extend XML model for graduated feature colours, group associated manual/auto annotati...

[jalview.git] / schemas / vamsas.xsd

diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
index b457bec..f438063 100755 (executable)
--- a/schemas/vamsas.xsd
+++ b/schemas/vamsas.xsd
@@ -1,4 +1,23 @@
 <?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
+-->
+
 <!-- 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">
@@ -89,9 +108,15 @@
                        <xs:sequence>
                                <xs:element name="alcodon" minOccurs="0" maxOccurs="unbounded">
                                        <xs:complexType>
-                                               <xs:attribute name="pos1" type="xs:integer"/>
-                                               <xs:attribute name="pos2" type="xs:integer"/>
-                                               <xs:attribute name="pos3" type="xs:integer"/>
+                                               <xs:annotation>
+                                                       <xs:documentation>
+                                                               specifies a series of aligned codons from an associated DNA sequence alignment that when translated correspond to columns of a peptide alignment.
+                                                               Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide).
+                                                       </xs:documentation>
+                                               </xs:annotation>
+                                               <xs:attribute name="pos1" type="xs:integer" use="optional"/>
+                                               <xs:attribute name="pos2" type="xs:integer" use="optional"/>
+                                               <xs:attribute name="pos3" type="xs:integer" use="optional"/>
                                        </xs:complexType>
                                </xs:element>
                                <xs:element name="alcodMap" minOccurs="0" maxOccurs="unbounded">
@@ -149,26 +174,46 @@
        <xs:element name="Annotation">
                <xs:complexType>
                        <xs:sequence>
-                               <xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded"/>
-                               <xs:element name="label" type="xs:string"/>
-                               <xs:element name="description" type="xs:string" minOccurs="0"/>
+                               <xs:element ref="vamsas:annotationElement" minOccurs="0"
+                                       maxOccurs="unbounded" />
+                               <xs:element name="label" type="xs:string" />
+                               <xs:element name="description" type="xs:string"
+                                       minOccurs="0" />
                                <xs:element name="thresholdLine" minOccurs="0">
                                        <xs:complexType>
-                                               <xs:attribute name="label" type="xs:string"/>
-                                               <xs:attribute name="value" type="xs:float"/>
-                                               <xs:attribute name="colour" type="xs:int"/>
+                                               <xs:attribute name="label" type="xs:string" />
+                                               <xs:attribute name="value" type="xs:float" />
+                                               <xs:attribute name="colour" type="xs:int" />
                                        </xs:complexType>
                                </xs:element>
                        </xs:sequence>
-                       <xs:attribute name="graph" type="xs:boolean" use="required"/>
-                       <xs:attribute name="graphType" type="xs:int" use="optional"/>
-                       <xs:attribute name="sequenceRef" type="xs:string" use="optional"/>
-                       <xs:attribute name="graphColour" type="xs:int" use="optional"/>
-                       <xs:attribute name="graphGroup" type="xs:int" use="optional"/>
-                       <xs:attribute name="id" type="xs:string" use="optional"/>
-                       <xs:attribute name="scoreOnly" type="xs:boolean" use="optional" default="false"/>
-                       <xs:attribute name="score" type="xs:double" use="optional"/>
-                       <xs:attribute name="visible" type="xs:boolean" use="optional"/>
+                       <xs:attribute name="graph" type="xs:boolean" use="required" />
+                       <xs:attribute name="graphType" type="xs:int" use="optional" />
+                       <xs:attribute name="sequenceRef" type="xs:string"
+                               use="optional" />
+                       <xs:attribute name="groupRef" type="xs:string"
+                               use="optional" />
+                       <xs:attribute name="graphColour" type="xs:int"
+                               use="optional" />
+                       <xs:attribute name="graphGroup" type="xs:int"
+                               use="optional" />
+                       <xs:attribute name="id" type="xs:string" use="optional" />
+                       <xs:attribute name="scoreOnly" type="xs:boolean"
+                               use="optional" default="false" />
+                       <xs:attribute name="score" type="xs:double" use="optional" />
+                       <xs:attribute name="visible" type="xs:boolean"
+                               use="optional" />
+                       <xs:attribute name="centreColLabels" type="xs:boolean"
+                               use="optional" />
+                       <xs:attribute name="scaleColLabels" type="xs:boolean"
+                               use="optional" />
+                       <xs:attribute name="showAllColLabels" type="xs:boolean"
+                               use="optional" />
+
+
+                       <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:complexType>
        </xs:element>   
        <xs:element name="SequenceSet">