From 37c1bc52d964f50df6604d50a381a8f5dae8a5aa Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 20 May 2005 08:16:59 +0000
Subject: [PATCH] xml schemas

---
 schemas/JalviewState.xsd |    9 +++
 schemas/jalview.xsd      |  136 ++++++++++++++++++++++++++++++++++++++++++++++
 schemas/vamsas.xsd       |   73 +++++++++++++++++++++++++
 3 files changed, 218 insertions(+)
 create mode 100755 schemas/JalviewState.xsd
 create mode 100755 schemas/jalview.xsd
 create mode 100755 schemas/vamsas.xsd

diff --git a/schemas/JalviewState.xsd b/schemas/JalviewState.xsd
new file mode 100755
index 0000000..e0274c6
--- /dev/null
+++ b/schemas/JalviewState.xsd
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" targetNamespace="www.jalview.org">
+    <xs:complexType name="JalviewState">
+        <xs:sequence>
+            <xs:element name="creationDate" type="xs:dateTime"/>
+            <xs:element name="file" maxOccurs="unbounded" type="xs:string"/>
+        </xs:sequence>
+    </xs:complexType>
+</xs:schema>
\ No newline at end of file
diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
new file mode 100755
index 0000000..77d701c
--- /dev/null
+++ b/schemas/jalview.xsd
@@ -0,0 +1,136 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" 
+			xmlns:vamsas="www.vamsas.org" 
+			xmlns:jalview="www.jalview.org" 
+			targetNamespace="www.jalview.org" 
+			elementFormDefault="qualified" 
+			attributeFormDefault="unqualified">
+
+<xs:import schemaLocation="vamsas.xsd" namespace="www.vamsas.org" />
+
+<xs:complexType name="JalviewModel">
+
+    <xs:sequence>
+
+	    <xs:element name="creationDate" type="xs:dateTime"/>
+
+        <xs:element name="vamsasModel" type="vamsas:VAMSAS"/>
+
+        <xs:sequence>
+
+            <xs:element name="JSeq" maxOccurs="unbounded">
+
+                <xs:complexType>
+                    
+					<xs:attribute name="colour" type="xs:int" use="optional"/>
+					
+                    <xs:attribute name="start" type="xs:int" use="required"/>
+
+                    <xs:attribute name="end" type="xs:int" use="required"/>
+
+                    <xs:attribute name="id" type="xs:int" use="required"/>
+
+                </xs:complexType>
+
+            </xs:element>
+
+            <xs:element name="JGroup" maxOccurs="unbounded">
+
+                <xs:complexType>
+
+                    <xs:sequence minOccurs="1">
+
+                        <xs:element name="seq" maxOccurs="unbounded" type="xs:int"/>
+					
+                    </xs:sequence>
+
+                        <xs:attribute name="start" type="xs:int"/>
+
+                        <xs:attribute name="end" type="xs:int"/>
+
+                        <xs:attribute name="name" type="xs:string"/>
+
+                        <xs:attribute name="colour" type="xs:string"/>
+
+						<xs:attribute name="consThreshold" type="xs:int"/>
+
+						<xs:attribute name="pidThreshold" type="xs:int"/>
+
+                        <xs:attribute name="outlineColour" type="xs:int"/>
+
+                        <xs:attribute name="displayBoxes" type="xs:boolean"/>
+
+                        <xs:attribute name="displayText" type="xs:boolean"/>
+
+                        <xs:attribute name="colourText" type="xs:boolean"/>
+
+                </xs:complexType>
+
+            </xs:element>
+
+            <xs:element name="Viewport" maxOccurs="unbounded">
+
+                <xs:complexType>
+				     	<xs:attribute name="conservationSelected" type="xs:boolean"/>
+
+						<xs:attribute name="pidSelected" type="xs:boolean"/>
+
+                        <xs:attribute name="bgColour" type="xs:string"/>
+
+						<xs:attribute name="consThreshold" type="xs:int"/>
+
+						<xs:attribute name="pidThreshold" type="xs:int"/>
+
+                        <xs:attribute name="title" type="xs:string"/>
+
