resources/uniprot_mapping.xml

   1 <?xml version="1.0"?>
   2 <mapping>
   3         <class name="jalview.datamodel.UniprotFile">
   4                  <map-to xml="uniprot"/>
   5                  <field name="UniprotEntries" type="jalview.datamodel.UniprotEntry" collection="vector">
   6                       <bind-xml name="entry"/>
   7                  </field>
   8         </class>
   9
  10          <class name="jalview.datamodel.UniprotEntry">
  11                 <field name="name" type="string" collection="vector"/>
  12                 <field name="accession" type="string" collection="vector"/>
  13                 <field name="protein" type="jalview.datamodel.UniprotProteinName"/>
  14             <field name="UniprotSequence" type="jalview.datamodel.UniprotSequence">
  15                 <bind-xml name="sequence"/>
  16             </field>
  17             <field name="feature" type="jalview.datamodel.SequenceFeature" collection="vector"/>
  18             <field name="dbReference" type="jalview.datamodel.PDBEntry" collection="vector"/>
  19
  20          </class>
  21         <class name="jalview.datamodel.UniprotProteinName">
  22                 <field name="name" collection="vector" type="string">
  23                         <bind-xml name="fullName" location="recommendedName" node="element"/>
  24                 </field>
  25         </class>
  26          <!-- uniprot protein name is now a collection of collections - the INCLUDES and CONTAINS entries of the uniprot
  27                 record. This means this doesn't exist anymore...
  28          <class name="jalview.datamodel.UniprotProteinName">
  29                 <field name="name" type="string" collection="vector">
  30                         <bind-xml name="name"/>
  31                 </field>
  32          </class>
  33          -->
  34
  35          <class name="jalview.datamodel.SequenceFeature">
  36                 <field name="type">
  37                         <bind-xml node="attribute"/>
  38                 </field>
  39                 <field name="description">
  40                          <bind-xml node="attribute"/>
  41                 </field>
  42                 <field name="status">
  43                         <bind-xml node="attribute"/>
  44                 </field>
  45                 <field name="position">
  46                  <bind-xml name="position" node="attribute" location="location/position"/>
  47                  </field>
  48                 <field name="begin">
  49                  <bind-xml name="position" node="attribute" location="location/begin"/>
  50                  </field>
  51                 <field name="end">
  52                  <bind-xml name="position" node="attribute" location="location/end"/>
  53                  </field>
  54          </class>
  55
  56           <class name="jalview.datamodel.UniprotSequence">
  57                      <field name="content" type="string">
  58                         <bind-xml name="sequence" node="text"/>
  59                      </field>
  60          </class>
  61
  62          <class name="jalview.datamodel.PDBEntry">
  63                 <field name="type"><bind-xml node="attribute"/></field>
  64                 <field name="id"><bind-xml node="attribute"/></field>
  65                 <field name="property" collection="hashtable">
  66                         <bind-xml name="property">
  67                            <class name="org.exolab.castor.mapping.MapItem">
  68                               <field name="key">
  69                                 <bind-xml name="type" node="attribute"/>
  70                               </field>
  71                               <field name="value">
  72                                 <bind-xml node="attribute"/>
  73                                 </field>
  74                            </class>
  75                         </bind-xml>
  76                 </field>
  77          </class>
  78
  79 </mapping>