X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fvamsas.xsd;fp=schemas%2Fvamsas.xsd;h=25ccc5500bce94059ff85eba14acb290ff39f371;hb=1b6e5d1b5e248e6c4455f748df970b9fabba4bb4;hp=bf17ca382a4689eff507ac06474de6e32fde223b;hpb=6944ad87af9e39a36c8dc42c077f836bee01599a;p=vamsas.git

diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
index bf17ca3..25ccc55 100644
--- a/schemas/vamsas.xsd
+++ b/schemas/vamsas.xsd
@@ -4,7 +4,7 @@
 <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:complexType name="rangeType">
 		<xs:annotation>
-			<xs:documentation>Specify positions and/or regions on the principle dimension of some associated vamsas objects
+			<xs:documentation>Specify positions and/or regions on the principle dimension of some associated vamsas object
 			TODO: this is abstract. should provide context to scope the range of ids for each use</xs:documentation>
 		<xs:documentation>Keeping to jaxb-1.0 specification for the moment - this choice should become a substitution group when we use jaxb-2.0 capable bindings
 		</xs:documentation></xs:annotation>
@@ -105,9 +105,7 @@
 				<xs:attribute name="group" type="xs:string" use="optional">
 				<xs:annotation><xs:documentation>Annotation with the same non-empty group name are grouped together</xs:documentation></xs:annotation></xs:attribute>
 				<xs:attribute name="type" type="xs:string" use="required"/>
-				<xs:attribute name="seqRef" type="xs:IDREF" use="optional">
-					<xs:annotation><xs:documentation>annotation may be associated with a particular sequence lying within the same reference frame as the rangeType's objRef</xs:documentation></xs:annotation>
-				</xs:attribute>
+				
 			</xs:extension>
 		</xs:complexContent>
 	</xs:complexType>
@@ -202,7 +200,11 @@
 						<xs:annotation><xs:documentation>Annotate over positions and regions of dataset sequences</xs:documentation>
 						</xs:annotation>
 						<xs:complexContent>
-							<xs:extension base="vamsas:rangeAnnotation"/>
+							<xs:extension base="vamsas:rangeAnnotation">
+								<xs:attribute name="seqRef" type="xs:IDREF" use="optional">
+									<xs:annotation><xs:documentation>annotation may be associated with a particular sequence lying within the same reference frame as the rangeType's objRef</xs:documentation></xs:annotation>
+								</xs:attribute>
+							</xs:extension>
 						</xs:complexContent>
 					</xs:complexType>
 				</xs:element>
@@ -212,9 +214,18 @@
 							<xs:element name="AlignmentFeatures" minOccurs="0" maxOccurs="unbounded"><xs:complexType><xs:annotation>
 								<xs:documentation>Annotate over positions and regions of the alignment</xs:documentation>
 							</xs:annotation><xs:complexContent>
-								<xs:extension base="vamsas:rangeAnnotation"></xs:extension>
+								<xs:extension base="vamsas:rangeAnnotation">								
+									<xs:attribute name="seqRef" type="xs:IDREF" use="optional">
+									<xs:annotation><xs:documentation>annotation may be associated with a particular sequence lying within the same reference frame as the rangeType's objRef</xs:documentation></xs:annotation>
+								</xs:attribute>
+								</xs:extension>
 							</xs:complexContent></xs:complexType></xs:element> 
 							<xs:element name="AlignmentAnnotations" minOccurs="0" maxOccurs="unbounded">
+								<xs:annotation>
+									<xs:documentation>
+										TODO: hard to distinguish this from the alignment features element. Do we merge them and leave the applications
+									</xs:documentation>
+								</xs:annotation>
 								<xs:complexType>
 									<xs:sequence>
 										<xs:element ref="vamsas:annotationElement" maxOccurs="unbounded"/>
@@ -233,19 +244,17 @@
 									<xs:complexContent>
 										<xs:extension base="vamsas:SequenceType">
 											<xs:sequence>
-												<xs:element name="AlignmentSequenceFeatures" minOccurs="0" maxOccurs="unbounded">
-													<xs:complexType><xs:annotation>
+												<xs:element name="AlignmentSequenceFeature" type="vamsas:rangeAnnotation" minOccurs="0" maxOccurs="unbounded">
+													<xs:annotation>
 													<xs:documentation>Annotate over positions and regions of the ungapped sequences in the alignment</xs:documentation>
 														<xs:documentation>TODO: have to remove id rangeSpec or require it to be the same as dataset sequence reference</xs:documentation>
-												</xs:annotation><xs:complexContent>
-													<xs:extension base="vamsas:rangeAnnotation"></xs:extension>
-												</xs:complexContent></xs:complexType>
+												</xs:annotation>
 												</xs:element> 
 											</xs:sequence>
 											<xs:attribute name="id" type="xs:ID" use="optional">
 												<xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation>
 											</xs:attribute>
-											<xs:attribute name="refid" type="xs:IDREF" use="required"/>
+											<xs:attribute name="refid" type="xs:IDREF" use="required"><xs:annotation><xs:documentation>Dataset Sequence from which this alignment sequence is taken from</xs:documentation></xs:annotation></xs:attribute>
 										</xs:extension>
 									</xs:complexContent>
 								</xs:complexType>
@@ -303,9 +312,9 @@
 	</xs:element>
 	<xs:complexType name="SequenceType">
 		<xs:sequence>
-			<xs:element name="sequence" type="xs:string"/>
-			<xs:element name="name" type="xs:string"/>
-			<xs:element name="description" type="xs:string"/>
+			<xs:element name="sequence" type="xs:string" minOccurs="1" maxOccurs="1"/>
+			<xs:element name="name" type="xs:string" minOccurs="1" maxOccurs="1"/>
+			<xs:element name="description" type="xs:string" minOccurs="0" maxOccurs="1"/>
 			<xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>additional typed properties</xs:documentation></xs:annotation></xs:element>
 		</xs:sequence>
 		<xs:attribute name="start" type="xs:integer" use="required"/>
@@ -343,6 +352,7 @@
 									<xs:extension base="vamsas:appData">
 										<xs:annotation>
 											<xs:documentation>Data available to just a specific instance of the application</xs:documentation>
+											<xs:documentation>VAMSAS/Pierre: Is this data volatile ?  Application instances may not be accessible after the session has closed - the user may have to be presented with the option of picking up the data in that instance</xs:documentation>
 										</xs:annotation>
 										<xs:attribute name="urn" type="xs:string" use="required"/>
 									</xs:extension>