resources/embl_mapping.xml

   1 <?xml version="1.0"?>
   2 <!--
   3   Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   4   Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
   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 -->
  19 <mapping xmlns="http://castor.exolab.org/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  20         xsi:schemaLocation="http://castor.exolab.org/ ../schemas/castor-mapping.xsd">
  21 <!--
  22         History: Originally created from EMBL_common_V1.0
  23         Updated on 24th April 2007 for WsDBFetch Service move to EMBL_Services_V1.1.xsd
  24         -->
  25         <class name="jalview.datamodel.xdb.embl.EmblFile">
  26                 <map-to xml="EMBL_Services"/>
  27                 <field name="entries" type="jalview.datamodel.xdb.embl.EmblEntry" collection="vector">
  28                         <bind-xml name="entry"/>
  29                 </field>
  30
  31                 <field name="errors" type="jalview.datamodel.xdb.embl.EmblError" collection="vector">
  32                         <bind-xml name="Error"/>
  33                 </field>
  34         </class>
  35         <class name="jalview.datamodel.xdb.embl.EmblEntry">
  36                 <map-to xml="entry"/>
  37                 <field name="accession" type="string">
  38                         <bind-xml location="accession" node="attribute"/>
  39                 </field>
  40                 <field name="lastUpdated" type="string">
  41                         <bind-xml location="last-updated" node="attribute"/>
  42                 </field>
  43                 <field name="version" type="string">
  44                         <bind-xml location="version" node="attribute"/>
  45                 </field>
  46
  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"/> <!-- location="sequence" node="element"/ -->
  67                 </field>
  68         </class>
  69         <class name="jalview.datamodel.xdb.embl.EmblSequence">
  70                 <map-to xml="sequence"/>
  71                 <field name="type" type="string">
  72                         <bind-xml name="type" node="attribute" location="type"/>
  73                 </field>
  74                 <field name="version" type="string">
  75                         <bind-xml name="version" node="attribute" location="version"/>
  76                 </field>
  77                 <field name="sequence" type="string">
  78                         <bind-xml node="text"/>
  79                 </field>
  80         </class>
  81         <class name="jalview.datamodel.xdb.embl.EmblFeature" verify-constructable="false">
  82                 <map-to xml="feature"/>
  83                 <field name="name" type="string">
  84                         <bind-xml name="name" node="attribute"/>
  85                 </field>
  86                 <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">
  87                         <bind-xml name="dbreference" node="element"/>
  88                 </field>
  89                 <field name="qualifiers" type="jalview.datamodel.xdb.embl.Qualifier" collection="vector">
  90                         <bind-xml name="qualifier"/>
  91                 </field>
  92                 <field name="locations" type="jalview.datamodel.xdb.embl.EmblFeatureLocations" collection="vector">
  93                         <bind-xml name="location"/>
  94                 </field>
  95         </class>
  96         <class name="jalview.datamodel.DBRefEntry" verify-constructable="false">
  97                 <field name="accessionId" type="java.lang.String"><!-- set-method="setAccessionId" get-method="getAccessionId"> -->
  98                         <bind-xml name="primary" node="attribute"/>
  99                 </field>
 100                 <field name="source" type="java.lang.String"> <!--set-method="setSource" get-method="getSource"> -->
 101                         <bind-xml name="db" node="attribute"/>
 102                 </field>
 103                 <field name="version" type="string"><!-- set-method="setVersion" get-method="getVersion"> -->
 104                         <bind-xml name="secondary" node="attribute"/>
 105                 </field>
 106         </class>
 107         <class  name="jalview.datamodel.xdb.embl.Qualifier" verify-constructable="false">
 108                 <map-to xml="Qualifier"/>
 109                 <field name="name">
 110                         <bind-xml name="name" node="attribute"/>
 111                 </field>
 112                 <field name="evidence" type="string" collection="array">
 113                         <bind-xml name="evidence" node="element"/>
 114                 </field>
 115                 <field name="values" type="string" collection="array">
 116                         <bind-xml name="value" node="element"/>
 117                 </field>
 118         </class>
 119         <class name="jalview.datamodel.xdb.embl.EmblFeatureLocations">
 120                 <map-to xml="location"/>
 121                 <field name="locationType" type="string">
 122                         <bind-xml name="type" node="attribute"/>
 123                 </field>
 124                 <field name="locationComplement" type="boolean">
 125                         <bind-xml name="complement" node="attribute"/>
 126                 </field>
 127                 <field name="locElements" type="jalview.datamodel.xdb.embl.EmblFeatureLocElement" collection="vector">
 128                         <bind-xml name="locationElement"/>
 129                 </field>
 130         </class>
 131         <class name="jalview.datamodel.xdb.embl.EmblFeatureLocElement">
 132                 <map-to xml="locationElement"/>
 133                 <field name="type" type="string">
 134                         <bind-xml name="type" node="attribute"/>
 135                 </field>
 136                 <field name="accession" type="string">
 137                         <bind-xml name="accession" node="attribute"/>
 138                 </field>
 139                 <field name="version" type="string">
 140                         <bind-xml name="version" node="attribute"/>
 141                 </field>
 142                 <field name="complement" type="boolean">
 143                         <bind-xml name="complement"/>
 144                 </field>
 145                 <field name="basePositions" type="jalview.datamodel.xdb.embl.BasePosition" collection="array">
 146                         <bind-xml name="basePosition" node="element"/>
 147                 </field>
 148         </class>
 149         <class name="jalview.datamodel.xdb.embl.BasePosition">
 150                 <map-to xml="basePosition"/>
 151                 <field name="type">
 152                         <bind-xml name="type" node="attribute"/>
 153                 </field>
 154                 <field name="pos">
 155                         <bind-xml node="text"/>
 156                 </field>
 157         </class>
 158 </mapping>