From: amwaterhouse <amwaterhouse@issues.jalview.org>
Date: Fri, 18 May 2007 09:26:55 +0000 (+0000)
Subject: sequenceMapping added
X-Git-Tag: Release_0.2~131
X-Git-Url: http://source.jalview.org/gitweb/?p=vamsas.git;a=commitdiff_plain;h=8bb95a7f692f143e519bdcfc11b7e0d6cd0a1332

sequenceMapping added

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@389 be28352e-c001-0410-b1a7-c7978e42abec
---

diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
index 7f01fd2..3b8d42b 100644
--- a/schemas/vamsas.xsd
+++ b/schemas/vamsas.xsd
@@ -1,9 +1,7 @@
 <?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 v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->
-<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes"
-	targetNamespace="http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes" elementFormDefault="qualified"
-	attributeFormDefault="unqualified">
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes" targetNamespace="http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes" elementFormDefault="qualified" attributeFormDefault="unqualified">
 	<xs:annotation>
 		<xs:documentation> Vorba ID - Vamsas Object Request Broker Address ID (name needs to be
 			worked on): Suggest it could be of the form documentRoot/datasetName/SequenceUID for a
@@ -25,8 +23,7 @@
 					<xs:documentation> Primary Key for vamsas object referencing </xs:documentation>
 				</xs:annotation>
 			</xs:attribute>
-			<xs:attribute name="modifiable" type="vamsas:locks" use="optional">
-			</xs:attribute>
+			<xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
 		</xs:complexType>
 	</xs:element>
 	<xs:annotation>
@@ -56,8 +53,7 @@
 										</xs:documentation>
 									</xs:annotation>
 								</xs:attribute>
-								<xs:attribute name="modifiable" type="vamsas:locks" use="optional">
-								</xs:attribute>
+								<xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
 							</xs:extension>
 						</xs:simpleContent>
 					</xs:complexType>
@@ -70,8 +66,7 @@
 					<xs:documentation> Primary Key for vamsas object referencing </xs:documentation>
 				</xs:annotation>
 			</xs:attribute>
-			<xs:attribute name="modifiable" type="vamsas:locks" use="optional">
-			</xs:attribute>
+			<xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
 		</xs:complexType>
 	</xs:element>
 	<xs:element name="property">
@@ -191,8 +186,7 @@
 						<xs:complexType>
 							<xs:simpleContent>
 								<xs:extension base="xs:float">
-									<xs:attribute name="name" type="xs:string" use="optional"
-										default="score"/>
+									<xs:attribute name="name" type="xs:string" use="optional" default="score"/>
 								</xs:extension>
 							</xs:simpleContent>
 						</xs:complexType>
@@ -211,8 +205,7 @@
 						</xs:documentation>
 					</xs:annotation>
 				</xs:attribute>
-				<xs:attribute name="modifiable" type="vamsas:locks" use="optional">
-				</xs:attribute>
+				<xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
 				<xs:attribute name="group" type="xs:string" use="optional" default="">
 					<xs:annotation>
 						<xs:documentation> Annotation with the same non-empty group name are grouped
@@ -360,9 +353,9 @@
 										</xs:annotation>
 										<xs:complexType>
 											<xs:sequence>
-												<xs:element name="map"
-													minOccurs="0" maxOccurs="unbounded">
-													<xs:annotation><xs:documentation> From: Offset to first
+												<xs:element name="map" minOccurs="0" maxOccurs="unbounded">
+													<xs:annotation>
+														<xs:documentation> From: Offset to first
 														position in dataset sequence record that
 														this database entry maps to To: Offset
 														to last position in dataset sequence
@@ -376,38 +369,31 @@
 													</xs:annotation>
 													<xs:complexType>
 														<xs:complexContent>
-															<xs:extension base="vamsas:mapList">
-																
-															</xs:extension>
+															<xs:extension base="vamsas:mapList"/>
 														</xs:complexContent>
-													</xs:complexType>												
+													</xs:complexType>
 												</xs:element>
-												<xs:element ref="vamsas:link" minOccurs="0"
-												maxOccurs="unbounded"/>
-												<xs:element ref="vamsas:property" minOccurs="0"
-												maxOccurs="unbounded"/>
+												<xs:element ref="vamsas:link" minOccurs="0" maxOccurs="unbounded"/>
+												<xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded"/>
 											</xs:sequence>
-											<xs:attribute name="source" type="xs:string"
-												use="required">
+											<xs:attribute name="source" type="xs:string" use="required">
 												<xs:annotation>
-												<xs:documentation> TODO Database Naming
+													<xs:documentation> TODO Database Naming
 												Convention: either start using LSID (so
 												change type to URI) or leave this as an
 												uncontrolled/unspecified string ID
 												</xs:documentation>
 												</xs:annotation>
 											</xs:attribute>
-											<xs:attribute name="version" type="xs:string"
-												use="required">
+											<xs:attribute name="version" type="xs:string" use="required">
 												<xs:annotation>
-												<xs:documentation> Version must be specified -
+													<xs:documentation> Version must be specified -
 												</xs:documentation>
 												</xs:annotation>
 											</xs:attribute>
-											<xs:attribute name="accessionId" type="xs:string"
-												use="required">
+											<xs:attribute name="accessionId" type="xs:string" use="required">
 												<xs:annotation>
-												<xs:documentation> TODO: make some specification
+													<xs:documentation> TODO: make some specification
 												of the database field from which this
 												accessionId is taken from - should that be a
 												special property of the dbRef object ?
