X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=resources%2Funiprot_mapping.xml;h=68868c4e378934bc21e5289695f0aa647d14b089;hb=cf7336a4d64f799b6f6362622d740693e251bf9a;hp=5664440e7f270092fc8ee708aa189437c0118b56;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/resources/uniprot_mapping.xml b/resources/uniprot_mapping.xml
index 5664440..68868c4 100755
--- a/resources/uniprot_mapping.xml
+++ b/resources/uniprot_mapping.xml
@@ -1,56 +1,57 @@
 <?xml version="1.0"?>
 <!--
-   * 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * 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/>.
+ * 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">