resources/uniprot_mapping.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
   4  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
   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 -->
  19 <mapping>
  20         <class name="jalview.datamodel.UniprotFile">
  21                  <map-to xml="uniprot"/>
  22                  <field name="UniprotEntries" type="jalview.datamodel.UniprotEntry" collection="vector">
  23                       <bind-xml name="entry"/>
  24                  </field>
  25         </class>
  26
  27          <class name="jalview.datamodel.UniprotEntry">
  28                 <field name="name" type="string" collection="vector"/>
  29                 <field name="accession" type="string" collection="vector"/>
  30                 <field name="protein" type="jalview.datamodel.UniprotProteinName"/>
  31             <field name="UniprotSequence" type="jalview.datamodel.UniprotSequence">
  32                 <bind-xml name="sequence"/>
  33             </field>
  34             <field name="feature" type="jalview.datamodel.SequenceFeature" collection="vector"/>
  35             <field name="dbReference" type="jalview.datamodel.PDBEntry" collection="vector"/>
  36
  37          </class>
  38         <class name="jalview.datamodel.UniprotProteinName">
  39                 <field name="name" collection="vector" type="string">
  40                         <bind-xml name="fullName" location="recommendedName" node="element"/>
  41                 </field>
  42         </class>
  43          <!-- uniprot protein name is now a collection of collections - the INCLUDES and CONTAINS entries of the uniprot
  44                 record. This means this doesn't exist anymore...
  45          <class name="jalview.datamodel.UniprotProteinName">
  46                 <field name="name" type="string" collection="vector">
  47                         <bind-xml name="name"/>
  48                 </field>
  49          </class>
  50          -->
  51
  52          <class name="jalview.datamodel.SequenceFeature">
  53                 <field name="type">
  54                         <bind-xml node="attribute"/>
  55                 </field>
  56                 <field name="description">
  57                          <bind-xml node="attribute"/>
  58                 </field>
  59                 <field name="status">
  60                         <bind-xml node="attribute"/>
  61                 </field>
  62                 <field name="position">
  63                  <bind-xml name="position" node="attribute" location="location/position"/>
  64                  </field>
  65                 <field name="begin">
  66                  <bind-xml name="position" node="attribute" location="location/begin"/>
  67                  </field>
  68                 <field name="end">
  69                  <bind-xml name="position" node="attribute" location="location/end"/>
  70                  </field>
  71          </class>
  72
  73           <class name="jalview.datamodel.UniprotSequence">
  74                      <field name="content" type="string">
  75                         <bind-xml name="sequence" node="text"/>
  76                      </field>
  77          </class>
  78
  79          <class name="jalview.datamodel.PDBEntry">
  80                 <field name="type"><bind-xml node="attribute"/></field>
  81                 <field name="id"><bind-xml node="attribute"/></field>
  82                 <field name="property" collection="hashtable">
  83                         <bind-xml name="property">
  84                            <class name="org.exolab.castor.mapping.MapItem">
  85                               <field name="key">
  86                                 <bind-xml name="type" node="attribute"/>
  87                               </field>
  88                               <field name="value">
  89                                 <bind-xml node="attribute"/>
  90                                 </field>
  91                            </class>
  92                         </bind-xml>
  93                 </field>
  94          </class>
  95
  96 </mapping>