@@ -416,7 +402,7 @@
 											</xs:attribute>
 											<xs:attribute name="id" type="xs:ID" use="optional">
 												<xs:annotation>
-												<xs:documentation> Primary Key for vamsas object
+													<xs:documentation> Primary Key for vamsas object
 												referencing </xs:documentation>
 												</xs:annotation>
 											</xs:attribute>
@@ -439,6 +425,24 @@
 						</xs:complexContent>
 					</xs:complexType>
 				</xs:element>
+				<xs:element name="sequenceMapping" minOccurs="0" maxOccurs="unbounded">
+					<xs:complexType>
+						<xs:sequence>
+							<xs:element name="range" maxOccurs="unbounded">
+								<xs:complexType>
+									<xs:attribute name="seqAStart" type="xs:int"/>
+									<xs:attribute name="seqAEnd" type="xs:int"/>
+									<xs:attribute name="seqBStart" type="xs:int"/>
+									<xs:attribute name="seqBEnd" type="xs:int"/>
+								</xs:complexType>
+							</xs:element>
+							<xs:element ref="vamsas:Provenance"/>
+						</xs:sequence>
+						<xs:attribute name="sequenceA" type="xs:IDREF" use="required"/>
+						<xs:attribute name="sequenceB" type="xs:IDREF" use="required"/>
+						<xs:attribute name="id" type="xs:ID" use="optional"/>
+					</xs:complexType>
+				</xs:element>
 				<xs:element name="DataSetAnnotations" minOccurs="0" maxOccurs="unbounded">
 					<xs:complexType>
 						<xs:annotation>
@@ -463,8 +467,7 @@
 				<xs:element name="Alignment" minOccurs="0" maxOccurs="unbounded">
 					<xs:complexType>
 						<xs:sequence>
-							<xs:element name="AlignmentAnnotation" minOccurs="0"
-								maxOccurs="unbounded">
+							<xs:element name="AlignmentAnnotation" minOccurs="0" maxOccurs="unbounded">
 								<xs:annotation>
 									<xs:documentation> This is annotation over the coordinate frame
 										defined by all the columns in the alignment.
