JAL-2920 JAL-3017 uniprot XML schema included in mappings doc

[jalview.git] / resources / uniprot_mapping.xml

diff --git a/resources/uniprot_mapping.xml b/resources/uniprot_mapping.xml
index 092a3c7..68868c4 100755 (executable)
--- a/resources/uniprot_mapping.xml
+++ b/resources/uniprot_mapping.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <!--
- * 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.
  * 
@@ -18,39 +18,40 @@
  * The Jalview Authors are detailed in the 'AUTHORS' file.
 -->
 <mapping>
-       <class name="jalview.datamodel.UniprotFile">
+  <!-- see https://www.uniprot.org/docs/uniprot.xsd for latest Uniprot XML schema -->
+       <class name="jalview.datamodel.xdb.uniprot.UniprotFile">
                  <map-to xml="uniprot"/>               
-                 <field name="UniprotEntries" type="jalview.datamodel.UniprotEntry" collection="vector">
+                 <field name="UniprotEntries" type="jalview.datamodel.xdb.uniprot.UniprotEntry" collection="vector">
                      <bind-xml name="entry"/>
                 </field>               
         </class>
                 
-        <class name="jalview.datamodel.UniprotEntry">
+        <class name="jalview.datamodel.xdb.uniprot.UniprotEntry">
                <field name="name" type="string" collection="vector"/>
                <field name="accession" type="string" collection="vector"/>
-               <field name="protein" type="jalview.datamodel.UniprotProteinName"/>
-           <field name="UniprotSequence" type="jalview.datamodel.UniprotSequence">
+               <field name="protein" type="jalview.datamodel.xdb.uniprot.UniprotProteinName"/>
+           <field name="UniprotSequence" type="jalview.datamodel.xdb.uniprot.UniprotSequence">
                <bind-xml name="sequence"/> 
            </field>
-           <field name="feature" type="jalview.datamodel.SequenceFeature" collection="vector"/>
+           <field name="feature" type="jalview.datamodel.xdb.uniprot.UniprotFeature" collection="vector"/>
            <field name="dbReference" type="jalview.datamodel.PDBEntry" collection="vector"/>
                       
         </class>
-       <class name="jalview.datamodel.UniprotProteinName">
+       <class name="jalview.datamodel.xdb.uniprot.UniprotProteinName">
                <field name="name" collection="vector" type="string">
                        <bind-xml name="fullName" location="recommendedName" node="element"/>
                </field>
        </class>
         <!-- uniprot protein name is now a collection of collections - the INCLUDES and CONTAINS entries of the uniprot
                record. This means this doesn't exist anymore...
-        <class name="jalview.datamodel.UniprotProteinName">
+        <class name="jalview.datamodel.xdb.uniprot.UniprotProteinName">
                <field name="name" type="string" collection="vector">
                        <bind-xml name="name"/>
                </field>                
         </class>
         -->
         
-        <class name="jalview.datamodel.SequenceFeature">
+        <class name="jalview.datamodel.xdb.uniprot.UniprotFeature">
                <field name="type">
                        <bind-xml node="attribute"/>
                </field>
@@ -62,16 +63,22 @@
                </field>
                <field name="position">
                 <bind-xml name="position" node="attribute" location="location/position"/>
-                </field>
+               </field>
                <field name="begin">
                 <bind-xml name="position" node="attribute" location="location/begin"/>
-                </field>
-               <field name="end">
-                <bind-xml name="position" node="attribute" location="location/end"/>
-                </field>
+               </field>
+    <field name="end">
+      <bind-xml name="position" node="attribute" location="location/end"/>
+    </field>
+    <field name="variation" collection="vector" type="string">
+     <bind-xml name="variation"/>
+    </field>
+    <field name="original">
+     <bind-xml name="original"/>
+    </field>
         </class>
        
-          <class name="jalview.datamodel.UniprotSequence">
+          <class name="jalview.datamodel.xdb.uniprot.UniprotSequence">
                     <field name="content" type="string">
                        <bind-xml name="sequence" node="text"/>
                     </field>
@@ -80,7 +87,7 @@
         <class name="jalview.datamodel.PDBEntry">
                <field name="type"><bind-xml node="attribute"/></field>
                <field name="id"><bind-xml node="attribute"/></field>
-               <field name="property" collection="hashtable">
+               <field name="props" collection="hashtable">
                        <bind-xml name="property">
                           <class name="org.exolab.castor.mapping.MapItem">
                              <field name="key">