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="entries" type="jalview.datamodel.xdb.embl.EmblEntry" collection="vector">
  32                         <bind-xml name="entry"/>
  33                 </field>
  34                 <field name="errors" type="jalview.datamodel.xdb.embl.EmblError" collection="vector">
  35                         <bind-xml name="Error"/>
  36                 </field>
  37         </class>
  38         <class name="jalview.datamodel.xdb.embl.EmblEntry">
  39                 <field name="accession" type="string">
  40                         <bind-xml name="accession" node="attribute"/>
  41                 </field>
  42                 <field name="lastUpdated" type="string">
  43                         <bind-xml name="lastUpdated" node="attribute"/>
  44                 </field>
  45                 <!--
  46                     in EMBL XML 1.2 sequence/@version becomes entry/version
  47                     entry/@version becomes 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="moleculeType" type="string">
  56                         <bind-xml name="moleculeType" node="attribute"/>
  57                 </field>
  58                 <field name="sequenceLength" type="string">
  59                         <bind-xml name="sequenceLength" node="attribute"/>
  60                 </field>
  61                 <field name="topology" type="string">
  62                         <bind-xml name="topology" node="attribute" location="type"/>
  63                 </field>
  64                 <field name="rCreated" type="string">
  65                         <bind-xml name="releaseCreated" node="attribute"/>
  66                 </field>
  67                 <field name="rLastUpdated" type="string">
  68                         <bind-xml name="releaseLastUpdated" node="attribute"/>
  69                 </field>
  70                 <field name="desc" type="string">
  71                         <bind-xml name="description" node="element"/>
  72                 </field>
  73                 <field name="keywords" type="string" collection="vector">
  74                         <bind-xml name="keyword" node="element"/>
  75                 </field>
  76                 <field name="features" type="jalview.datamodel.xdb.embl.EmblFeature" collection="vector">
  77                         <bind-xml name="feature"/>
  78                 </field>
  79                 <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">
  80                         <bind-xml name="xref" />
  81                 </field>
  82                 <field name="sequence" type="jalview.datamodel.xdb.embl.EmblSequence">
  83                         <bind-xml name="sequence"/>
  84                 </field>
  85         </class>
  86         <class name="jalview.datamodel.xdb.embl.EmblSequence">
  87                 <field name="sequence" type="string">
  88                         <bind-xml node="text"/>
  89                 </field>
  90         </class>
  91         <class name="jalview.datamodel.xdb.embl.EmblFeature" verify-constructable="false">
  92                 <field name="name" type="string">
  93                         <bind-xml name="name" node="attribute"/>
  94                 </field>
  95                 <field name="location" type="string">
  96                         <bind-xml name="location" node="attribute"/>
  97                 </field>
  98                 <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">
  99                         <bind-xml name="xref" node="element"/>
 100                 </field>
 101                 <field name="qualifiers" type="jalview.datamodel.xdb.embl.Qualifier" collection="vector">
 102                         <bind-xml name="qualifier"/>
 103                 </field>
 104         </class>
 105         <class name="jalview.datamodel.DBRefEntry" verify-constructable="false">
 106                 <field name="accessionId" type="java.lang.String">
 107                         <bind-xml name="id" node="attribute"/>
 108                 </field>
 109                 <field name="source" type="java.lang.String">
 110                         <bind-xml name="db" node="attribute"/>
 111                 </field>
 112                 <field name="version" type="string">
 113                         <bind-xml name="secondaryId" node="attribute"/>
 114                 </field>
 115         </class>
 116         <class  name="jalview.datamodel.xdb.embl.Qualifier" verify-constructable="false">
 117                 <field name="name">
 118                         <bind-xml name="name" node="attribute"/>
 119                 </field>
 120                 <field name="evidence" type="string" collection="array">
 121                         <bind-xml name="evidence" node="element"/>
 122                 </field>
 123                 <field name="values" type="string" collection="array">
 124                         <bind-xml name="value" node="element"/>
 125                 </field>
 126         </class>
 127         <class name="jalview.datamodel.xdb.embl.EmblFeatureLocations">
 128                 <field name="locationType" type="string">
 129                         <bind-xml name="type" node="attribute"/>
 130                 </field>
 131                 <field name="locationComplement" type="boolean">
 132                         <bind-xml name="complement" node="attribute"/>
 133                 </field>
 134                 <field name="locElements" type="jalview.datamodel.xdb.embl.EmblFeatureLocElement" collection="vector">
 135                         <bind-xml name="locationElement"/>
 136                 </field>
 137         </class>
 138         <class name="jalview.datamodel.xdb.embl.EmblFeatureLocElement">
 139                 <field name="type" type="string">
 140                         <bind-xml name="type" node="attribute"/>
 141                 </field>
 142                 <field name="accession" type="string">
 143                         <bind-xml name="accession" node="attribute"/>
 144                 </field>
 145                 <field name="version" type="string">
 146                         <bind-xml name="version" node="attribute"/>
 147                 </field>
 148                 <field name="complement" type="boolean">
 149                         <bind-xml name="complement"/>
 150                 </field>
 151                 <field name="basePositions" type="jalview.datamodel.xdb.embl.BasePosition" collection="array">
 152                         <bind-xml name="basePosition" node="element"/>
 153                 </field>
 154         </class>
 155         <class name="jalview.datamodel.xdb.embl.BasePosition">
 156                 <field name="type">
 157                         <bind-xml name="type" node="attribute"/>
 158                 </field>
 159                 <field name="pos">
 160                         <bind-xml node="text"/>
 161                 </field>
 162         </class>
 163 </mapping>