resources/embl_mapping.xml

   1 <?xml version="1.0"?>\r
   2 <!--\r
   3    * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
   4    * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   5    * \r
   6    * This program is free software; you can redistribute it and/or\r
   7    * modify it under the terms of the GNU General Public License\r
   8    * as published by the Free Software Foundation; either version 2\r
   9    * of the License, or (at your option) any later version.\r
  10    * \r
  11    * This program is distributed in the hope that it will be useful,\r
  12    * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  13    * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  14    * GNU General Public License for more details.\r
  15    * \r
  16    * You should have received a copy of the GNU General Public License\r
  17    * along with this program; if not, write to the Free Software\r
  18    * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  19 -->\r
  20 <mapping xmlns="http://castor.exolab.org/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"\r
  21         xsi:schemaLocation="http://castor.exolab.org/ ../schemas/castor-mapping.xsd">\r
  22 <!--\r
  23         History: Originally created from EMBL_common_V1.0\r
  24         Updated on 24th April 2007 for WsDBFetch Service move to EMBL_Services_V1.1.xsd\r
  25         -->\r
  26         <class name="jalview.datamodel.xdb.embl.EmblFile">\r
  27                 <map-to xml="EMBL_Services"/>\r
  28                 <field name="entries" type="jalview.datamodel.xdb.embl.EmblEntry" collection="vector">\r
  29                         <bind-xml name="entry"/>\r
  30                 </field>\r
  31                 \r
  32                 <field name="errors" type="jalview.datamodel.xdb.embl.EmblError" collection="vector">\r
  33                         <bind-xml name="Error"/>\r
  34                 </field>\r
  35         </class>\r
  36         <class name="jalview.datamodel.xdb.embl.EmblEntry">\r
  37                 <map-to xml="entry"/>\r
  38                 <field name="accession" type="string">\r
  39                         <bind-xml location="accession" node="attribute"/>\r
  40                 </field>\r
  41                 <field name="lastUpdated" type="string">\r
  42                         <bind-xml location="last-updated" node="attribute"/>\r
  43                 </field>\r
  44                 <field name="version" type="string">\r
  45                         <bind-xml location="version" node="attribute"/>\r
  46                 </field>\r
  47                 \r
  48                 <field name="rCreated" type="string">\r
  49                         <bind-xml location="releaseCreated" node="attribute"/>\r
  50                 </field>\r
  51                 <field name="rLastUpdated" type="string">\r
  52                         <bind-xml location="releaseLastUpdated" node="attribute"/>\r
  53                 </field>\r
  54                 <field name="desc" type="string">\r
  55                         <bind-xml name="description" node="element"/>\r
  56                 </field>\r
  57                 <field name="Keywords" type="string" collection="vector">\r
  58                         <bind-xml name="keyword" node="element"/>\r
  59                 </field>\r
  60                 <field name="features" type="jalview.datamodel.xdb.embl.EmblFeature" collection="vector">\r
  61                         <bind-xml name="feature"/>\r
  62                 </field>\r
  63                 <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">\r
  64                         <bind-xml name="dbreference" />\r
  65                 </field>\r
  66                 <field name="sequence" type="jalview.datamodel.xdb.embl.EmblSequence">\r
  67                         <bind-xml name="sequence"/> <!-- location="sequence" node="element"/ -->\r
  68                 </field>\r
  69         </class>\r
  70         <class name="jalview.datamodel.xdb.embl.EmblSequence">\r
  71                 <map-to xml="sequence"/>\r
  72                 <field name="type" type="string">\r
  73                         <bind-xml name="type" node="attribute" location="type"/>\r
  74                 </field>\r
  75                 <field name="version" type="string">\r
  76                         <bind-xml name="version" node="attribute" location="version"/>\r
  77                 </field>\r
  78                 <field name="sequence" type="string">\r
  79                         <bind-xml node="text"/>\r
  80                 </field>\r
  81         </class>\r
