X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fjalview.xsd;h=eab650040cef4637326cf1ceb361470e87bfdd24;hb=cb7c4a276c52b0bb3e448e6761886fecc0e9d05c;hp=03c572844e4a47d3f8c1a5a7a382da79deca3334;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index 03c5728..eab6500 100755
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -1,20 +1,21 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
-  Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
-  Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
-  
-  This file is part of Jalview.
-  
-  Jalview is free software: you can redistribute it and/or
-  modify it under the terms of the GNU General Public License 
-  as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
-   
-  Jalview is distributed in the hope that it will be useful, but 
-  WITHOUT ANY WARRANTY; without even the implied warranty 
-  of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
-  PURPOSE.  See the GNU General Public License for more details.
-  
-  You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
 -->
 <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" xmlns:jvws="www.jalview.org/xml/wsparamset" targetNamespace="www.jalview.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
 		<xs:import namespace="www.vamsas.ac.uk/jalview/version2" schemaLocation="vamsas.xsd"/>
@@ -26,7 +27,7 @@
 			<xs:element name="version" type="xs:string" />
 			<xs:element name="vamsasModel" type="vamsas:VAMSAS" />
 			<xs:sequence>
-				<xs:element name="JSeq" maxOccurs="unbounded">
+				<xs:element name="JSeq" maxOccurs="unbounded" minOccurs="0">
 					<xs:complexType>
 						<xs:sequence>
 							<xs:element name="features"
@@ -202,6 +203,15 @@
 																		</xs:documentation>
 																	</xs:annotation>
 																</xs:attribute>
+																<xs:attribute name="type" type="xs:string"
+																	use="optional">
+																	<xs:annotation>
+																		<xs:documentation>
+																			An identifier for the viewer type, currently either
+																			JMOL or CHIMERA
+																		</xs:documentation>
+																	</xs:annotation>
+																</xs:attribute>
 
 															</xs:extension>
 														</xs:simpleContent>
@@ -229,9 +239,10 @@
 				<xs:element name="JGroup" minOccurs="0"
 					maxOccurs="unbounded">
 					<xs:complexType>
-						<xs:sequence>
-							<xs:element name="seq" type="xs:string"
-								maxOccurs="unbounded" />
+            <xs:sequence>
+							<xs:element name="seq" type="xs:string" maxOccurs="unbounded" />
+							<xs:element name="annotationColours" type="jv:AnnotationColourScheme"
+								minOccurs="0" maxOccurs="1" />
 						</xs:sequence>
 						<xs:attribute name="start" type="xs:int" />
 						<xs:attribute name="end" type="xs:int" />
@@ -274,25 +285,11 @@
 						</xs:attribute>
 					</xs:complexType>
 				</xs:element>
-				<xs:element name="Viewport" maxOccurs="unbounded">
+				<xs:element name="Viewport" maxOccurs="unbounded" minOccurs="0">
 					<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 name="AnnotationColours" type="jv:AnnotationColourScheme" 
+								minOccurs="0" maxOccurs="1">
 							</xs:element>
 							<xs:element name="hiddenColumns"
 								minOccurs="0" maxOccurs="unbounded">
@@ -371,12 +368,11 @@
 							type="xs:boolean" use="optional" default="true" />
 						<xs:attribute name="showSequenceLogo"
 							type="xs:boolean" use="optional" default="false" />
-            <xs:attribute name="normaliseSequenceLogo"
-              type="xs:boolean" use="optional" default="false" />
+			            <xs:attribute name="normaliseSequenceLogo"
+			              type="xs:boolean" use="optional" default="false" />
 						<xs:attribute name="ignoreGapsinConsensus"
 							type="xs:boolean" use="optional" default="true" />
-
-						<xs:attribute name="startRes" 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" />
@@ -400,6 +396,14 @@
 								</xs:documentation>
 							</xs:annotation>
 						</xs:attribute>
+						<xs:attribute name="complementId" type="xs:string"
+							use="optional">
+							<xs:annotation>
+								<xs:documentation>
+									The viewport id of this viewport's (cdna/protein) coding complement, if any
+								</xs:documentation>
+							</xs:annotation>
+						</xs:attribute>
 					</xs:complexType>
 				</xs:element>
 				<xs:element name="UserColours" minOccurs="0"
@@ -566,4 +570,16 @@
       <xs:attribute name="xpos" type="xs:int"/>
       <xs:attribute name="ypos" type="xs:int"/>
     </xs:attributeGroup>
+  <xs:complexType name="AnnotationColourScheme">
+	<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:attribute name="perSequence" type="xs:boolean" use="optional" />
+	<xs:attribute name="predefinedColours" type="xs:boolean"
+		use="optional" />
+  </xs:complexType>
+  
 </xs:schema>