@@ -476,10 +479,9 @@
 											<xs:sequence>
 												<xs:element ref="vamsas:Provenance"/>
 											</xs:sequence>
-											<xs:attribute name="graph" type="xs:boolean"
-												use="required">
+											<xs:attribute name="graph" type="xs:boolean" use="required">
 												<xs:annotation>
-												<xs:documentation> TODO: decide if this flag is
+													<xs:documentation> TODO: decide if this flag is
 												redundant - when true it would suggest that
 												the annotationElement values together form a
 												graph </xs:documentation>
@@ -495,38 +497,34 @@
 									<xs:complexContent>
 										<xs:extension base="vamsas:SequenceType">
 											<xs:sequence>
-												<xs:element name="AlignmentSequenceAnnotation"
-												minOccurs="0" maxOccurs="unbounded">
-												<xs:complexType>
-												<xs:annotation>
-												<xs:documentation> Annotate over
+												<xs:element name="AlignmentSequenceAnnotation" minOccurs="0" maxOccurs="unbounded">
+													<xs:complexType>
+														<xs:annotation>
+															<xs:documentation> Annotate over
 												positions and regions of the
 												ungapped sequence in the context of
 												the alignment </xs:documentation>
-												<xs:documentation/>
-												</xs:annotation>
-												<xs:complexContent>
-												<xs:extension
-												base="vamsas:rangeAnnotation">
-												<xs:sequence>
-												<xs:element
-												ref="vamsas:Provenance"/>
-												</xs:sequence>
-												<xs:attribute name="graph"
-												type="xs:boolean" use="required">
-												<xs:annotation>
-												<xs:documentation> TODO:
+															<xs:documentation/>
+														</xs:annotation>
+														<xs:complexContent>
+															<xs:extension base="vamsas:rangeAnnotation">
+																<xs:sequence>
+																	<xs:element ref="vamsas:Provenance"/>
+																</xs:sequence>
+																<xs:attribute name="graph" type="xs:boolean" use="required">
+																	<xs:annotation>
+																		<xs:documentation> TODO:
 												decide if this flag is
 												redundant - when true it
 												would suggest that the
 												annotationElement values
 												together form a graph
 												</xs:documentation>
-												</xs:annotation>
-												</xs:attribute>
-												</xs:extension>
-												</xs:complexContent>
-												<!--  								
+																	</xs:annotation>
+																</xs:attribute>
+															</xs:extension>
+														</xs:complexContent>
+														<!--  								
 															This replaces the flat list of sequenceFeatures.
 															<xs:element name="AlignmentFeatures" minOccurs="0" maxOccurs="unbounded"><xs:complexType><xs:annotation>
 															<xs:documentation>Annotate over positions and regions of the alignment</xs:documentation>
@@ -537,19 +535,18 @@
 															</xs:attribute>
 															</xs:extension>
 															</xs:complexContent></xs:complexType></xs:element> -->
-												</xs:complexType>
+													</xs:complexType>
 												</xs:element>
 											</xs:sequence>
 											<xs:attribute name="id" type="xs:ID" use="optional">
 												<xs:annotation>
-												<xs:documentation> Primary Key for vamsas object
+													<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
+													<xs:documentation> Dataset Sequence from which
 												this alignment sequence is taken from
 												</xs:documentation>
 												</xs:annotation>
@@ -574,9 +571,7 @@
 								</xs:documentation>
 							</xs:annotation>
 						</xs:attribute>
-						<xs:attribute name="modifiable" type="vamsas:locks" use="optional">
-						</xs:attribute>
-						
+						<xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
 					</xs:complexType>
 				</xs:element>
 				<xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
@@ -610,8 +605,7 @@
 					<xs:complexType>
 						<xs:simpleContent>
 							<xs:extension base="xs:string">
-								<xs:attribute name="dict" type="xs:string" use="optional"
-									default="utf8">
+								<xs:attribute name="dict" type="xs:string" use="optional" default="utf8">
 									<xs:annotation>
 										<xs:documentation> specifies the symbol dictionary for this
 											glyph - eg utf8 (the default), aasecstr_3 or
@@ -667,20 +661,6 @@
 					<xs:documentation> additional typed properties </xs:documentation>
 				</xs:annotation>
 			</xs:element>
-			<xs:element name="mapping" minOccurs="0" maxOccurs="unbounded">
-				<xs:complexType>
-					<xs:complexContent>
-						<xs:extension base="vamsas:mapList">
-							<xs:attribute name="onto" type="xs:IDREF" use="required">
-								<xs:annotation>
-									<xs:documentation> object to which the mapping is being mapped
-									</xs:documentation>
-								</xs:annotation>
-							</xs:attribute>
-						</xs:extension>
-					</xs:complexContent>
-				</xs:complexType>
-			</xs:element>
 		</xs:sequence>
 		<xs:attribute name="start" type="xs:integer" use="required"/>
 		<xs:attribute name="end" type="xs:integer" use="required"/>
@@ -702,10 +682,8 @@
 											<xs:documentation> Data available to just a particular
 												user </xs:documentation>
 										</xs:annotation>
-										<xs:attribute name="fullname" type="xs:string"
-											use="required"/>
-										<xs:attribute name="organization" type="xs:string"
-											use="required"/>
+										<xs:attribute name="fullname" type="xs:string" use="required"/>
+										<xs:attribute name="organization" type="xs:string" use="required"/>
 									</xs:extension>
 								</xs:complexContent>
 							</xs:complexType>