X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=schemas%2Fjalview.xsd;h=65cf2f89e55dd97e6e05fdbd16da4b1d041520f8;hb=70103cf21e1f8f4e6d645a752b46ab8870bd65af;hp=2bedcd6d331b877ddaf0bf41fa3167ae46bdddfc;hpb=4ac0fe29bbaaafc4d120c8369061391b9ae015f6;p=jalview.git

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index 2bedcd6..65cf2f8 100755
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -1,12 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
-				 xmlns:vamsas="www.vamsas.ac.uk/jalview/version2"
-				 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.ac.uk/jalview/version2"/>
-	<xs:import schemaLocation="JalviewUserColours.xsd" namespace="www.jalview.org/colours"/>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" xmlns:jalview="www.jalview.org/colours" xmlns:jv="www.jalview.org" targetNamespace="www.jalview.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
+	<xs:import namespace="www.vamsas.ac.uk/jalview/version2" schemaLocation="vamsas.xsd"/>
+	<xs:import namespace="www.jalview.org/colours" schemaLocation="JalviewUserColours.xsd"/>
 	<xs:complexType name="JalviewModel">
 		<xs:sequence>
 			<xs:element name="creationDate" type="xs:dateTime"/>
@@ -16,20 +11,21 @@
 				<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 name="features" type="jv:feature" minOccurs="0" maxOccurs="unbounded"/>
+							<xs:element name="pdbids" type="jv:pdbentry" minOccurs="0" maxOccurs="unbounded"/>
+							<xs:element name="hiddenSequences" type="xs:int" 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:attribute name="hidden" type="xs:boolean"/>
+					</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:element name="seq" type="xs:int" maxOccurs="unbounded"/>
 						</xs:sequence>
 						<xs:attribute name="start" type="xs:int"/>
 						<xs:attribute name="end" type="xs:int"/>
@@ -41,10 +37,31 @@
 						<xs:attribute name="displayBoxes" type="xs:boolean"/>
 						<xs:attribute name="displayText" type="xs:boolean"/>
 						<xs:attribute name="colourText" type="xs:boolean"/>
+						<xs:attribute name="textCol1" type="xs:int"/>
+						<xs:attribute name="textCol2" type="xs:int"/>
+						<xs:attribute name="textColThreshold" type="xs:int"/>
 					</xs:complexType>
 				</xs:element>
 				<xs:element name="Viewport" maxOccurs="unbounded">
 					<xs:complexType>
+						<xs:sequence>
+							<xs:element name="AnnotationColours" minOccurs="0">
+								<xs:complexType>
+									<xs:attribute name="aboveThreshold" type="xs:int"/>
+									<xs:attribute name="annotation" type="xs:string"/>
+									<xs:attribute name="minColour" type="xs:int"/>
+									<xs:attribute name="maxColour" type="xs:int"/>
+									<xs:attribute name="colourScheme" type="xs:string"/>
+									<xs:attribute name="threshold" type="xs:float"/>
+								</xs:complexType>
+							</xs:element>
+							<xs:element name="hiddenColumns" minOccurs="0" maxOccurs="unbounded">
+								<xs:complexType>
+									<xs:attribute name="start" type="xs:int"/>
+									<xs:attribute name="end" type="xs:int"/>
+								</xs:complexType>
+							</xs:element>
+						</xs:sequence>
 						<xs:attribute name="conservationSelected" type="xs:boolean"/>
 						<xs:attribute name="pidSelected" type="xs:boolean"/>
 						<xs:attribute name="bgColour" type="xs:string"/>
@@ -52,6 +69,7 @@
 						<xs:attribute name="pidThreshold" type="xs:int"/>
 						<xs:attribute name="title" type="xs:string"/>
 						<xs:attribute name="showFullId" type="xs:boolean"/>
+						<xs:attribute name="rightAlignIds" type="xs:boolean"/>
 						<xs:attribute name="showText" type="xs:boolean"/>
