resources/uniprot_mapping.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   4  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   5  *
   6  * This file is part of Jalview.
   7  *
   8  * Jalview is free software: you can redistribute it and/or
   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  18  * The Jalview Authors are detailed in the 'AUTHORS' file.
  19 -->
  20 <mapping>
  21   <!-- see https://www.uniprot.org/docs/uniprot.xsd for latest Uniprot XML schema -->
  22         <class name="jalview.datamodel.xdb.uniprot.UniprotFile">
  23                  <map-to xml="uniprot"/>
  24                  <field name="UniprotEntries" type="jalview.datamodel.xdb.uniprot.UniprotEntry" collection="vector">
  25                       <bind-xml name="entry"/>
  26                  </field>
  27         </class>
  28
  29          <class name="jalview.datamodel.xdb.uniprot.UniprotEntry">
  30                 <field name="name" type="string" collection="vector"/>
  31                 <field name="accession" type="string" collection="vector"/>
  32                 <field name="protein" type="jalview.datamodel.xdb.uniprot.UniprotProteinName"/>
  33             <field name="UniprotSequence" type="jalview.datamodel.xdb.uniprot.UniprotSequence">
  34                 <bind-xml name="sequence"/>
  35             </field>
  36             <field name="feature" type="jalview.datamodel.xdb.uniprot.UniprotFeature" collection="vector"/>
  37             <field name="dbReference" type="jalview.datamodel.PDBEntry" collection="vector"/>
  38
  39          </class>
  40         <class name="jalview.datamodel.xdb.uniprot.UniprotProteinName">
  41                 <field name="name" collection="vector" type="string">
  42                         <bind-xml name="fullName" location="recommendedName" node="element"/>
  43                 </field>
  44         </class>
  45          <!-- uniprot protein name is now a collection of collections - the INCLUDES and CONTAINS entries of the uniprot
  46                 record. This means this doesn't exist anymore...
  47          <class name="jalview.datamodel.xdb.uniprot.UniprotProteinName">
  48                 <field name="name" type="string" collection="vector">
  49                         <bind-xml name="name"/>
  50                 </field>
  51          </class>
  52          -->
  53
  54          <class name="jalview.datamodel.xdb.uniprot.UniprotFeature">
  55                 <field name="type">
  56                         <bind-xml node="attribute"/>
  57                 </field>
  58                 <field name="description">
  59                          <bind-xml node="attribute"/>
  60                 </field>
  61                 <field name="status">
  62                         <bind-xml node="attribute"/>
  63                 </field>
  64                 <field name="position">
  65                  <bind-xml name="position" node="attribute" location="location/position"/>
  66                 </field>
  67                 <field name="begin">
  68                  <bind-xml name="position" node="attribute" location="location/begin"/>
  69                 </field>
  70     <field name="end">
  71       <bind-xml name="position" node="attribute" location="location/end"/>
  72     </field>
  73     <field name="variation" collection="vector" type="string">
  74      <bind-xml name="variation"/>
  75     </field>
  76     <field name="original">
  77      <bind-xml name="original"/>
  78     </field>
  79          </class>
  80
  81           <class name="jalview.datamodel.xdb.uniprot.UniprotSequence">
  82                      <field name="content" type="string">
  83                         <bind-xml name="sequence" node="text"/>
  84                      </field>
  85          </class>
  86
  87          <class name="jalview.datamodel.PDBEntry">
  88                 <field name="type"><bind-xml node="attribute"/></field>
  89                 <field name="id"><bind-xml node="attribute"/></field>
  90                 <field name="props" collection="hashtable">
  91                         <bind-xml name="property">
  92                            <class name="org.exolab.castor.mapping.MapItem">
  93                               <field name="key">
  94                                 <bind-xml name="type" node="attribute"/>
  95                               </field>
  96                               <field name="value">
  97                                 <bind-xml node="attribute"/>
  98                                 </field>
  99                            </class>
 100                         </bind-xml>
 101                 </field>
 102          </class>
 103
 104 </mapping>