resources/uniprot_mapping.xml

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