  82         <class name="jalview.datamodel.xdb.embl.EmblFeature" verify-constructable="false">\r
  83                 <map-to xml="feature"/>\r
  84                 <field name="name" type="string">\r
  85                         <bind-xml name="name" node="attribute"/>\r
  86                 </field>\r
  87                 <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">\r
  88                         <bind-xml name="dbreference" node="element"/>\r
  89                 </field>\r
  90                 <field name="qualifiers" type="jalview.datamodel.xdb.embl.Qualifier" collection="vector">\r
  91                         <bind-xml name="qualifier"/>\r
  92                 </field>                                        \r
  93                 <field name="locations" type="jalview.datamodel.xdb.embl.EmblFeatureLocations" collection="vector">\r
  94                         <bind-xml name="location"/>\r
  95                 </field>\r
  96         </class>\r
  97         <class name="jalview.datamodel.DBRefEntry" verify-constructable="false">\r
  98                 <field name="accessionId" type="java.lang.String"><!-- set-method="setAccessionId" get-method="getAccessionId"> -->\r
  99                         <bind-xml name="primary" node="attribute"/>\r
 100                 </field>\r
 101                 <field name="source" type="java.lang.String"> <!--set-method="setSource" get-method="getSource"> -->\r
 102                         <bind-xml name="db" node="attribute"/>\r
 103                 </field>\r
 104                 <field name="version" type="string"><!-- set-method="setVersion" get-method="getVersion"> -->\r
 105                         <bind-xml name="secondary" node="attribute"/>\r
 106                 </field>\r
 107         </class>\r
 108         <class  name="jalview.datamodel.xdb.embl.Qualifier" verify-constructable="false">\r
 109                 <map-to xml="Qualifier"/>\r
 110                 <field name="name">\r
 111                         <bind-xml name="name" node="attribute"/>\r
 112                 </field>\r
 113                 <field name="evidence" type="string" collection="array">\r
 114                         <bind-xml name="evidence" node="element"/>\r
 115                 </field>\r
 116                 <field name="values" type="string" collection="array">\r
 117                         <bind-xml name="value" node="element"/>\r
 118                 </field>\r
 119         </class>\r
 120         <class name="jalview.datamodel.xdb.embl.EmblFeatureLocations">\r
 121                 <map-to xml="location"/>\r
 122                 <field name="locationType" type="string">\r
 123                         <bind-xml name="type" node="attribute"/>\r
 124                 </field>\r
 125                 <field name="locationComplement" type="boolean">\r
 126                         <bind-xml name="complement" node="attribute"/>\r
 127                 </field>\r
 128                 <field name="locElements" type="jalview.datamodel.xdb.embl.EmblFeatureLocElement" collection="vector">\r
 129                         <bind-xml name="locationElement"/>\r
 130                 </field>\r
 131         </class>\r
 132         <class name="jalview.datamodel.xdb.embl.EmblFeatureLocElement">\r
 133                 <map-to xml="locationElement"/>\r
 134                 <field name="type" type="string">\r
 135                         <bind-xml name="type" node="attribute"/>\r
 136                 </field>\r
 137                 <field name="accession" type="string">\r
 138                         <bind-xml name="accession" node="attribute"/>                   \r
 139                 </field>\r
 140                 <field name="version" type="string">\r
 141                         <bind-xml name="version" node="attribute"/>\r
 142                 </field>\r
 143                 <field name="complement" type="boolean">\r
 144                         <bind-xml name="complement"/>\r
 145                 </field>\r
 146                 <field name="basePositions" type="jalview.datamodel.xdb.embl.BasePosition" collection="array">\r
 147                         <bind-xml name="basePosition" node="element"/>\r
 148                 </field>\r
 149         </class>\r
 150         <class name="jalview.datamodel.xdb.embl.BasePosition">\r
 151                 <map-to xml="basePosition"/>\r
 152                 <field name="type">\r
 153                         <bind-xml name="type" node="attribute"/>\r
 154                 </field>\r
 155                 <field name="pos">\r
 156                         <bind-xml node="text"/>\r
 157                 </field>\r
 158         </class>\r
 159 </mapping>\r