From a2fb36f510f24b4f0f24554452cf63b7f8d1f10b Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 22 Sep 2005 09:56:04 +0000
Subject: [PATCH] created new schema to define the document XML file. Added
 two well formed schema examples.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@46 be28352e-c001-0410-b1a7-c7978e42abec
---
 schemas/coreObject.xml     |    9 +++-
 schemas/document.xml       |  104 ++++++++++++++++++++++++++++++++++++++++++++
 schemas/vamsas.xsd         |   37 ++++++----------
 schemas/vamsasDocument.xsd |   25 +++++++++++
 4 files changed, 150 insertions(+), 25 deletions(-)
 create mode 100644 schemas/document.xml
 create mode 100644 schemas/vamsasDocument.xsd

diff --git a/schemas/coreObject.xml b/schemas/coreObject.xml
index 810dde4..63d2180 100755
--- a/schemas/coreObject.xml
+++ b/schemas/coreObject.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version="1.0" encoding="UTF-8"?>	
 <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">
 	<SequenceSet>
@@ -83,5 +83,12 @@ http://www.vamsas.ac.uk/build/VamsasClient/schemas/vamsas.xsd">
 				</entry>
 			</Provenance>
 		</Alignment>
+		<Provenance>
+			<entry>
+				<User>jim</User>
+				<Action>edited</Action>
+				<Date>2005-11-21</Date>
+			</entry>
+		</Provenance>
 	</SequenceSet>
 </VAMSAS>
diff --git a/schemas/document.xml b/schemas/document.xml
new file mode 100644
index 0000000..ef21892
--- /dev/null
+++ b/schemas/document.xml
@@ -0,0 +1,104 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<VamsasDocument xmlns="http://www.vamsas.ac.uk/vamsasDocument"
+     xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+     xsi:schemaLocation="http://www.vamsas.ac.uk/vamsasDocument file:/homes/jimp/prj/new-eclipse/VamsasClient/schemas/vamsasDocument.xsd">
+    <Version></Version>
+    <LockFile></LockFile>
+    <Provenance xmlns="http://www.vamsas.org"></Provenance>
+    <VAMSAS xmlns="http://www.vamsas.org"></VAMSAS>
+    <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">
+        <SequenceSet>
+            <Sequence start="1" end="167" id="a1127235554296">
+                <sequence>KTAIITGGSRGIGKSIAIKLGKLGASIVLNYRNNTDALKNTIRELEDLNINVIAVQGDISNYKECEKIIKAALDKFNGIDILVNNAGITADNLILRMKEEEFDKVIETNLKGTFNCVKHCIPMIKRRYGKIINISSVVGVAGNVGQCNYAAAKAGVIGFTKSLAKEL</sequence>
+                <name>Q899P0</name>
+            </Sequence>
+            <Sequence start="1" end="168" id="a1127235554297">
+                <sequence>KIAIVTGASSGIGRAIAFKLASRGANLILGDVKIDELRKVAEEIAKETKVKVIPLYVNVGDFNSTKEFYNKGISELGVDYVDILVNNAGINRDALFVKMTYEQWDEVIKVDLYSMFNMTKQVVDMVKRNYGRIINISSLSWLGNIGQANYSAAKAGVIGFTKTLAREL</sequence>
+                <name>Q972M3</name>
+            </Sequence>
+            <Sequence start="1" end="167" id="a1127235554298">
+                <sequence>KVIVITGASSGIGEQVAMQVAEQGATPVLMARTEEKLKALADKIKETYNTPCYYYVLDVSEETEVQSVFSKVLQEVGRIDILVNNAGFGIFKTFEDASMDEVKDMFQVNVFGLVACTKAVLPYMVKRNGHIINIASLAGKIATPKSSAYAATKHAVLGFTNSLRMEL</sequence>
+                <name>Q81M93</name>
+            </Sequence>
+            <Sequence start="1" end="167" id="a1127235554299">
+                <sequence>KIALVTGAMGGLGTAICQALAKDGCIVAANCLPNFEPAAAWLGQQEALGFKFYVAEGDVSDFESCKAMVAKIEADLGPVDILVNNAGITRDKFFAKMDKAQWDAVIATNLSSLFNVTQQVSPKMERGWGRIINISSVNGVKGQAGQTNYSAAKAGVIGFTKALAAEL</sequence>
