resources/embl_mapping.xml

   1 <?xml version="1.0"?>\r
   2 <!--\r
   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
   4  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\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 -->\r
  19 <mapping xmlns="http://castor.exolab.org/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"\r
  20         xsi:schemaLocation="http://castor.exolab.org/ ../schemas/castor-mapping.xsd">\r
  21 <!--\r
  22         History: Originally created from EMBL_common_V1.0\r
  23         Updated on 24th April 2007 for WsDBFetch Service move to EMBL_Services_V1.1.xsd\r
  24         -->\r
  25         <class name="jalview.datamodel.xdb.embl.EmblFile">\r
  26                 <map-to xml="EMBL_Services"/>\r
  27                 <field name="entries" type="jalview.datamodel.xdb.embl.EmblEntry" collection="vector">\r
  28                         <bind-xml name="entry"/>\r
  29                 </field>\r
  30                 \r
  31                 <field name="errors" type="jalview.datamodel.xdb.embl.EmblError" collection="vector">\r
  32                         <bind-xml name="Error"/>\r
  33                 </field>\r
  34         </class>\r
  35         <class name="jalview.datamodel.xdb.embl.EmblEntry">\r
  36                 <map-to xml="entry"/>\r
  37                 <field name="accession" type="string">\r
  38                         <bind-xml location="accession" node="attribute"/>\r
  39                 </field>\r
  40                 <field name="lastUpdated" type="string">\r
  41                         <bind-xml location="last-updated" node="attribute"/>\r
  42                 </field>\r
  43                 <field name="version" type="string">\r
  44                         <bind-xml location="version" node="attribute"/>\r
  45                 </field>\r
  46                 \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"/> <!-- location="sequence" node="element"/ -->\r
  67                 </field>\r
  68         </class>\r
  69         <class name="jalview.datamodel.xdb.embl.EmblSequence">\r
  70                 <map-to xml="sequence"/>\r
  71                 <field name="type" type="string">\r
  72                         <bind-xml name="type" node="attribute" location="type"/>\r
  73                 </field>\r
  74                 <field name="version" type="string">\r
  75                         <bind-xml name="version" node="attribute" location="version"/>\r
  76                 </field>\r
  77                 <field name="sequence" type="string">\r
  78                         <bind-xml node="text"/>\r
  79                 </field>\r
  80         </class>\r
  81         <class name="jalview.datamodel.xdb.embl.EmblFeature" verify-constructable="false">\r
  82                 <map-to xml="feature"/>\r
  83                 <field name="name" type="string">\r
  84                         <bind-xml name="name" node="attribute"/>\r
  85                 </field>\r
  86                 <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">\r
  87                         <bind-xml name="dbreference" node="element"/>\r
  88                 </field>\r
  89                 <field name="qualifiers" type="jalview.datamodel.xdb.embl.Qualifier" collection="vector">\r
  90                         <bind-xml name="qualifier"/>\r
  91                 </field>                                        \r
  92                 <field name="locations" type="jalview.datamodel.xdb.embl.EmblFeatureLocations" collection="vector">\r
  93                         <bind-xml name="location"/>\r
  94                 </field>\r
  95         </class>\r
  96         <class name="jalview.datamodel.DBRefEntry" verify-constructable="false">\r
  97                 <field name="accessionId" type="java.lang.String"><!-- set-method="setAccessionId" get-method="getAccessionId"> -->\r
  98                         <bind-xml name="primary" node="attribute"/>\r
  99                 </field>\r
 100                 <field name="source" type="java.lang.String"> <!--set-method="setSource" get-method="getSource"> -->\r
 101                         <bind-xml name="db" node="attribute"/>\r
 102                 </field>\r
 103                 <field name="version" type="string"><!-- set-method="setVersion" get-method="getVersion"> -->\r
 104                         <bind-xml name="secondary" node="attribute"/>\r
 105                 </field>\r
 106         </class>\r
 107         <class  name="jalview.datamodel.xdb.embl.Qualifier" verify-constructable="false">\r
 108                 <map-to xml="Qualifier"/>\r
 109                 <field name="name">\r
 110                         <bind-xml name="name" node="attribute"/>\r
 111                 </field>\r
 112                 <field name="evidence" type="string" collection="array">\r
 113                         <bind-xml name="evidence" node="element"/>\r
 114                 </field>\r
 115                 <field name="values" type="string" collection="array">\r
 116                         <bind-xml name="value" node="element"/>\r
 117                 </field>\r
 118         </class>\r
 119         <class name="jalview.datamodel.xdb.embl.EmblFeatureLocations">\r
 120                 <map-to xml="location"/>\r
 121                 <field name="locationType" type="string">\r
 122                         <bind-xml name="type" node="attribute"/>\r
 123                 </field>\r
 124                 <field name="locationComplement" type="boolean">\r
 125                         <bind-xml name="complement" node="attribute"/>\r
 126                 </field>\r
 127                 <field name="locElements" type="jalview.datamodel.xdb.embl.EmblFeatureLocElement" collection="vector">\r
 128                         <bind-xml name="locationElement"/>\r
 129                 </field>\r
 130         </class>\r
 131         <class name="jalview.datamodel.xdb.embl.EmblFeatureLocElement">\r
 132                 <map-to xml="locationElement"/>\r
 133                 <field name="type" type="string">\r
 134                         <bind-xml name="type" node="attribute"/>\r
 135                 </field>\r
 136                 <field name="accession" type="string">\r
 137                         <bind-xml name="accession" node="attribute"/>                   \r
 138                 </field>\r
 139                 <field name="version" type="string">\r
 140                         <bind-xml name="version" node="attribute"/>\r
 141                 </field>\r
 142                 <field name="complement" type="boolean">\r
 143                         <bind-xml name="complement"/>\r
 144                 </field>\r
 145                 <field name="basePositions" type="jalview.datamodel.xdb.embl.BasePosition" collection="array">\r
 146                         <bind-xml name="basePosition" node="element"/>\r
 147                 </field>\r
 148         </class>\r
 149         <class name="jalview.datamodel.xdb.embl.BasePosition">\r
 150                 <map-to xml="basePosition"/>\r
 151                 <field name="type">\r
 152                         <bind-xml name="type" node="attribute"/>\r
 153                 </field>\r
 154                 <field name="pos">\r
 155                         <bind-xml node="text"/>\r
 156                 </field>\r
 157         </class>\r
 158 </mapping>\r