X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fjalview.xsd;h=d5cd5bcfe3c8704018abccac0534d9020e3c3425;hb=fa18a41c0cd9438a527615cce1d49d49a426e096;hp=7e995ddf151e7e9d8810a5dbae99693dd64bae21;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index 7e995dd..d5cd5bc 100755
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<!-- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1) 
-	* Copyright (C) 2015 The Jalview Authors * * This file is part of 
+<!-- * 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) 
@@ -287,12 +287,18 @@
 									</xs:attribute>
 								</xs:complexType>
 							</xs:element>
+							<xs:element name="hmmerProfile" minOccurs="0" type="xs:string">
+								<xs:annotation>
+									<xs:documentation>name of the project jar entry that holds the HMM file with the profile for the sequence</xs:documentation>
+								</xs:annotation>
+							</xs:element>
 						</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:string" use="required" />
 						<xs:attribute name="hidden" type="xs:boolean" />
+						<xs:attribute name="viewreference" type="xs:boolean" use="optional"/>
 					</xs:complexType>
 				</xs:element>
 				<xs:element name="JGroup" minOccurs="0" maxOccurs="unbounded">
@@ -499,6 +505,18 @@
 						<xs:sequence>
 							<xs:element name="setting" minOccurs="0" maxOccurs="unbounded">
 								<xs:complexType>
+									<xs:sequence>
+									    <xs:element name="attributeName" type="xs:string" minOccurs="0" maxOccurs="2">
+										    	<xs:annotation>
+										    		<xs:documentation>name of feature attribute to colour by, or attribute and sub-attribute</xs:documentation>
+										    	</xs:annotation>
+									    </xs:element> 
+			    			  		   		<xs:element name="matcherSet" minOccurs="0" type="jalview:FeatureMatcherSet">
+										    	<xs:annotation>
+										    		<xs:documentation>optional filter(s) applied to the feature type</xs:documentation>
+										    	</xs:annotation>
+										</xs:element>
+								  	</xs:sequence>
 									<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"
@@ -514,6 +532,7 @@
 											</xs:documentation>
 										</xs:annotation>
 									</xs:attribute>
+									<xs:attribute name="noValueColour" use="optional" type="jalview:NoValueColour" default="Min" />
 									<xs:attribute name="threshold" type="xs:float"
 										use="optional">
 										<xs:annotation>
@@ -558,6 +577,11 @@
 			<xs:element name="otherData" minOccurs="0" maxOccurs="unbounded">
 				<xs:complexType>
 					<xs:attribute name="key" type="xs:string" use="required" />
+					<xs:attribute name="key2" type="xs:string" use="optional">
+						<xs:annotation>
+							<xs:documentation>key2 may be used for a sub-attribute of key</xs:documentation>
+						</xs:annotation>
+					</xs:attribute>
 					<xs:attribute name="value" type="xs:string" use="required" />
 				</xs:complexType>
 			</xs:element>