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         Updated May 2016 for EMBL XML 1.2 JAL-2113 JAL-2114
  26           see ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_5/ENA.embl.xsd
  27           see http://www.ebi.ac.uk/ena/submit/data-formats
  28         -->
  29         <class name="jalview.datamodel.xdb.embl.EmblFile">
  30                 <map-to xml="ROOT"/>
  31                 <field name="text" type="string">
  32                         <bind-xml node="text"/>
  33                 </field>
  34                 <field name="entries" type="jalview.datamodel.xdb.embl.EmblEntry" collection="vector">
  35                         <bind-xml name="entry"/>
  36                 </field>
  37                 <field name="errors" type="jalview.datamodel.xdb.embl.EmblError" collection="vector">
  38                         <bind-xml name="Error"/>
  39                 </field>
  40         </class>
  41         <class name="jalview.datamodel.xdb.embl.EmblEntry">
  42                 <field name="accession" type="string">
  43                         <bind-xml name="accession" node="attribute"/>
  44                 </field>
  45                 <!--
  46                     in EMBL XML 1.2 sequence/@version became entry/version
  47                     entry/@version became entry/@entryVersion
  48                 -->
  49                 <field name="sequenceVersion" type="string">
  50                         <bind-xml name="version" node="attribute"/>
  51                 </field>
  52                 <field name="entryVersion" type="string">
  53                         <bind-xml name="entryVersion" node="attribute"/>
  54                 </field>
  55                 <field name="dataClass" type="string">
  56                         <bind-xml name="dataClass" node="attribute"/>
  57                 </field>
  58                 <field name="taxonomicDivision" type="string">
  59                         <bind-xml name="taxonomicDivision" node="attribute"/>
  60                 </field>
  61                 <field name="moleculeType" type="string">
  62                         <bind-xml name="moleculeType" node="attribute"/>
  63                 </field>
  64                 <field name="sequenceLength" type="string">
  65                         <bind-xml name="sequenceLength" node="attribute"/>
  66                 </field>
  67                 <field name="topology" type="string">
  68                         <bind-xml name="topology" node="attribute" location="type"/>
  69                 </field>
  70                 <field name="firstPublicDate" type="string">
  71                         <bind-xml name="firstPublic" node="attribute"/>
  72                 </field>
  73                 <field name="firstPublicRelease" type="string">
  74                         <bind-xml name="firstPublicRelease" node="attribute"/>
  75                 </field>
  76                 <field name="lastUpdatedDate" type="string">
  77                         <bind-xml name="lastUpdated" node="attribute"/>
  78                 </field>
  79                 <field name="lastUpdatedRelease" type="string">
  80                         <bind-xml name="lastUpdatedRelease" node="attribute"/>
  81                 </field>
  82                 <field name="description" type="string">
  83                         <bind-xml name="description" node="element"/>
  84                 </field>
  85                 <field name="keywords" type="string" collection="vector">
  86                         <bind-xml name="keyword" node="element"/>
  87                 </field>
  88                 <field name="features" type="jalview.datamodel.xdb.embl.EmblFeature" collection="vector">
  89                         <bind-xml name="feature"/>
  90                 </field>
  91                 <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">
  92                         <bind-xml name="xref" />
  93                 </field>
  94                 <field name="sequence" type="jalview.datamodel.xdb.embl.EmblSequence">
  95                         <bind-xml name="sequence"/>
  96                 </field>
  97         </class>
  98         <class name="jalview.datamodel.xdb.embl.EmblSequence">
  99                 <field name="sequence" type="string">
 100                         <bind-xml node="text"/>
 101                 </field>
 102         </class>
 103         <class name="jalview.datamodel.xdb.embl.EmblFeature" verify-constructable="false">
 104                 <field name="name" type="string">
 105                         <bind-xml name="name" node="attribute"/>
 106                 </field>
 107                 <field name="location" type="string">
 108                         <bind-xml name="location" node="attribute"/>
 109                 </field>
 110                 <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">
 111                         <bind-xml name="xref" node="element"/>
 112                 </field>
 113                 <field name="qualifiers" type="jalview.datamodel.xdb.embl.Qualifier" collection="vector">
 114                         <bind-xml name="qualifier"/>
 115                 </field>
 116         </class>
 117         <class name="jalview.datamodel.DBRefEntry" verify-constructable="false">
 118                 <field name="accessionId" type="java.lang.String">
 119                         <bind-xml name="id" node="attribute"/>
 120                 </field>
 121                 <field name="source" type="java.lang.String">
 122                         <bind-xml name="db" node="attribute"/>
 123                 </field>
 124                 <field name="version" type="string">
 125                         <bind-xml name="secondaryId" node="attribute"/>
 126                 </field>
 127         </class>
 128         <class  name="jalview.datamodel.xdb.embl.Qualifier" verify-constructable="false">
 129                 <field name="name">
 130                         <bind-xml name="name" node="attribute"/>
 131                 </field>
 132                 <field name="evidence" type="string" collection="array">
 133                         <bind-xml name="evidence" node="element"/>
 134                 </field>
 135                 <field name="values" type="string" collection="array">
 136                         <bind-xml name="value" node="element"/>
 137                 </field>
 138         </class>
 139 </mapping>