X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fvamsas.xsd;h=22b7aac75111e71bb35d2817f5f7ab8ad52bb6c5;hb=1d6ce1bd2d0cf108d6207694e4aa6b845de11049;hp=f4380630fc72b0c3ad646745ed44f2abe1671c8b;hpb=c636e45f030b140229ec8d0748245da4a53411b5;p=jalview.git

diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
index f438063..22b7aac 100755
--- a/schemas/vamsas.xsd
+++ b/schemas/vamsas.xsd
@@ -1,24 +1,28 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
-  Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
-  Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-  
-  This program 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 2
-  of the License, or (at your option) any later version.
-  
-  This program 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 this program; if not, write to the Free Software
-  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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.
 -->
-
 <!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->
+<!-- 
+	Java JAXB binding classes are generated by running command line tool xjc:
+ 	    xjc schemas/jalview.xsd -d src -p jalview.xml.binding.jalview
+ 	Note this also generates code for included schemas
+-->
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" targetNamespace="www.vamsas.ac.uk/jalview/version2" elementFormDefault="qualified" attributeFormDefault="unqualified">
 	<xs:complexType name="VAMSAS">
 		<xs:sequence>
@@ -186,6 +190,12 @@
 						<xs:attribute name="colour" type="xs:int" />
 					</xs:complexType>
 				</xs:element>
+				<xs:element name="property" minOccurs="0" maxOccurs="unbounded">
+					<xs:complexType>
+						<xs:attribute name="name" type="xs:string" />
+						<xs:attribute name="value" type="xs:string" />
+					</xs:complexType>
+				</xs:element>
 			</xs:sequence>
 			<xs:attribute name="graph" type="xs:boolean" use="required" />
 			<xs:attribute name="graphType" type="xs:int" use="optional" />
@@ -197,6 +207,8 @@
 				use="optional" />
 			<xs:attribute name="graphGroup" type="xs:int"
 				use="optional" />
+			<xs:attribute name="graphHeight" type="xs:int" use="optional">
+			<xs:annotation><xs:documentation>height in pixels for the graph if this is a graph-type annotation.</xs:documentation></xs:annotation></xs:attribute>
 			<xs:attribute name="id" type="xs:string" use="optional" />
 			<xs:attribute name="scoreOnly" type="xs:boolean"
 				use="optional" default="false" />
@@ -214,6 +226,11 @@
 			<xs:attribute name="autoCalculated" type="xs:boolean" use="optional" default="false">
 			<xs:annotation><xs:documentation>is an autocalculated annotation row</xs:documentation>
 			</xs:annotation></xs:attribute>
+			<xs:attribute name="belowAlignment" type="xs:boolean" use="optional" default="true">
+			<xs:annotation><xs:documentation>is to be shown below the alignment - introduced in Jalview 2.8 for visualizing T-COFFEE alignment scores</xs:documentation></xs:annotation></xs:attribute>
+			<xs:attribute name="calcId" type="xs:string" use="optional">
+			<xs:annotation><xs:documentation>Optional string identifier used to group sets of annotation produced by a particular calculation. Values are opaque strings but have semantic meaning to Jalview's renderer, data importer and calculation system.</xs:documentation></xs:annotation>
+			</xs:attribute>
 		</xs:complexType>
 	</xs:element>	
 	<xs:element name="SequenceSet">