+                <name>NODG_AZOBR</name>
+            </Sequence>
+            <Sequence start="1" end="166" id="a1127235554300">
+                <sequence>QTAVVTGGGKGIGRAICLALAREGADIVIAARTEKDIRETARMVEKEGRKALPVSTDIRVEEDVENMISEAVDAFGRIDILVNNAGVAYRKYMVETSTEEYDNIMDTNLKGMFFCTKYALPYLLKREGRIINISSGAGKHGIPKLSIYSASKFAVIGFTESIAYEI</sequence>
+                <name>Q8PS57</name>
+            </Sequence>
+            <Sequence start="1" end="167" id="a1127235554301">
+                <sequence>KTAIVTGAARGIGKAIALKFAAEGANIAFTDLVIDENAEKTRVELEAMGVKAKGYASNAANFEDTAKVVEEIHKDFGRIDILVNNAGITRDGLMMRMSEQQWDMVINVNLKSAFNFIHACTPMMRQKAGSIINMASVVGVHGNAGQANYAASKAGMIALAKSIAQEL</sequence>
+                <name>Q8A195</name>
+            </Sequence>
+            <Sequence start="1" end="164" id="a1127235554302">
+                <sequence>KVVVVTGAGSGIGEATAKRFAHEGASVVLVGRNQEKLAKVAAQLKGAEHLIRATDVADLTDVEALFKEVAERFGRLDVLVNNAGVVKSGKVTELGVEDWKAVMSVDLDGVFYCTRTAMPALIASKGNIINVSSVSGLGGDWGMSFYNAAKGAITNFTRALALD</sequence>
+                <name>Q888G8</name>
+            </Sequence>
+            <Sequence start="1" end="164" id="a1127235554303">
+                <sequence>KVALVTGAANGIGLAIAERLYQEGATLALADWNEEQLAIVIEQFDSARVYAQKVDVSDPEQVQALVRKTVERFGRLDILVNNAGIHIPGTVLECSVQDWRRIASVNIDGVVYCAMHALPELIKTRGCMVNTASVSGLGGDWGAAFYCATKGAVVNFTRALALD</sequence>
+                <name>Q9KRP5</name>
+            </Sequence>
+            <Sequence start="1" end="163" id="a1127235554304">
+                <sequence>KIALVTGASRGIGRAIAELLVERGATVIGTATSEGGAAAISEYLGENGKGLALNVTDVESIEATLKAINDEFGAIDILVNNAGITRDNLLMRMKDDEWNDIINTNLTPIYRMSKAVLRMMKKRAGRIINVGSVVGTMGNAGQTNYAAAKAGVIGFTKSMAREV</sequence>
+                <name>Q87N22</name>
+            </Sequence>
+            <Alignment gapChar="-">
+                <alignmentSequence start="1" end="167" refid="a1127235554296">
+                    <sequence>KTAIITGGSRGIGKSIAIKLGKLGASIVLNYRNNTDALKNTIRELEDLN--INVIAVQGDISNYKECEKIIKAALDKFNG--IDILVNNAGITADNLILRMKEEEFDKVIETNLKGTFNCVKHCIPMIKRRYGKIINISSVVGVAGNVGQCNYAAAKAGVIGFTKSLAKEL</sequence>
+                    <name>Q899P0</name>
+                </alignmentSequence>
+                <alignmentSequence start="1" end="168" refid="a1127235554297">
+                    <sequence>KIAIVTGASSGIGRAIAFKLASRGANLILGDVKIDEL--RKVAEEIAKETKVKVIPLYVNVGDFNSTKEFYNKGISELGVDYVDILVNNAGINRDALFVKMTYEQWDEVIKVDLYSMFNMTKQVVDMVKRNYGRIINISSLSWL-GNIGQANYSAAKAGVIGFTKTLAREL</sequence>
+                    <name>Q972M3</name>
+                </alignmentSequence>
+                <alignmentSequence start="1" end="167" refid="a1127235554298">
+                    <sequence>KVIVITGASSGIGEQVAMQVAEQGATPVLMARTEEKL--KALADKIKETYNTPCYYYVLDVSEETEVQSVFSKVLQEVGR--IDILVNNAGFGIFKTFEDASMDEVKDMFQVNVFGLVACTKAVLPYMVKRNGHIINIASLAGKIATPKSSAYAATKHAVLGFTNSLRMEL</sequence>
+                    <name>Q81M93</name>
+                </alignmentSequence>
+                <alignmentSequence start="1" end="167" refid="a1127235554299">
+                    <sequence>KIALVTGAMGGLGTAICQALAKDGCIVAANCLPNFEPAAAWLGQQEALG--FKFYVAEGDVSDFESCKAMVAKIEADLGP--VDILVNNAGITRDKFFAKMDKAQWDAVIATNLSSLFNVTQQVSPKMERGWGRIINISSVNGVKGQAGQTNYSAAKAGVIGFTKALAAEL</sequence>
+                    <name>NODG_AZOBR</name>
+                </alignmentSequence>
