From 1b6e5d1b5e248e6c4455f748df970b9fabba4bb4 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 19 May 2006 16:53:59 +0000
Subject: [PATCH] still refactoring the rangeType and features/annotation
 elements.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@220 be28352e-c001-0410-b1a7-c7978e42abec
---
 schemas/document.xml |   29 +++++++++++++++++++----------
 schemas/vamsas.xsd   |   40 +++++++++++++++++++++++++---------------
 2 files changed, 44 insertions(+), 25 deletions(-)

diff --git a/schemas/document.xml b/schemas/document.xml
index 9bdefd8..860934a 100644
--- a/schemas/document.xml
+++ b/schemas/document.xml
@@ -7,6 +7,7 @@
     <Provenance xmlns="http://www.vamsas.org">
         <entry>
             <User>Jim</User>
+            <App>Jalview</App>
             <Action>updated the xml schema</Action>
             <Date>2006-01-17</Date>
         </entry>
@@ -15,39 +16,39 @@
     <VAMSAS xmlns="http://www.vamsas.org" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.vamsas.org
         http://www.vamsas.ac.uk/build/VamsasClient/schemas/vamsas.xsd">
         <DataSet>
-            <Sequence start="1" end="167" id="a1127235554296">
+            <Sequence start="1" end="167" dictionary="vamsas:aa" id="a1127235554296">
                 <sequence>KTAIITGGSRGIGKSIAIKLGKLGASIVLNYRNNTDALKNTIRELEDLNINVIAVQGDISNYKECEKIIKAALDKFNGIDILVNNAGITADNLILRMKEEEFDKVIETNLKGTFNCVKHCIPMIKRRYGKIINISSVVGVAGNVGQCNYAAAKAGVIGFTKSLAKEL</sequence>
                 <name>Q899P0</name>
             </Sequence>
-            <Sequence start="1" end="168" id="a1127235554297">
+            <Sequence start="1" end="168" dictionary="vamsas:aa" id="a1127235554297">
                 <sequence>KIAIVTGASSGIGRAIAFKLASRGANLILGDVKIDELRKVAEEIAKETKVKVIPLYVNVGDFNSTKEFYNKGISELGVDYVDILVNNAGINRDALFVKMTYEQWDEVIKVDLYSMFNMTKQVVDMVKRNYGRIINISSLSWLGNIGQANYSAAKAGVIGFTKTLAREL</sequence>
                 <name>Q972M3</name>
             </Sequence>
-            <Sequence start="1" end="167" id="a1127235554298">
+            <Sequence start="1" end="167" dictionary="vamsas:aa" id="a1127235554298">
                 <sequence>KVIVITGASSGIGEQVAMQVAEQGATPVLMARTEEKLKALADKIKETYNTPCYYYVLDVSEETEVQSVFSKVLQEVGRIDILVNNAGFGIFKTFEDASMDEVKDMFQVNVFGLVACTKAVLPYMVKRNGHIINIASLAGKIATPKSSAYAATKHAVLGFTNSLRMEL</sequence>
                 <name>Q81M93</name>
             </Sequence>
-            <Sequence start="1" end="167" id="a1127235554299">
+            <Sequence start="1" end="167" dictionary="vamsas:aa" id="a1127235554299">
                 <sequence>KIALVTGAMGGLGTAICQALAKDGCIVAANCLPNFEPAAAWLGQQEALGFKFYVAEGDVSDFESCKAMVAKIEADLGPVDILVNNAGITRDKFFAKMDKAQWDAVIATNLSSLFNVTQQVSPKMERGWGRIINISSVNGVKGQAGQTNYSAAKAGVIGFTKALAAEL</sequence>
                 <name>NODG_AZOBR</name>
             </Sequence>
-            <Sequence start="1" end="166" id="a1127235554300">
+            <Sequence start="1" end="166" dictionary="vamsas:aa" id="a1127235554300">
                 <sequence>QTAVVTGGGKGIGRAICLALAREGADIVIAARTEKDIRETARMVEKEGRKALPVSTDIRVEEDVENMISEAVDAFGRIDILVNNAGVAYRKYMVETSTEEYDNIMDTNLKGMFFCTKYALPYLLKREGRIINISSGAGKHGIPKLSIYSASKFAVIGFTESIAYEI</sequence>
                 <name>Q8PS57</name>
             </Sequence>