+                        <xs:attribute name="showFullId" type="xs:boolean"/>
+
+                        <xs:attribute name="showText" type="xs:boolean"/>
+
+                        <xs:attribute name="showColourText" type="xs:boolean"/>
+
+                        <xs:attribute name="showBoxes" type="xs:boolean"/>
+
+                        <xs:attribute name="wrapAlignment" type="xs:boolean"/>
+
+                        <xs:attribute name="renderGaps" type="xs:boolean"/>
+
+                        <xs:attribute name="showSequenceFeatures" type="xs:boolean"/>
+
+						<xs:attribute name="showAnnotation" type="xs:boolean"/>
+
+                        <xs:attribute name="showConservation" type="xs:boolean"/>
+
+                        <xs:attribute name="showQuality" type="xs:boolean"/>
+
+						<xs:attribute name="showIdentity" type="xs:boolean"/>
+
+                    <xs:attribute name="xpos" type="xs:int"/>
+
+                    <xs:attribute name="ypos" type="xs:int"/>
+
+                    <xs:attribute name="width" type="xs:int"/>
+
+                    <xs:attribute name="height" type="xs:int"/>
+
+				    <xs:attribute name="startRes" type="xs:int"/>
+					<xs:attribute name="startSeq" type="xs:int"/>
+					<xs:attribute name="fontName" type="xs:string"/>
+					<xs:attribute name="fontSize" type="xs:int"/>
+					<xs:attribute name="fontStyle" type="xs:int"/>
+				
+
+                </xs:complexType>
+
+            </xs:element>
+
+        </xs:sequence>
+
+    </xs:sequence>
+
+</xs:complexType>
+
+
+
+
+</xs:schema>
diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
new file mode 100755
index 0000000..08a70af
--- /dev/null
+++ b/schemas/vamsas.xsd
@@ -0,0 +1,73 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- 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="www.vamsas.org" targetNamespace="www.vamsas.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
+	<xs:complexType name="VAMSAS">
+		<xs:sequence>
+			<xs:element name="Alignment" minOccurs="0" maxOccurs="unbounded">
+				<xs:complexType>
+					<xs:sequence>
+						<xs:element name="Annotation" minOccurs="0">
+							<xs:complexType>
+								<xs:sequence>
+									<xs:element ref="vamsas:annotationElement" maxOccurs="unbounded"/>
+									<xs:element name="label" type="xs:string"/>
+									<xs:element name="description" type="xs:string"/>
+								</xs:sequence>
+								<xs:attribute name="graph" type="xs:boolean" use="required"/>
+							</xs:complexType>
+						</xs:element>
+						<xs:element ref="vamsas:SequenceSet"/>
+					</xs:sequence>
+				</xs:complexType>
+			</xs:element>
+			<xs:element name="Tree" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
+			<xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
+		</xs:sequence>
+	</xs:complexType>
+	<xs:element name="SequenceSet">
+		<xs:complexType>
+			<xs:sequence>
+				<xs:element name="Sequence" type="vamsas:SequenceType" maxOccurs="unbounded"/>
+				<xs:element name="Annotation" 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: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="seqRef" type="xs:string" use="required"/>
+					</xs:complexType>
+				</xs:element>
+			</xs:sequence>
+			<xs:attribute name="gapChar" type="xs:string" use="required"/>
+			<xs:attribute name="aligned" type="xs:boolean" 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:simpleType>
+						<xs:restriction base="xs:string">
+							<xs:length value="1"/>
+						</xs:restriction>
+					</xs:simpleType>
+				</xs:element>
+				<xs:element name="value" type="xs:float"/>
+			</xs:sequence>
+			<xs:attribute name="position" type="xs:int" use="required"/>
+		</xs:complexType>
+	</xs:element>
+	<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="id" type="xs:string"/>
+	</xs:complexType>
+</xs:schema>
-- 
1.7.10.2