JAL-1286 check if local file ends with .gz and opens as a gzip stream

[jalview.git] / schemas / vamsas.xsd

diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
index c144d97..ec6ec7c 100755 (executable)
--- a/schemas/vamsas.xsd
+++ b/schemas/vamsas.xsd
@@ -1,20 +1,20 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
-   * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
-   * Copyright (C) 2010 J Procter, AM Waterhouse, 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 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/>.
 -->
 <!-- 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">
@@ -195,6 +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" />
@@ -212,6 +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">