resources/embl_mapping.xml

   1 <?xml version="1.0"?>\r
   2 <!--\r
   3         History: Originally created from EMBL_common_V1.0\r
   4         Updated on 24th April 2007 for WsDBFetch Service move to EMBL_Services_V1.1.xsd\r
   5         -->
   6         \r
   7 <mapping xmlns="http://castor.exolab.org/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"\r
   8         xsi:schemaLocation="http://castor.exolab.org/ ../schemas/castor-mapping.xsd">\r
   9         <!-- -->\r
  10         <class name="jalview.datamodel.xdb.embl.EmblFile">\r
  11                 <map-to xml="EMBL_Services"/>\r
  12                 <field name="entries" type="jalview.datamodel.xdb.embl.EmblEntry" collection="vector">\r
  13                         <bind-xml name="entry"/>\r
  14                 </field>\r
  15                 \r
  16                 <field name="errors" type="jalview.datamodel.xdb.embl.EmblError" collection="vector">\r
  17                         <bind-xml name="Error"/>\r
  18                 </field>\r
  19         </class>\r
  20         <class name="jalview.datamodel.xdb.embl.EmblEntry">\r
  21                 <map-to xml="entry"/>\r
  22                 <field name="accession" type="string">
  23                         <bind-xml location="accession" node="attribute"/>
  24                 </field>\r
  25                 <field name="lastUpdated" type="string">\r
  26                         <bind-xml location="last-updated" node="attribute"/>\r
  27                 </field>\r
  28                 <field name="version" type="string">\r
  29                         <bind-xml location="version" node="attribute"/>\r
  30                 </field>\r
  31                 \r
  32                 <field name="rCreated" type="string">\r
  33                         <bind-xml location="releaseCreated" node="attribute"/>\r
  34                 </field>\r
  35                 <field name="rLastUpdated" type="string">\r
  36                         <bind-xml location="releaseLastUpdated" node="attribute"/>\r
  37                 </field>\r
  38                 <field name="desc" type="string">
  39                         <bind-xml name="description" node="element"/>
  40                 </field>\r
  41                 <field name="Keywords" type="string" collection="vector">\r
  42                         <bind-xml name="keyword" node="element"/>\r
  43                 </field>\r
  44                 <field name="features" type="jalview.datamodel.xdb.embl.EmblFeature" collection="vector">\r
  45                         <bind-xml name="feature"/>
  46                 </field>\r
  47                 <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">\r
  48                         <bind-xml name="dbreference" />\r
  49                 </field>\r
  50                 <field name="sequence" type="jalview.datamodel.xdb.embl.EmblSequence">\r
  51                         <bind-xml name="sequence"/> <!-- location="sequence" node="element"/ -->\r
  52                 </field>\r
  53         </class>\r
  54         <class name="jalview.datamodel.xdb.embl.EmblSequence">
  55                 <map-to xml="sequence"/>\r
  56                 <field name="type" type="string">\r
  57                         <bind-xml name="type" node="attribute" location="type"/>\r
  58                 </field>\r
  59                 <field name="version" type="string">\r
  60                         <bind-xml name="version" node="attribute" location="version"/>\r
  61                 </field>\r
  62                 <field name="sequence" type="string">\r
  63                         <bind-xml node="text"/>\r
  64                 </field>
  65         </class>\r
  66         <class name="jalview.datamodel.xdb.embl.EmblFeature" verify-constructable="false">\r
  67                 <map-to xml="feature"/>\r
  68                 <field name="name" type="string">
  69                         <bind-xml name="name" node="attribute"/>
  70                 </field>\r
  71                 <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">
  72                         <bind-xml name="dbreference" node="element"/>
  73                 </field>\r
  74                 <field name="qualifiers" type="jalview.datamodel.xdb.embl.Qualifier" collection="vector">\r
  75                         <bind-xml name="qualifier"/>\r
  76                 </field>                                        \r
  77                 <field name="locations" type="jalview.datamodel.xdb.embl.EmblFeatureLocations" collection="vector">\r
  78                         <bind-xml name="location"/>\r
  79                 </field>\r
  80         </class>\r
  81         <class name="jalview.datamodel.DBRefEntry" verify-constructable="false">\r
  82                 <field name="accessionId" type="java.lang.String"><!-- set-method="setAccessionId" get-method="getAccessionId"> -->\r
  83                         <bind-xml name="primary" node="attribute"/>\r
  84                 </field>\r
  85                 <field name="source" type="java.lang.String"> <!--set-method="setSource" get-method="getSource"> -->\r
  86                         <bind-xml name="db" node="attribute"/>\r
  87                 </field>\r
  88                 <field name="version" type="string"><!-- set-method="setVersion" get-method="getVersion"> -->\r
  89                         <bind-xml name="secondary" node="attribute"/>\r
  90                 </field>\r
  91         </class>\r
  92         <class  name="jalview.datamodel.xdb.embl.Qualifier" verify-constructable="false">
  93                 <map-to xml="Qualifier"/>\r
  94                 <field name="name">\r
  95                         <bind-xml name="name" node="attribute"/>\r
  96                 </field>\r
  97                 <field name="evidence" type="string" collection="array">\r
  98                         <bind-xml name="evidence" node="element"/>\r
  99                 </field>\r
 100                 <field name="values" type="string" collection="array">\r
 101                         <bind-xml name="value" node="element"/>\r
 102                 </field>\r
 103         </class>\r
 104         <class name="jalview.datamodel.xdb.embl.EmblFeatureLocations">\r
 105                 <map-to xml="location"/>\r
 106                 <field name="locationType" type="string">\r
 107                         <bind-xml name="type" node="attribute"/>\r
 108                 </field>\r
 109                 <field name="locationComplement" type="boolean">\r
 110                         <bind-xml name="complement" node="attribute"/>\r
 111                 </field>\r
 112                 <field name="locElements" type="jalview.datamodel.xdb.embl.EmblFeatureLocElement" collection="vector">\r
 113                         <bind-xml name="locationElement"/>\r
 114                 </field>\r
 115         </class>\r
 116         <class name="jalview.datamodel.xdb.embl.EmblFeatureLocElement">\r
 117                 <map-to xml="locationElement"/>\r
 118                 <field name="type" type="string">\r
 119                         <bind-xml name="type" node="attribute"/>\r
 120                 </field>\r
 121                 <field name="accession" type="string">\r
 122                         <bind-xml name="accession" node="attribute"/>                   \r
 123                 </field>\r
 124                 <field name="version" type="string">\r
 125                         <bind-xml name="version" node="attribute"/>\r
 126                 </field>\r
 127                 <field name="complement" type="boolean">\r
 128                         <bind-xml name="complement"/>\r
 129                 </field>\r
 130                 <field name="basePositions" type="jalview.datamodel.xdb.embl.BasePosition" collection="array">\r
 131                         <bind-xml name="basePosition" node="element"/>\r
 132                 </field>\r
 133         </class>\r
 134         <class name="jalview.datamodel.xdb.embl.BasePosition">
 135                 <map-to xml="basePosition"/>\r
 136                 <field name="type">
 137                         <bind-xml name="type" node="attribute"/>
 138                 </field>\r
 139                 <field name="pos">
 140                         <bind-xml node="text"/>\r
 141                 </field>\r
 142         </class>\r
 143 </mapping>\r