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         <class name="jalview.datamodel.UniprotFile">
  22                  <map-to xml="uniprot"/>
  23                  <field name="UniprotEntries" type="jalview.datamodel.UniprotEntry" collection="vector">
  24                       <bind-xml name="entry"/>
  25                  </field>
  26         </class>
  27
  28          <class name="jalview.datamodel.UniprotEntry">
  29                 <field name="name" type="string" collection="vector"/>
  30                 <field name="accession" type="string" collection="vector"/>
  31                 <field name="protein" type="jalview.datamodel.UniprotProteinName"/>
  32             <field name="UniprotSequence" type="jalview.datamodel.UniprotSequence">
  33                 <bind-xml name="sequence"/>
  34             </field>
  35             <field name="feature" type="jalview.datamodel.SequenceFeature" collection="vector"/>
  36             <field name="dbReference" type="jalview.datamodel.PDBEntry" collection="vector"/>
  37
  38          </class>
  39         <class name="jalview.datamodel.UniprotProteinName">
  40                 <field name="name" collection="vector" type="string">
  41                         <bind-xml name="fullName" location="recommendedName" node="element"/>
  42                 </field>
  43         </class>
  44          <!-- uniprot protein name is now a collection of collections - the INCLUDES and CONTAINS entries of the uniprot
  45                 record. This means this doesn't exist anymore...
  46          <class name="jalview.datamodel.UniprotProteinName">
  47                 <field name="name" type="string" collection="vector">
  48                         <bind-xml name="name"/>
  49                 </field>
  50          </class>
  51          -->
  52
  53          <class name="jalview.datamodel.SequenceFeature">
  54                 <field name="type">
  55                         <bind-xml node="attribute"/>
  56                 </field>
  57                 <field name="description">
  58                          <bind-xml node="attribute"/>
  59                 </field>
  60                 <field name="status">
  61                         <bind-xml node="attribute"/>
  62                 </field>
  63                 <field name="position">
  64                  <bind-xml name="position" node="attribute" location="location/position"/>
  65                  </field>
  66                 <field name="begin">
  67                  <bind-xml name="position" node="attribute" location="location/begin"/>
  68                  </field>
  69                 <field name="end">
  70                  <bind-xml name="position" node="attribute" location="location/end"/>
  71                  </field>
  72          </class>
  73
  74           <class name="jalview.datamodel.UniprotSequence">
  75                      <field name="content" type="string">
  76                         <bind-xml name="sequence" node="text"/>
  77                      </field>
  78          </class>
  79
  80          <class name="jalview.datamodel.PDBEntry">
  81                 <field name="type"><bind-xml node="attribute"/></field>
  82                 <field name="id"><bind-xml node="attribute"/></field>
  83                 <field name="property" collection="hashtable">
  84                         <bind-xml name="property">
  85                            <class name="org.exolab.castor.mapping.MapItem">
  86                               <field name="key">
  87                                 <bind-xml name="type" node="attribute"/>
  88                               </field>
  89                               <field name="value">
  90                                 <bind-xml node="attribute"/>
  91                                 </field>
  92                            </class>
  93                         </bind-xml>
  94                 </field>
  95          </class>
  96
  97 </mapping>