X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fjalview.xsd;h=3fdf20c8b408dac477d9fa99cd01870b30c265f0;hb=8fb68bdd03fd4be2a8dd536e547c9b1d59b60734;hp=e1fbb677055b34925b5f5ac382e5263f04523953;hpb=a2094092396efa4d6736b11f3b1e1415098c3d12;p=jalview.git

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index e1fbb67..3fdf20c 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 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 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"
@@ -229,9 +230,10 @@
 				<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" />
@@ -260,7 +262,9 @@
 							type="xs:boolean" use="optional" default="true" />
 						<xs:attribute name="showSequenceLogo"
 							type="xs:boolean" use="optional" default="false" />
-						<xs:attribute name="id" type="xs:string"
+						<xs:attribute name="normaliseSequenceLogo"
+              type="xs:boolean" use="optional" default="false" />
+            <xs:attribute name="id" type="xs:string"
 							use="optional">
 							<xs:annotation>
 								<xs:documentation>
@@ -272,25 +276,11 @@
 						</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">
@@ -369,6 +359,8 @@
 							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="ignoreGapsinConsensus"
 							type="xs:boolean" use="optional" default="true" />
 
@@ -562,4 +554,16 @@
       <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>