resources/embl_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 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                 <field name="accession" type="string">\r
  38                         <bind-xml location="accession" node="attribute"/>\r
  39                 </field>\r
  40                 <!--  May 2015 changed from last-updated to match xml -->\r
  41                 <field name="lastUpdated" type="string">\r
  42                         <bind-xml location="lastUpdated" 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                 <field name="rCreated" type="string">\r
  48                         <bind-xml location="releaseCreated" node="attribute"/>\r
  49                 </field>\r
  50                 <field name="rLastUpdated" type="string">\r
  51                         <bind-xml location="releaseLastUpdated" node="attribute"/>\r
  52                 </field>\r
  53                 <field name="desc" type="string">\r
  54                         <bind-xml name="description" node="element"/>\r
  55                 </field>\r
  56                 <field name="keywords" type="string" collection="vector">\r
  57                         <bind-xml name="keyword" node="element"/>\r
  58                 </field>\r
  59                 <field name="features" type="jalview.datamodel.xdb.embl.EmblFeature" collection="vector">\r
  60                         <bind-xml name="feature"/>\r
  61                 </field>\r
  62                 <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">\r
  63                         <bind-xml name="dbreference" />\r
  64                 </field>\r
  65                 <field name="sequence" type="jalview.datamodel.xdb.embl.EmblSequence">\r
  66                         <bind-xml name="sequence"/>\r
  67                 </field>\r
  68         </class>\r
  69         <class name="jalview.datamodel.xdb.embl.EmblSequence">\r
  70                 <field name="type" type="string">\r
  71                         <bind-xml name="type" node="attribute" location="type"/>\r
  72                 </field>\r
  73                 <field name="version" type="string">\r
  74                         <bind-xml name="version" node="attribute" location="version"/>\r
  75                 </field>\r
  76                 <field name="sequence" type="string">\r
  77                         <bind-xml node="text"/>\r
  78                 </field>\r
  79         </class>\r
  80         <class name="jalview.datamodel.xdb.embl.EmblFeature" verify-constructable="false">\r
  81                 <field name="name" type="string">\r
  82                         <bind-xml name="name" node="attribute"/>\r
  83                 </field>\r
  84                 <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">\r
  85                         <bind-xml name="dbreference" node="element"/>\r
  86                 </field>\r
  87                 <field name="qualifiers" type="jalview.datamodel.xdb.embl.Qualifier" collection="vector">\r
  88                         <bind-xml name="qualifier"/>\r
  89                 </field>                                        \r
  90                 <field name="locations" type="jalview.datamodel.xdb.embl.EmblFeatureLocations" collection="vector">\r
  91                         <bind-xml name="location"/>\r
  92                 </field>\r
  93         </class>\r
  94         <class name="jalview.datamodel.DBRefEntry" verify-constructable="false">\r
  95                 <field name="accessionId" type="java.lang.String">\r
  96                         <bind-xml name="primary" node="attribute"/>\r
  97                 </field>\r
  98                 <field name="source" type="java.lang.String"> \r
  99                         <bind-xml name="db" node="attribute"/>\r
 100                 </field>\r
 101                 <field name="version" type="string">\r
 102                         <bind-xml name="secondary" node="attribute"/>\r
 103                 </field>\r
 104         </class>\r
 105         <class  name="jalview.datamodel.xdb.embl.Qualifier" verify-constructable="false">\r
 106                 <field name="name">\r
 107                         <bind-xml name="name" node="attribute"/>\r
 108                 </field>\r
 109                 <field name="evidence" type="string" collection="array">\r
 110                         <bind-xml name="evidence" node="element"/>\r
 111                 </field>\r
 112                 <field name="values" type="string" collection="array">\r
 113                         <bind-xml name="value" node="element"/>\r
 114                 </field>\r
 115         </class>\r
 116         <class name="jalview.datamodel.xdb.embl.EmblFeatureLocations">\r
 117                 <field name="locationType" type="string">\r
 118                         <bind-xml name="type" node="attribute"/>\r
 119                 </field>\r
 120                 <field name="locationComplement" type="boolean">\r
 121                         <bind-xml name="complement" node="attribute"/>\r
 122                 </field>\r
 123                 <field name="locElements" type="jalview.datamodel.xdb.embl.EmblFeatureLocElement" collection="vector">\r
 124                         <bind-xml name="locationElement"/>\r
 125                 </field>\r
 126         </class>\r
 127         <class name="jalview.datamodel.xdb.embl.EmblFeatureLocElement">\r
 128                 <field name="type" type="string">\r
 129                         <bind-xml name="type" node="attribute"/>\r
 130                 </field>\r
 131                 <field name="accession" type="string">\r
 132                         <bind-xml name="accession" node="attribute"/>                   \r
 133                 </field>\r
 134                 <field name="version" type="string">\r
 135                         <bind-xml name="version" node="attribute"/>\r
 136                 </field>\r
 137                 <field name="complement" type="boolean">\r
 138                         <bind-xml name="complement"/>\r
 139                 </field>\r
 140                 <field name="basePositions" type="jalview.datamodel.xdb.embl.BasePosition" collection="array">\r
 141                         <bind-xml name="basePosition" node="element"/>\r
 142                 </field>\r
 143         </class>\r
 144         <class name="jalview.datamodel.xdb.embl.BasePosition">\r
 145                 <field name="type">\r
 146                         <bind-xml name="type" node="attribute"/>\r
 147                 </field>\r
 148                 <field name="pos">\r
 149                         <bind-xml node="text"/>\r
 150                 </field>\r
 151         </class>\r
 152 </mapping>\r