-            <Sequence start="1" end="167" id="a1127235554301">
+            <Sequence start="1" end="167" dictionary="vamsas:aa" id="a1127235554301">
                 <sequence>KTAIVTGAARGIGKAIALKFAAEGANIAFTDLVIDENAEKTRVELEAMGVKAKGYASNAANFEDTAKVVEEIHKDFGRIDILVNNAGITRDGLMMRMSEQQWDMVINVNLKSAFNFIHACTPMMRQKAGSIINMASVVGVHGNAGQANYAASKAGMIALAKSIAQEL</sequence>
                 <name>Q8A195</name>
             </Sequence>
-            <Sequence start="1" end="164" id="a1127235554302">
+            <Sequence start="1" end="164" dictionary="vamsas:aa" id="a1127235554302">
                 <sequence>KVVVVTGAGSGIGEATAKRFAHEGASVVLVGRNQEKLAKVAAQLKGAEHLIRATDVADLTDVEALFKEVAERFGRLDVLVNNAGVVKSGKVTELGVEDWKAVMSVDLDGVFYCTRTAMPALIASKGNIINVSSVSGLGGDWGMSFYNAAKGAITNFTRALALD</sequence>
                 <name>Q888G8</name>
             </Sequence>
-            <Sequence start="1" end="164" id="a1127235554303">
+            <Sequence start="1" end="164" dictionary="vamsas:aa" id="a1127235554303">
                 <sequence>KVALVTGAANGIGLAIAERLYQEGATLALADWNEEQLAIVIEQFDSARVYAQKVDVSDPEQVQALVRKTVERFGRLDILVNNAGIHIPGTVLECSVQDWRRIASVNIDGVVYCAMHALPELIKTRGCMVNTASVSGLGGDWGAAFYCATKGAVVNFTRALALD</sequence>
                 <name>Q9KRP5</name>
             </Sequence>
-            <Sequence start="1" end="163" id="a1127235554304">
+            <Sequence start="1" end="163" dictionary="vamsas:aa" id="a1127235554304">
                 <sequence>KIALVTGASRGIGRAIAELLVERGATVIGTATSEGGAAAISEYLGENGKGLALNVTDVESIEATLKAINDEFGAIDILVNNAGITRDNLLMRMKDDEWNDIINTNLTPIYRMSKAVLRMMKKRAGRIINVGSVVGTMGNAGQTNYAAAKAGVIGFTKSMAREV</sequence>
                 <name>Q87N22</name>
             </Sequence>
@@ -91,6 +92,7 @@
                 <Provenance>
                     <entry>
                         <User>jim</User>
+                        <App>Jalview</App>
                         <Action>edited</Action>
                         <Date>2005-12-21</Date>
                     </entry>
@@ -99,17 +101,24 @@
             <Provenance>
                 <entry>
                     <User>jim</User>
+                    <App>Jalview</App>
                     <Action>edited</Action>
                     <Date>2005-11-21</Date>
                 </entry>
             </Provenance>
         </DataSet>
     </VAMSAS>
-    <ApplicationData xmlns="http://www.vamsas.org" version="" name="" urn="">
+    <ApplicationData xmlns="http://www.vamsas.org" version="" name="">
         <dataReference>name of accompanying jar entry containing data</dataReference> <!-- alternative is base64 encoded string in <data></data> -->
         <User fullname="a user" organization="probably very little">
             <dataReference>another accompanying jar entry or the data tag with embedded data.</dataReference>
         </User>
+        <Common><dataReference>another bogus reference</dataReference></Common>
     </ApplicationData>
+    <ApplicationData xmlns="http://www.vamsas.org" version="alpha" name="hmm">
+        <data>somedata</data>
+        <Instance urn="hmm://myInstancetype"><dataReference>some reference</dataReference></Instance>
+    </ApplicationData>
+    
 </VamsasDocument>
 
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>
-- 
1.7.10.2