resources/uniprot_mapping.xml

   1 <?xml version="1.0"?>\r
   2 <mapping>\r
   3         <class name="jalview.datamodel.UniprotFile">\r
   4                  <map-to xml="uniprot"/>               \r
   5                  <field name="UniprotEntries" type="jalview.datamodel.UniprotEntry"  collection="vector">\r
   6                       <bind-xml name="entry"/>\r
   7                  </field>               \r
   8         </class>\r
   9                  \r
  10          <class name="jalview.datamodel.UniprotEntry">\r
  11                 <field name="name" type="string" collection="vector"/>\r
  12                 <field name="accession" type="string" collection="vector"/>\r
  13                 <field name="proteinName" type="string" collection="vector">\r
  14                         <bind-xml name="name" location="entry/protein"/>\r
  15                 </field>\r
  16                 \r
  17               \r
  18               <field name="UniprotSequence" type="jalview.datamodel.UniprotSequence">\r
  19                 <bind-xml name="sequence"/> \r
  20                </field>\r
  21                <field name="feature" type="jalview.datamodel.SequenceFeature" collection="vector"/>\r
  22                <field name="dbReference" type="jalview.datamodel.PDBEntry" collection="vector"/>\r
  23                        \r
  24          </class>\r
  25          \r
  26          \r
  27          <class name="jalview.datamodel.SequenceFeature">\r
  28                 <field name="type">\r
  29                         <bind-xml node="attribute"/>\r
  30                 </field>\r
  31                 <field name="description">\r
  32                          <bind-xml node="attribute"/>\r
  33                 </field>\r
  34                 <field name="status">\r
  35                         <bind-xml node="attribute"/>\r
  36                 </field>\r
  37                 <field name="position">\r
  38                  <bind-xml name="position" node="attribute" location="location/position"/>\r
  39                  </field>\r
  40                 <field name="begin">\r
  41                  <bind-xml name="position" node="attribute" location="location/begin"/>\r
  42                  </field>\r
  43                 <field name="end">\r
  44                  <bind-xml name="position" node="attribute" location="location/end"/>\r
  45                  </field>\r
  46          </class>\r
  47         \r
  48           <class name="jalview.datamodel.UniprotSequence">\r
  49                      <field name="content" type="string">\r
  50                         <bind-xml name="sequence" node="text"/>\r
  51                      </field>\r
  52          </class>\r
  53          \r
  54          <class name="jalview.datamodel.PDBEntry">\r
  55                 <field name="type"><bind-xml node="attribute"/></field>\r
  56                 <field name="id"><bind-xml node="attribute"/></field>\r
  57                 <field name="property" collection="hashtable">\r
  58                         <bind-xml name="property">\r
  59                            <class name="org.exolab.castor.mapping.MapItem">\r
  60                               <field name="key">\r
  61                                 <bind-xml name="type" node="attribute"/>\r
  62                               </field>\r
  63                               <field name="value">\r
  64                                 <bind-xml node="attribute"/>\r
  65                                 </field>\r
  66                            </class>\r
  67                         </bind-xml>\r
  68                 </field>\r
  69          </class>\r
  70 \r
  71 </mapping>\r