+                <alignmentSequence start="1" end="166" refid="a1127235554300">
+                    <sequence>QTAVVTGGGKGIGRAICLALAREGADIVIAARTEKDI--RETARMVEKEG-RKALPVSTDIRVEEDVENMISEAVDAFGR--IDILVNNAGVAYRKYMVETSTEEYDNIMDTNLKGMFFCTKYALPYLLKREGRIINISSGAGKHGIPKLSIYSASKFAVIGFTESIAYEI</sequence>
+                    <name>Q8PS57</name>
+                </alignmentSequence>
+                <alignmentSequence start="1" end="167" refid="a1127235554301">
+                    <sequence>KTAIVTGAARGIGKAIALKFAAEGANIAFTDLVIDENAEKTRVELEAMG--VKAKGYASNAANFEDTAKVVEEIHKDFGR--IDILVNNAGITRDGLMMRMSEQQWDMVINVNLKSAFNFIHACTPMMRQKAGSIINMASVVGVHGNAGQANYAASKAGMIALAKSIAQEL</sequence>
+                    <name>Q8A195</name>
+                </alignmentSequence>
+                <alignmentSequence start="1" end="164" refid="a1127235554302">
+                    <sequence>KVVVVTGAGSGIGEATAKRFAHEGASVVLVGRNQEKL--AKVAAQLKG---AEHLIRATDVADLTDVEALFKEVAERFGR--LDVLVNNAGVVKSGKVTELGVEDWKAVMSVDLDGVFYCTRTAMPALIASKGNIINVSSVSGLGGDWGMSFYNAAKGAITNFTRALALD-</sequence>
+                    <name>Q888G8</name>
+                </alignmentSequence>
+                <alignmentSequence start="1" end="164" refid="a1127235554303">
+                    <sequence>KVALVTGAANGIGLAIAERLYQEGATLALADWNEEQL--AIVIEQFDS---ARVYAQKVDVSDPEQVQALVRKTVERFGR--LDILVNNAGIHIPGTVLECSVQDWRRIASVNIDGVVYCAMHALPELIKTRGCMVNTASVSGLGGDWGAAFYCATKGAVVNFTRALALD-</sequence>
+                    <name>Q9KRP5</name>
+                </alignmentSequence>
+                <alignmentSequence start="1" end="163" refid="a1127235554304">
+                    <sequence>KIALVTGASRGIGRAIAELLVERGATVIGTATSEGGA--AAISEYLG----ENGKGLALNVTDVESIEATLKAINDEFGA--IDILVNNAGITRDNLLMRMKDDEWNDIINTNLTPIYRMSKAVLRMMKKRAGRIINVGSVVGTMGNAGQTNYAAAKAGVIGFTKSMAREV</sequence>
+                    <name>Q87N22</name>
+                </alignmentSequence>
+                <Provenance>
+                    <entry>
+                        <User>jim</User>
+                        <Action>edited</Action>
+                        <Date>2005-12-21</Date>
+                    </entry>
+                </Provenance>
+            </Alignment>
+            <Provenance>
+                <entry>
+                    <User>jim</User>
+                    <Action>edited</Action>
+                    <Date>2005-11-21</Date>
+                </entry>
+            </Provenance>
+        </SequenceSet>
+    </VAMSAS>
+    <ApplicationData xmlns="http://www.vamsas.org"></ApplicationData>
+</VamsasDocument>
+
diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
index 9487eca..19b2a4b 100644
--- a/schemas/vamsas.xsd
+++ b/schemas/vamsas.xsd
@@ -2,17 +2,6 @@
 <!-- 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:annotation>
-		<xs:documentation>Vamsas Document Version Number</xs:documentation>
-	</xs:annotation>
-	<xs:element name="LockFile">
-		<xs:complexType>
-			<xs:simpleContent>
-				<xs:extension base="xs:string"/>
-			</xs:simpleContent>
-		</xs:complexType>
-	</xs:element>
 	<xs:element name="VAMSAS">
 		<xs:complexType>
 			<xs:sequence>
@@ -129,7 +118,7 @@
 					</xs:complexType>
 				</xs:element>
 				<xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
-				<xs:element ref="vamsas:Provenance"/>
+				<xs:element ref="vamsas:Provenance" minOccurs="1" maxOccurs="unbounded"/>
