From 650ef1d3df9818bdc29698bcc532b08db8ccfae5 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 29 Nov 2005 17:57:00 +0000
Subject: [PATCH] Save features and pdbids in jar file

---
 schemas/jalview.xsd |  283 ++++++++++++++++++++++-----------------------------
 1 file changed, 121 insertions(+), 162 deletions(-)

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index e94bd58..46f63d2 100755
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -1,171 +1,130 @@
 <?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/colours" 
-			targetNamespace="www.jalview.org" 
-			elementFormDefault="qualified" 
-			attributeFormDefault="unqualified">
-
-<xs:import schemaLocation="vamsas.xsd" namespace="www.vamsas.org" />
-<xs:import schemaLocation="jalviewUserColours.xsd" namespace="www.jalview.org/colours"/>
-
-<xs:complexType name="JalviewModel">
-
-    <xs:sequence>
-
-	    <xs:element name="creationDate" type="xs:dateTime"/>
-	    
-	    <xs:element name="version" type="xs:string"/>
-
-        <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" minOccurs="0" 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:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
+				 xmlns:vamsas="www.vamsas.org"
+				 xmlns:jalview="www.jalview.org/colours"
+				 xmlns:jv="www.jalview.org" 
+				 targetNamespace="www.jalview.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
+				 
+	<xs:import schemaLocation="vamsas.xsd" namespace="www.vamsas.org"/>
+	<xs:import schemaLocation="jalviewUserColours.xsd" namespace="www.jalview.org/colours"/>
+	<xs:complexType name="JalviewModel">
+		<xs:sequence>
+			<xs:element name="creationDate" type="xs:dateTime"/>
+			<xs:element name="version" type="xs:string"/>
+			<xs:element name="vamsasModel" type="vamsas:VAMSAS"/>
+			<xs:sequence>
+				<xs:element name="JSeq" maxOccurs="unbounded">
+					<xs:complexType>
+						<xs:sequence>
+						         <xs:element name="features" type="jv:feature" minOccurs="0" maxOccurs="unbounded"/>
+						         <xs:element name="pdbids" type="jv:pdbentry" minOccurs="0" maxOccurs="unbounded"/>
+					      </xs:sequence>
+					      
+						    <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" minOccurs="0" 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="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="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="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="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:element name="UserColours" minOccurs="0" maxOccurs="unbounded">
-                <xs:complexType>  
-					 <xs:sequence minOccurs="1">
-					 	<xs:element name="UserColourScheme" type="jalview:JalviewUserColours"/>
-					 </xs:sequence>
-					 <xs:attribute name="id" type="xs:string"/>
-                 </xs:complexType>
-            </xs:element>
-            
-               			<xs:element name="tree" minOccurs="0" maxOccurs="unbounded">
-                <xs:complexType>  
-					 <xs:sequence minOccurs="0" maxOccurs="1">
-					    <xs:element name="title" type="xs:string"/>
-					 	<xs:element name="newick" type="xs:string"/>
-					 </xs:sequence>
-					 <xs:attribute name="width" type="xs:int"/>
-					  <xs:attribute name="height" type="xs:int"/>
-					   <xs:attribute name="xpos" type="xs:int"/>
-					    <xs:attribute name="ypos" 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:attribute name="threshold" type="xs:float"/>
-					 <xs:attribute name="showBootstrap" type="xs:boolean"/>
-					 <xs:attribute name="showDistances" type="xs:boolean"/>
-					 <xs:attribute name="markUnlinked" type="xs:boolean"/>
-					 <xs:attribute name="fitToWindow" type="xs:boolean"/>
-					 <xs:attribute name="currentTree" type="xs:boolean"/>
-                 </xs:complexType>
-            </xs:element>     
-
-	</xs:sequence>
-
-    </xs:sequence>
-
-</xs:complexType>
-
-
-
-
+						<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:element name="UserColours" minOccurs="0" maxOccurs="unbounded">
+					<xs:complexType>
+						<xs:sequence minOccurs="1">
+							<xs:element name="UserColourScheme" type="jalview:JalviewUserColours"/>
+						</xs:sequence>
+						<xs:attribute name="id" type="xs:string"/>
+					</xs:complexType>
+				</xs:element>
+				<xs:element name="tree" minOccurs="0" maxOccurs="unbounded">
+					<xs:complexType>
+						<xs:sequence minOccurs="0" maxOccurs="1">
+							<xs:element name="title" type="xs:string"/>
+							<xs:element name="newick" type="xs:string"/>
+						</xs:sequence>
+						<xs:attribute name="width" type="xs:int"/>
+						<xs:attribute name="height" type="xs:int"/>
+						<xs:attribute name="xpos" type="xs:int"/>
+						<xs:attribute name="ypos" 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:attribute name="threshold" type="xs:float"/>
+						<xs:attribute name="showBootstrap" type="xs:boolean"/>
+						<xs:attribute name="showDistances" type="xs:boolean"/>
+						<xs:attribute name="markUnlinked" type="xs:boolean"/>
+						<xs:attribute name="fitToWindow" type="xs:boolean"/>
+						<xs:attribute name="currentTree" type="xs:boolean"/>
+					</xs:complexType>
+				</xs:element>
+			</xs:sequence>
+		</xs:sequence>
+	</xs:complexType>
+	
+	<xs:complexType name="feature">
+		<xs:attribute name="begin" type="xs:int" use="required"/>
+		<xs:attribute name="end" type="xs:int" use="required"/>
+		<xs:attribute name="type" type="xs:string" use="required"/>
+		<xs:attribute name="description" type="xs:string" use="optional"/>
+		<xs:attribute name="status" type="xs:string" use="optional"/>
+	</xs:complexType>
+	
+	<xs:complexType name="pdbentry">
+		<xs:sequence minOccurs="0" maxOccurs="unbounded">
+			<xs:element name="property" minOccurs="0" maxOccurs="unbounded">
+				<xs:complexType>
+					<xs:attribute name="name" type="xs:string" use="required"/>
+					<xs:attribute name="value" type="xs:string" use="required"/>
+				</xs:complexType>
+			</xs:element>
+		</xs:sequence>
+		<xs:attribute name="id" type="xs:string" use="required"/>
+		<xs:attribute name="type" type="xs:string" use="optional"/>
+	</xs:complexType>
+	
 </xs:schema>
-- 
1.7.10.2