<?xml version="1.0"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
<!--
History: Originally created from EMBL_common_V1.0
Updated on 24th April 2007 for WsDBFetch Service move to EMBL_Services_V1.1.xsd
+ Updated May 2016 for EMBL XML 1.2 JAL-2113 JAL-2114
+ see ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_5/ENA.embl.xsd
+ see http://www.ebi.ac.uk/ena/submit/data-formats
-->
<class name="jalview.datamodel.xdb.embl.EmblFile">
- <map-to xml="EMBL_Services"/>
+ <map-to xml="ROOT"/>
+ <field name="text" type="string">
+ <bind-xml node="text"/>
+ </field>
<field name="entries" type="jalview.datamodel.xdb.embl.EmblEntry" collection="vector">
<bind-xml name="entry"/>
</field>
-
<field name="errors" type="jalview.datamodel.xdb.embl.EmblError" collection="vector">
<bind-xml name="Error"/>
</field>
</class>
<class name="jalview.datamodel.xdb.embl.EmblEntry">
- <map-to xml="entry"/>
<field name="accession" type="string">
- <bind-xml location="accession" node="attribute"/>
+ <bind-xml name="accession" node="attribute"/>
</field>
- <field name="lastUpdated" type="string">
- <bind-xml location="last-updated" node="attribute"/>
+ <!--
+ in EMBL XML 1.2 sequence/@version became entry/version
+ entry/@version became entry/@entryVersion
+ -->
+ <field name="sequenceVersion" type="string">
+ <bind-xml name="version" node="attribute"/>
</field>
- <field name="version" type="string">
- <bind-xml location="version" node="attribute"/>
+ <field name="entryVersion" type="string">
+ <bind-xml name="entryVersion" node="attribute"/>
+ </field>
+ <field name="dataClass" type="string">
+ <bind-xml name="dataClass" node="attribute"/>
+ </field>
+ <field name="taxonomicDivision" type="string">
+ <bind-xml name="taxonomicDivision" node="attribute"/>
+ </field>
+ <field name="moleculeType" type="string">
+ <bind-xml name="moleculeType" node="attribute"/>
+ </field>
+ <field name="sequenceLength" type="string">
+ <bind-xml name="sequenceLength" node="attribute"/>
+ </field>
+ <field name="topology" type="string">
+ <bind-xml name="topology" node="attribute" location="type"/>
</field>
-
- <field name="rCreated" type="string">
- <bind-xml location="releaseCreated" node="attribute"/>
+ <field name="firstPublicDate" type="string">
+ <bind-xml name="firstPublic" node="attribute"/>
</field>
- <field name="rLastUpdated" type="string">
- <bind-xml location="releaseLastUpdated" node="attribute"/>
+ <field name="firstPublicRelease" type="string">
+ <bind-xml name="firstPublicRelease" node="attribute"/>
</field>
- <field name="desc" type="string">
+ <field name="lastUpdatedDate" type="string">
+ <bind-xml name="lastUpdated" node="attribute"/>
+ </field>
+ <field name="lastUpdatedRelease" type="string">
+ <bind-xml name="lastUpdatedRelease" node="attribute"/>
+ </field>
+ <field name="description" type="string">
<bind-xml name="description" node="element"/>
</field>
- <field name="Keywords" type="string" collection="vector">
+ <field name="keywords" type="string" collection="vector">
<bind-xml name="keyword" node="element"/>
</field>
<field name="features" type="jalview.datamodel.xdb.embl.EmblFeature" collection="vector">
<bind-xml name="feature"/>
</field>
<field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">
- <bind-xml name="dbreference" />
+ <bind-xml name="xref" />
</field>
<field name="sequence" type="jalview.datamodel.xdb.embl.EmblSequence">
- <bind-xml name="sequence"/> <!-- location="sequence" node="element"/ -->
+ <bind-xml name="sequence"/>
</field>
</class>
<class name="jalview.datamodel.xdb.embl.EmblSequence">
- <map-to xml="sequence"/>
- <field name="type" type="string">
- <bind-xml name="type" node="attribute" location="type"/>
- </field>
- <field name="version" type="string">
- <bind-xml name="version" node="attribute" location="version"/>
- </field>
<field name="sequence" type="string">
<bind-xml node="text"/>
</field>
</class>
<class name="jalview.datamodel.xdb.embl.EmblFeature" verify-constructable="false">
- <map-to xml="feature"/>
<field name="name" type="string">
<bind-xml name="name" node="attribute"/>
</field>
+ <field name="location" type="string">
+ <bind-xml name="location" node="attribute"/>
+ </field>
<field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">
- <bind-xml name="dbreference" node="element"/>
+ <bind-xml name="xref" node="element"/>
</field>
<field name="qualifiers" type="jalview.datamodel.xdb.embl.Qualifier" collection="vector">
<bind-xml name="qualifier"/>
</field>
- <field name="locations" type="jalview.datamodel.xdb.embl.EmblFeatureLocations" collection="vector">
- <bind-xml name="location"/>
- </field>
</class>
<class name="jalview.datamodel.DBRefEntry" verify-constructable="false">
- <field name="accessionId" type="java.lang.String"><!-- set-method="setAccessionId" get-method="getAccessionId"> -->
- <bind-xml name="primary" node="attribute"/>
+ <field name="accessionId" type="java.lang.String">
+ <bind-xml name="id" node="attribute"/>
</field>
- <field name="source" type="java.lang.String"> <!--set-method="setSource" get-method="getSource"> -->
+ <field name="source" type="java.lang.String">
<bind-xml name="db" node="attribute"/>
</field>
- <field name="version" type="string"><!-- set-method="setVersion" get-method="getVersion"> -->
- <bind-xml name="secondary" node="attribute"/>
+ <field name="version" type="string">
+ <bind-xml name="secondaryId" node="attribute"/>
</field>
</class>
<class name="jalview.datamodel.xdb.embl.Qualifier" verify-constructable="false">
- <map-to xml="Qualifier"/>
<field name="name">
<bind-xml name="name" node="attribute"/>
</field>
<bind-xml name="value" node="element"/>
</field>
</class>
- <class name="jalview.datamodel.xdb.embl.EmblFeatureLocations">
- <map-to xml="location"/>
- <field name="locationType" type="string">
- <bind-xml name="type" node="attribute"/>
- </field>
- <field name="locationComplement" type="boolean">
- <bind-xml name="complement" node="attribute"/>
- </field>
- <field name="locElements" type="jalview.datamodel.xdb.embl.EmblFeatureLocElement" collection="vector">
- <bind-xml name="locationElement"/>
- </field>
- </class>
- <class name="jalview.datamodel.xdb.embl.EmblFeatureLocElement">
- <map-to xml="locationElement"/>
- <field name="type" type="string">
- <bind-xml name="type" node="attribute"/>
- </field>
- <field name="accession" type="string">
- <bind-xml name="accession" node="attribute"/>
- </field>
- <field name="version" type="string">
- <bind-xml name="version" node="attribute"/>
- </field>
- <field name="complement" type="boolean">
- <bind-xml name="complement"/>
- </field>
- <field name="basePositions" type="jalview.datamodel.xdb.embl.BasePosition" collection="array">
- <bind-xml name="basePosition" node="element"/>
- </field>
- </class>
- <class name="jalview.datamodel.xdb.embl.BasePosition">
- <map-to xml="basePosition"/>
- <field name="type">
- <bind-xml name="type" node="attribute"/>
- </field>
- <field name="pos">
- <bind-xml node="text"/>
- </field>
- </class>
</mapping>
git://source.jalview.org / jalview.git / blobdiff