X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fvamsas.xsd;h=ec6ec7c6d821b281871a8fdd241b6820e2b1f8d0;hb=02e9934037787599aefda03a6af9b7501e867dc3;hp=f4380630fc72b0c3ad646745ed44f2abe1671c8b;hpb=c636e45f030b140229ec8d0748245da4a53411b5;p=jalview.git

diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
index f438063..ec6ec7c 100755
--- a/schemas/vamsas.xsd
+++ b/schemas/vamsas.xsd
@@ -1,23 +1,21 @@
 <?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
+  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 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 file is part of Jalview.
   
-  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.
+  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 this program; if not, write to the Free Software
-  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+  You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 -->
-
 <!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->
 <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">
@@ -197,6 +195,8 @@
 				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 +214,11 @@
 			<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">