resources/embl_mapping.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   4  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   5  *
   6  * This file is part of Jalview.
   7  *
   8  * Jalview is free software: you can redistribute it and/or
   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  18  * The Jalview Authors are detailed in the 'AUTHORS' file.
  19 -->
  20 <mapping xmlns="http://castor.exolab.org/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  21         xsi:schemaLocation="http://castor.exolab.org/ ../schemas/castor-mapping.xsd">
  22 <!--
  23         History: Originally created from EMBL_common_V1.0
  24         Updated on 24th April 2007 for WsDBFetch Service move to EMBL_Services_V1.1.xsd
  25         -->
  26         <class name="jalview.datamodel.xdb.embl.EmblFile">
  27                 <map-to xml="EMBL_Services"/>
  28                 <field name="entries" type="jalview.datamodel.xdb.embl.EmblEntry" collection="vector">
  29                         <bind-xml name="entry"/>
  30                 </field>
  31
  32                 <field name="errors" type="jalview.datamodel.xdb.embl.EmblError" collection="vector">
  33                         <bind-xml name="Error"/>
  34                 </field>
  35         </class>
  36         <class name="jalview.datamodel.xdb.embl.EmblEntry">
  37                 <field name="accession" type="string">
  38                         <bind-xml location="accession" node="attribute"/>
  39                 </field>
  40                 <!--  May 2015 changed from last-updated to match xml -->
  41                 <field name="lastUpdated" type="string">
  42                         <bind-xml location="lastUpdated" node="attribute"/>
  43                 </field>
  44                 <field name="version" type="string">
  45                         <bind-xml location="version" node="attribute"/>
  46                 </field>
  47                 <field name="rCreated" type="string">
  48                         <bind-xml location="releaseCreated" node="attribute"/>
  49                 </field>
  50                 <field name="rLastUpdated" type="string">
  51                         <bind-xml location="releaseLastUpdated" node="attribute"/>
  52                 </field>
  53                 <field name="desc" type="string">
  54                         <bind-xml name="description" node="element"/>
  55                 </field>
  56                 <field name="keywords" type="string" collection="vector">
  57                         <bind-xml name="keyword" node="element"/>
  58                 </field>
  59                 <field name="features" type="jalview.datamodel.xdb.embl.EmblFeature" collection="vector">
  60                         <bind-xml name="feature"/>
  61                 </field>
  62                 <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">
  63                         <bind-xml name="dbreference" />
  64                 </field>
  65                 <field name="sequence" type="jalview.datamodel.xdb.embl.EmblSequence">
  66                         <bind-xml name="sequence"/>
  67                 </field>
  68         </class>
  69         <class name="jalview.datamodel.xdb.embl.EmblSequence">
  70                 <field name="type" type="string">
  71                         <bind-xml name="type" node="attribute" location="type"/>
  72                 </field>
  73                 <field name="version" type="string">
  74                         <bind-xml name="version" node="attribute" location="version"/>
  75                 </field>
  76                 <field name="sequence" type="string">
  77                         <bind-xml node="text"/>
  78                 </field>
  79         </class>
  80         <class name="jalview.datamodel.xdb.embl.EmblFeature" verify-constructable="false">
  81                 <field name="name" type="string">
  82                         <bind-xml name="name" node="attribute"/>
  83                 </field>
  84                 <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">
  85                         <bind-xml name="dbreference" node="element"/>
  86                 </field>
  87                 <field name="qualifiers" type="jalview.datamodel.xdb.embl.Qualifier" collection="vector">
  88                         <bind-xml name="qualifier"/>
  89                 </field>
  90                 <field name="locations" type="jalview.datamodel.xdb.embl.EmblFeatureLocations" collection="vector">
  91                         <bind-xml name="location"/>
  92                 </field>
  93         </class>
  94         <class name="jalview.datamodel.DBRefEntry" verify-constructable="false">
  95                 <field name="accessionId" type="java.lang.String">
  96                         <bind-xml name="primary" node="attribute"/>
  97                 </field>
  98                 <field name="source" type="java.lang.String">
  99                         <bind-xml name="db" node="attribute"/>
 100                 </field>
 101                 <field name="version" type="string">
 102                         <bind-xml name="secondary" node="attribute"/>
 103                 </field>
 104         </class>
 105         <class  name="jalview.datamodel.xdb.embl.Qualifier" verify-constructable="false">
 106                 <field name="name">
 107                         <bind-xml name="name" node="attribute"/>
 108                 </field>
 109                 <field name="evidence" type="string" collection="array">
 110                         <bind-xml name="evidence" node="element"/>
 111                 </field>
 112                 <field name="values" type="string" collection="array">
 113                         <bind-xml name="value" node="element"/>
 114                 </field>
 115         </class>
 116         <class name="jalview.datamodel.xdb.embl.EmblFeatureLocations">
 117                 <field name="locationType" type="string">
 118                         <bind-xml name="type" node="attribute"/>
 119                 </field>
 120                 <field name="locationComplement" type="boolean">
 121                         <bind-xml name="complement" node="attribute"/>
 122                 </field>
 123                 <field name="locElements" type="jalview.datamodel.xdb.embl.EmblFeatureLocElement" collection="vector">
 124                         <bind-xml name="locationElement"/>
 125                 </field>
 126         </class>
 127         <class name="jalview.datamodel.xdb.embl.EmblFeatureLocElement">
 128                 <field name="type" type="string">
 129                         <bind-xml name="type" node="attribute"/>
 130                 </field>
 131                 <field name="accession" type="string">
 132                         <bind-xml name="accession" node="attribute"/>
 133                 </field>
 134                 <field name="version" type="string">
 135                         <bind-xml name="version" node="attribute"/>
 136                 </field>
 137                 <field name="complement" type="boolean">
 138                         <bind-xml name="complement"/>
 139                 </field>
 140                 <field name="basePositions" type="jalview.datamodel.xdb.embl.BasePosition" collection="array">
 141                         <bind-xml name="basePosition" node="element"/>
 142                 </field>
 143         </class>
 144         <class name="jalview.datamodel.xdb.embl.BasePosition">
 145                 <field name="type">
 146                         <bind-xml name="type" node="attribute"/>
 147                 </field>
 148                 <field name="pos">
 149                         <bind-xml node="text"/>
 150                 </field>
 151         </class>
 152 </mapping>