 			</xs:sequence>
 			<xs:attribute name="id" type="xs:ID" use="optional"/>
 		</xs:complexType>
@@ -137,16 +126,16 @@
 	<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" maxOccurs="1" minOccurs="0"/>
+				<xs:element name="description" type="xs:string" maxOccurs="1" minOccurs="0"/>
+				<xs:element name="secondaryStructure" maxOccurs="1" 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" maxOccurs="1" minOccurs="0"/>
 			</xs:sequence>
 			<xs:attribute name="position" type="xs:int" use="required"/>
 			<xs:attribute name="id" type="xs:ID" use="optional"/>
@@ -154,8 +143,8 @@
 	</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="sequence" type="xs:string" maxOccurs="1" minOccurs="1"/>
+			<xs:element name="name" type="xs:string" maxOccurs="1" minOccurs="1"/>
 		</xs:sequence>
 		<xs:attribute name="start" type="xs:int" use="required"/>
 		<xs:attribute name="end" type="xs:int" use="required"/>
@@ -163,10 +152,10 @@
 	<xs:element name="ApplicationData">
 		<xs:complexType>
 			<xs:sequence>
-				<xs:element name="Application">
+				<xs:element name="Application" minOccurs="0" maxOccurs="unbounded">
 					<xs:complexType>
 						<xs:sequence>
-							<xs:element name="User">
+							<xs:element name="User" minOccurs="1" maxOccurs="unbounded">
 								<xs:complexType>
 									<xs:attribute name="fullname" type="xs:string"/>
 									<xs:attribute name="organization" type="xs:string"/>
@@ -174,10 +163,10 @@
 								</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: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:attribute name="data" type="xs:string" use="required"/>
 					</xs:complexType>
 				</xs:element>
 			</xs:sequence>
diff --git a/schemas/vamsasDocument.xsd b/schemas/vamsasDocument.xsd
new file mode 100644
index 0000000..c56a41b
--- /dev/null
+++ b/schemas/vamsasDocument.xsd
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vdoc="http://www.vamsas.ac.uk/vamsasDocument" xmlns:vamsas="http://www.vamsas.org" targetNamespace="http://www.vamsas.ac.uk/vamsasDocument" elementFormDefault="qualified">
+    <xs:import namespace="http://www.vamsas.org" schemaLocation="vamsas.xsd"/>
+    <xs:element name="VamsasDocument" nillable="false">
+        <xs:complexType>
+            <xs:sequence>
+                <xs:element name="Version" type="xs:string" minOccurs="1" maxOccurs="1">
+                    <xs:annotation>
+                        <xs:documentation>Vamsas Document Version Number</xs:documentation>
+                    </xs:annotation>
+                </xs:element>
+                <xs:element name="LockFile" minOccurs="0" maxOccurs="1">
+                    <xs:complexType>
+                        <xs:simpleContent>
+                            <xs:extension base="xs:string"/>
+                        </xs:simpleContent>
+                    </xs:complexType>
+                </xs:element>
+                <xs:element ref="vamsas:Provenance" minOccurs="0" maxOccurs="1"/>
+                <xs:element ref="vamsas:VAMSAS" minOccurs="1" maxOccurs="unbounded"/>
+                <xs:element ref="vamsas:ApplicationData" minOccurs="0" maxOccurs="1"/>
+            </xs:sequence>
+        </xs:complexType>
+    </xs:element> 
+</xs:schema>
\ No newline at end of file
-- 
1.7.10.2