Merge branch 'feature/JAL-3063JAXB' into Jalview-BH/JAL-3026-JAL-3063-JAXB

[jalview.git] / resources / uniprot_mapping.xml

diff --git a/resources/uniprot_mapping.xml b/resources/uniprot_mapping.xml
deleted file mode 100755 (executable)
index 832d3e5..0000000
--- a/resources/uniprot_mapping.xml
+++ /dev/null
@@ -1,103 +0,0 @@
-<?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">
-     <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>