element name="description" type="xs:string" minOccurs="0"/>
+				<xs:element name="secondaryStructure" minOccurs="0">
 					<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:element name="value" type="xs:float" minOccurs="0"/>
 			</xs:sequence>
-			<xs:attribute name="position" type="xs:int" use="required"/>
-			<xs:attribute name="id" type="xs:ID"  minOccurs="0" maxOccurs="1"/>
+			<xs:attribute name="position" type="xs:integer" use="required"/>
+			<xs:attribute name="id" type="xs:ID" use="optional"/>
 		</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"/>
 		</xs:sequence>
-		<xs:attribute name="start" type="xs:int" use="required"/>
-		<xs:attribute name="end" type="xs:int" use="required"/>
+		<xs:attribute name="start" type="xs:integer" use="required"/>
+		<xs:attribute name="end" type="xs:integer" use="required"/>
 	</xs:complexType>
-	
-    <xs:complexType name="ApplicationData">
+	<xs:element name="ApplicationData">
+		<xs:complexType>
+			<xs:complexContent>
+				<xs:extension base="vamsas:appData">
+					<xs:attribute name="version" type="xs:string" use="required"/>
+					<xs:attribute name="name" type="xs:string" use="required"/>
+					<xs:attribute name="urn" type="xs:string" use="required"/>
+				</xs:extension>
+			</xs:complexContent>
+		</xs:complexType>
+	</xs:element>
+	<xs:complexType name="appData">
 		<xs:sequence>
-			<xs:element name="Application">
+			<xs:choice>
+				<xs:element name="data" type="xs:base64Binary"/>
+				<xs:element name="dataReference" type="xs:string"/>
+			</xs:choice>
+			<xs:element name="User" maxOccurs="unbounded">
 				<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:complexContent>
+						<xs:extension base="vamsas:appData">
+							<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:sequence>