JAL-4020 class reformatting

[jalview.git] / schemas / vamsas.xsd

diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
index e56a6c8..333a4e4 100755 (executable)
--- a/schemas/vamsas.xsd
+++ b/schemas/vamsas.xsd
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -18,6 +18,11 @@
  * 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>
@@ -98,6 +103,11 @@
                                                        </xs:element>
                                                </xs:choice>
                                        </xs:sequence>
+                                       <xs:attribute name="mappingType" type="xs:string" use="optional">
+                                               <xs:annotation>
+                                                       <xs:documentation>Biotype of the mapping e.g. CdsToPeptide</xs:documentation>
+                                               </xs:annotation>
+                                       </xs:attribute>
                                </xs:extension>
                        </xs:complexContent>    
                </xs:complexType>
@@ -156,6 +166,20 @@
                                                                <xs:attribute name="source" type="xs:string"/>
                                                                <xs:attribute name="version" type="xs:string"/>
                                                                <xs:attribute name="accessionId" type="xs:string"/>
+                                                               <xs:attribute name="locus" type="xs:boolean" default="false">
+                                                                       <xs:annotation>
+                                                                               <xs:documentation>
+                                                                                       true for gene locus mapping, source=species, version=assembly, accession=chromosome
+                                                                               </xs:documentation>
+                                                                       </xs:annotation>
+                                                               </xs:attribute>
+                                                               <xs:attribute name="canonical" type="xs:boolean" default="false">
+                                                                       <xs:annotation>
+                                                                               <xs:documentation>
+                                                                                       true for the representative accession for databases where multiple accessions map to the same entry (eg. Uniprot)
+                                                                               </xs:documentation>
+                                                                       </xs:annotation>
+                                                               </xs:attribute>
                                                        </xs:complexType>
                                                </xs:element>
                                        </xs:sequence>
@@ -166,6 +190,13 @@
                                                        </xs:documentation>
                                                </xs:annotation>
                                        </xs:attribute>
+                                       <xs:attribute name="biotype" type="xs:string" use="optional">
+                                               <xs:annotation>
+                                                       <xs:documentation>
+                                                               Biotype of the sequence (if known)
+                                                       </xs:documentation>
+                                               </xs:annotation>
+                                       </xs:attribute>
                                </xs:extension>
                        </xs:complexContent>
                </xs:complexType>
@@ -185,6 +216,12 @@
                                                <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" />