X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=resources%2Funiprot_mapping.xml;h=4c9ad5f3eec1674fee6da61af7519bf065e3232d;hb=be77f1e015d9b97391e23541850f37ea03b41b9b;hp=d6961aa3402d050d8ac21cf4f2515e6885bbc237;hpb=010b61b99e344283e1042e0a15d7082128fa0311;p=jalview.git

diff --git a/resources/uniprot_mapping.xml b/resources/uniprot_mapping.xml
index d6961aa..4c9ad5f 100755
--- a/resources/uniprot_mapping.xml
+++ b/resources/uniprot_mapping.xml
@@ -1,71 +1,103 @@
-<?xml version="1.0"?>
-<mapping>
-	<class name="jalview.datamodel.UniprotFile">
-                 <map-to xml="uniprot"/>               
-                 <field name="UniprotEntries" type="jalview.datamodel.UniprotEntry"  collection="vector">
-		      <bind-xml name="entry"/>
-		 </field>		
-        </class>
-		 
-	 <class name="jalview.datamodel.UniprotEntry">
-	        <field name="name" type="string" collection="vector"/>
-	 	<field name="accession" type="string" collection="vector"/>
-	      	<field name="proteinName" type="string" collection="vector">
-	      		<bind-xml name="name" location="entry/protein"/>
-	      	</field>
-	      	
-	      
-	      <field name="UniprotSequence" type="jalview.datamodel.UniprotSequence">
-	      	<bind-xml name="sequence"/> 
-	       </field>
-	       <field name="feature" type="jalview.datamodel.SequenceFeature" collection="vector"/>
-	       <field name="dbReference" type="jalview.datamodel.PDBEntry" collection="vector"/>
-	   	       
-	 </class>
-	 
-	 
-	 <class name="jalview.datamodel.SequenceFeature">
-	 	<field name="type">
-	 		<bind-xml node="attribute"/>
-	 	</field>
-	 	<field name="description">
-			 <bind-xml node="attribute"/>
-	 	</field>
-	 	<field name="status">
-			<bind-xml node="attribute"/>
-	 	</field>
-	 	<field name="position">
-	 	 <bind-xml name="position" node="attribute" location="location/position"/>
-	 	 </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>
-	 </class>
-	
-          <class name="jalview.datamodel.UniprotSequence">
-		     <field name="content" type="string">
-		        <bind-xml name="sequence" node="text"/>
-		     </field>
-	 </class>
-	 
-	 <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">
-			<bind-xml name="property">
-			   <class name="org.exolab.castor.mapping.MapItem">
-			      <field name="key">
-				<bind-xml name="type" node="attribute"/>
-			      </field>
-			      <field name="value">
-			      	<bind-xml node="attribute"/>
-			      	</field>
-			   </class>
-			</bind-xml>
-		</field>
-	 </class>
-
-</mapping>
+<?xml version="1.0"?>
+<!--
+ * 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.xdb.uniprot.UniprotFile">
+                 <map-to xml="uniprot"/>               
+                 <field name="UniprotEntries" type="jalview.datamodel.xdb.uniprot.UniprotEntry" collection="vector">
+		      <bind-xml name="entry"/>
+		 </field>		
+        </class>
+		 
+	 <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.xdb.uniprot.UniprotProteinName"/>
+	    <field name="UniprotSequence" type="jalview.datamodel.xdb.uniprot.UniprotSequence">
+	      	<bind-xml name="sequence"/> 
+	    </field>
+	    <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.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.xdb.uniprot.UniprotProteinName">
+	 	<field name="name" type="string" collection="vector">
+	 		<bind-xml name="name"/>
+	 	</field>	 	
+	 </class>
+	 -->
+	 
+	 <class name="jalview.datamodel.xdb.uniprot.UniprotFeature">
+	 	<field name="type">
+	 		<bind-xml node="attribute"/>
+	 	</field>
+	 	<field name="description">
+			 <bind-xml node="attribute"/>
+	 	</field>
+	 	<field name="status">
+			<bind-xml node="attribute"/>
+	 	</field>
+	 	<field name="position">
+	 	 <bind-xml name="position" node="attribute" location="location/position"/>
+	 	</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 name="variation" collection="vector" type="string">
+     <bind-xml name="variation"/>
+    </field>
+    <field name="original">
+     <bind-xml name="original"/>
+    </field>
+	 </class>
+	
+          <class name="jalview.datamodel.xdb.uniprot.UniprotSequence">
+		     <field name="content" type="string">
+		        <bind-xml name="sequence" node="text"/>
+		     </field>
+	 </class>
+	 
+	 <class name="jalview.datamodel.PDBEntry">
+	 	<field name="type"><bind-xml node="attribute"/></field>
+	 	<field name="id"><bind-xml node="attribute"/></field>
+	 	<field name="props" collection="hashtable">
+			<bind-xml name="property">
+			   <class name="org.exolab.castor.mapping.MapItem">
+			      <field name="key">
+				<bind-xml name="type" node="attribute"/>
+			      </field>
+			      <field name="value">
+			      	<bind-xml node="attribute"/>
+			      	</field>
+			   </class>
+			</bind-xml>
+		</field>
+	 </class>
+
+</mapping>