 						<xs:attribute name="showColourText" type="xs:boolean"/>
 						<xs:attribute name="showBoxes" type="xs:boolean"/>
@@ -59,9 +77,6 @@
 						<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"/>
@@ -71,11 +86,17 @@
 						<xs:attribute name="fontName" type="xs:string"/>
 						<xs:attribute name="fontSize" type="xs:int"/>
 						<xs:attribute name="fontStyle" type="xs:int"/>
+						<xs:attribute name="viewName" type="xs:string"/>
+						<xs:attribute name="sequenceSetId" type="xs:string"/>
+						<xs:attribute name="gatheredViews" type="xs:boolean"/>
+						<xs:attribute name="textCol1" type="xs:int"/>
+						<xs:attribute name="textCol2" type="xs:int"/>
+						<xs:attribute name="textColThreshold" type="xs:int"/>
 					</xs:complexType>
 				</xs:element>
 				<xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">
 					<xs:complexType>
-						<xs:sequence minOccurs="1">
+						<xs:sequence>
 							<xs:element name="UserColourScheme" type="jalview:JalviewUserColours"/>
 						</xs:sequence>
 						<xs:attribute name="id" type="xs:string"/>
@@ -83,7 +104,7 @@
 				</xs:element>
 				<xs:element name="tree" minOccurs="0" maxOccurs="unbounded">
 					<xs:complexType>
-						<xs:sequence minOccurs="0" maxOccurs="1">
+						<xs:sequence minOccurs="0">
 							<xs:element name="title" type="xs:string"/>
 							<xs:element name="newick" type="xs:string"/>
 						</xs:sequence>
@@ -102,34 +123,39 @@
 						<xs:attribute name="currentTree" type="xs:boolean"/>
 					</xs:complexType>
 				</xs:element>
-				
-				<xs:element name="FeatureSettings" minOccurs="0" maxOccurs="1">
-						<xs:complexType>
-				<xs:sequence>
-					<xs:element name="setting" minOccurs="0" maxOccurs="unbounded">
-						<xs:complexType>
-							<xs:attribute name="type" type="xs:string" use="required"/>
-							<xs:attribute name="colour" type="xs:int" use="required"/>
-							<xs:attribute name="display" type="xs:boolean" use="required"/>
-						</xs:complexType>
-					</xs:element>
-				</xs:sequence>
-				</xs:complexType>
+				<xs:element name="FeatureSettings" minOccurs="0">
+					<xs:complexType>
+						<xs:sequence>
+							<xs:element name="setting" minOccurs="0" maxOccurs="unbounded">
+								<xs:complexType>
+									<xs:attribute name="type" type="xs:string" use="required"/>
+									<xs:attribute name="colour" type="xs:int" use="required"/>
+									<xs:attribute name="display" type="xs:boolean" use="required"/>
+								</xs:complexType>
+							</xs:element>
+						</xs:sequence>
+					</xs:complexType>
 				</xs:element>
-				
 			</xs:sequence>
 		</xs:sequence>
 	</xs:complexType>
-	
 	<xs:complexType name="feature">
+		<xs:sequence>
+			<xs:element name="otherData" minOccurs="0" maxOccurs="unbounded">
+				<xs:complexType>
+					<xs:attribute name="key" type="xs:string" use="required"/>
+					<xs:attribute name="value" type="xs:string" use="required"/>
+				</xs:complexType>
+			</xs:element>
+		</xs:sequence>
 		<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:attribute name="featureGroup" type="xs:string" use="optional"/>
+		<xs:attribute name="score" type="xs:float" use="optional"/>
 	</xs:complexType>
-		
 	<xs:complexType name="pdbentry">
 		<xs:sequence minOccurs="0" maxOccurs="unbounded">
 			<xs:element name="property" minOccurs="0" maxOccurs="unbounded">
@@ -141,6 +167,6 @@
 		</xs:sequence>
 		<xs:attribute name="id" type="xs:string" use="required"/>
 		<xs:attribute name="type" type="xs:string" use="optional"/>
+		<xs:attribute name="file" type="xs:string"/>
 	</xs:complexType>
-	
 </xs:schema>