resources/embl_mapping.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   4  * Copyright (C) 2014 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                 <map-to xml="entry"/>
  38                 <field name="accession" type="string">
  39                         <bind-xml location="accession" node="attribute"/>
  40                 </field>
  41                 <field name="lastUpdated" type="string">
  42                         <bind-xml location="last-updated" node="attribute"/>
  43                 </field>
  44                 <field name="version" type="string">
  45                         <bind-xml location="version" node="attribute"/>
  46                 </field>
  47
  48                 <field name="rCreated" type="string">
  49                         <bind-xml location="releaseCreated" node="attribute"/>
  50                 </field>
  51                 <field name="rLastUpdated" type="string">
  52                         <bind-xml location="releaseLastUpdated" node="attribute"/>
  53                 </field>
  54                 <field name="desc" type="string">
  55                         <bind-xml name="description" node="element"/>
  56                 </field>
  57                 <field name="Keywords" type="string" collection="vector">
  58                         <bind-xml name="keyword" node="element"/>
  59                 </field>
  60                 <field name="features" type="jalview.datamodel.xdb.embl.EmblFeature" collection="vector">
  61                         <bind-xml name="feature"/>
  62                 </field>
  63                 <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">
  64                         <bind-xml name="dbreference" />
  65                 </field>
  66                 <field name="sequence" type="jalview.datamodel.xdb.embl.EmblSequence">
  67                         <bind-xml name="sequence"/> <!-- location="sequence" node="element"/ -->
  68                 </field>
  69         </class>
  70         <class name="jalview.datamodel.xdb.embl.EmblSequence">
  71                 <map-to xml="sequence"/>
  72                 <field name="type" type="string">
  73                         <bind-xml name="type" node="attribute" location="type"/>
  74                 </field>
  75                 <field name="version" type="string">
  76                         <bind-xml name="version" node="attribute" location="version"/>
  77                 </field>
  78                 <field name="sequence" type="string">
  79                         <bind-xml node="text"/>
  80                 </field>
  81         </class>
  82         <class name="jalview.datamodel.xdb.embl.EmblFeature" verify-constructable="false">
  83                 <map-to xml="feature"/>
  84                 <field name="name" type="string">
  85                         <bind-xml name="name" node="attribute"/>
  86                 </field>
  87                 <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">
  88                         <bind-xml name="dbreference" node="element"/>
  89                 </field>
  90                 <field name="qualifiers" type="jalview.datamodel.xdb.embl.Qualifier" collection="vector">
  91                         <bind-xml name="qualifier"/>
  92                 </field>
  93                 <field name="locations" type="jalview.datamodel.xdb.embl.EmblFeatureLocations" collection="vector">
  94                         <bind-xml name="location"/>
  95                 </field>
  96         </class>
  97         <class name="jalview.datamodel.DBRefEntry" verify-constructable="false">
  98                 <field name="accessionId" type="java.lang.String"><!-- set-method="setAccessionId" get-method="getAccessionId"> -->
  99                         <bind-xml name="primary" node="attribute"/>
 100                 </field>
 101                 <field name="source" type="java.lang.String"> <!--set-method="setSource" get-method="getSource"> -->
 102                         <bind-xml name="db" node="attribute"/>
 103                 </field>
 104                 <field name="version" type="string"><!-- set-method="setVersion" get-method="getVersion"> -->
 105                         <bind-xml name="secondary" node="attribute"/>
 106                 </field>
 107         </class>
 108         <class  name="jalview.datamodel.xdb.embl.Qualifier" verify-constructable="false">
 109                 <map-to xml="Qualifier"/>
 110                 <field name="name">
 111                         <bind-xml name="name" node="attribute"/>
 112                 </field>
 113                 <field name="evidence" type="string" collection="array">
 114                         <bind-xml name="evidence" node="element"/>
 115                 </field>
 116                 <field name="values" type="string" collection="array">
 117                         <bind-xml name="value" node="element"/>
 118                 </field>
 119         </class>
 120         <class name="jalview.datamodel.xdb.embl.EmblFeatureLocations">
 121                 <map-to xml="location"/>
 122                 <field name="locationType" type="string">
 123                         <bind-xml name="type" node="attribute"/>
 124                 </field>
 125                 <field name="locationComplement" type="boolean">
 126                         <bind-xml name="complement" node="attribute"/>
 127                 </field>
 128                 <field name="locElements" type="jalview.datamodel.xdb.embl.EmblFeatureLocElement" collection="vector">
 129                         <bind-xml name="locationElement"/>
 130                 </field>
 131         </class>
 132         <class name="jalview.datamodel.xdb.embl.EmblFeatureLocElement">
 133                 <map-to xml="locationElement"/>
 134                 <field name="type" type="string">
 135                         <bind-xml name="type" node="attribute"/>
 136                 </field>
 137                 <field name="accession" type="string">
 138                         <bind-xml name="accession" node="attribute"/>
 139                 </field>
 140                 <field name="version" type="string">
 141                         <bind-xml name="version" node="attribute"/>
 142                 </field>
 143                 <field name="complement" type="boolean">
 144                         <bind-xml name="complement"/>
 145                 </field>
 146                 <field name="basePositions" type="jalview.datamodel.xdb.embl.BasePosition" collection="array">
 147                         <bind-xml name="basePosition" node="element"/>
 148                 </field>
 149         </class>
 150         <class name="jalview.datamodel.xdb.embl.BasePosition">
 151                 <map-to xml="basePosition"/>
 152                 <field name="type">
 153                         <bind-xml name="type" node="attribute"/>
 154                 </field>
 155                 <field name="pos">
 156                         <bind-xml node="text"/>
 157                 </field>
 158         </class>
 159 </mapping>