-<?xml version="1.0"?>\r
-<!--\r
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- * \r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- * \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
--->\r
-<mapping xmlns="http://castor.exolab.org/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"\r
- xsi:schemaLocation="http://castor.exolab.org/ ../schemas/castor-mapping.xsd">\r
-<!--\r
- History: Originally created from EMBL_common_V1.0\r
- Updated on 24th April 2007 for WsDBFetch Service move to EMBL_Services_V1.1.xsd\r
- -->\r
- <class name="jalview.datamodel.xdb.embl.EmblFile">\r
- <map-to xml="EMBL_Services"/>\r
- <field name="entries" type="jalview.datamodel.xdb.embl.EmblEntry" collection="vector">\r
- <bind-xml name="entry"/>\r
- </field>\r
- \r
- <field name="errors" type="jalview.datamodel.xdb.embl.EmblError" collection="vector">\r
- <bind-xml name="Error"/>\r
- </field>\r
- </class>\r
- <class name="jalview.datamodel.xdb.embl.EmblEntry">\r
- <map-to xml="entry"/>\r
- <field name="accession" type="string">\r
- <bind-xml location="accession" node="attribute"/>\r
- </field>\r
- <field name="lastUpdated" type="string">\r
- <bind-xml location="last-updated" node="attribute"/>\r
- </field>\r
- <field name="version" type="string">\r
- <bind-xml location="version" node="attribute"/>\r
- </field>\r
- \r
- <field name="rCreated" type="string">\r
- <bind-xml location="releaseCreated" node="attribute"/>\r
- </field>\r
- <field name="rLastUpdated" type="string">\r
- <bind-xml location="releaseLastUpdated" node="attribute"/>\r
- </field>\r
- <field name="desc" type="string">\r
- <bind-xml name="description" node="element"/>\r
- </field>\r
- <field name="Keywords" type="string" collection="vector">\r
- <bind-xml name="keyword" node="element"/>\r
- </field>\r
- <field name="features" type="jalview.datamodel.xdb.embl.EmblFeature" collection="vector">\r
- <bind-xml name="feature"/>\r
- </field>\r
- <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">\r
- <bind-xml name="dbreference" />\r
- </field>\r
- <field name="sequence" type="jalview.datamodel.xdb.embl.EmblSequence">\r
- <bind-xml name="sequence"/> <!-- location="sequence" node="element"/ -->\r
- </field>\r
- </class>\r
- <class name="jalview.datamodel.xdb.embl.EmblSequence">\r
- <map-to xml="sequence"/>\r
- <field name="type" type="string">\r
- <bind-xml name="type" node="attribute" location="type"/>\r
- </field>\r
- <field name="version" type="string">\r
- <bind-xml name="version" node="attribute" location="version"/>\r
- </field>\r
- <field name="sequence" type="string">\r
- <bind-xml node="text"/>\r
- </field>\r
- </class>\r
- <class name="jalview.datamodel.xdb.embl.EmblFeature" verify-constructable="false">\r
- <map-to xml="feature"/>\r
- <field name="name" type="string">\r
- <bind-xml name="name" node="attribute"/>\r
- </field>\r
- <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">\r
- <bind-xml name="dbreference" node="element"/>\r
- </field>\r
- <field name="qualifiers" type="jalview.datamodel.xdb.embl.Qualifier" collection="vector">\r
- <bind-xml name="qualifier"/>\r
- </field> \r
- <field name="locations" type="jalview.datamodel.xdb.embl.EmblFeatureLocations" collection="vector">\r
- <bind-xml name="location"/>\r
- </field>\r
- </class>\r
- <class name="jalview.datamodel.DBRefEntry" verify-constructable="false">\r
- <field name="accessionId" type="java.lang.String"><!-- set-method="setAccessionId" get-method="getAccessionId"> -->\r
- <bind-xml name="primary" node="attribute"/>\r
- </field>\r
- <field name="source" type="java.lang.String"> <!--set-method="setSource" get-method="getSource"> -->\r
- <bind-xml name="db" node="attribute"/>\r
- </field>\r
- <field name="version" type="string"><!-- set-method="setVersion" get-method="getVersion"> -->\r
- <bind-xml name="secondary" node="attribute"/>\r
- </field>\r
- </class>\r
- <class name="jalview.datamodel.xdb.embl.Qualifier" verify-constructable="false">\r
- <map-to xml="Qualifier"/>\r
- <field name="name">\r
- <bind-xml name="name" node="attribute"/>\r
- </field>\r
- <field name="evidence" type="string" collection="array">\r
- <bind-xml name="evidence" node="element"/>\r
- </field>\r
- <field name="values" type="string" collection="array">\r
- <bind-xml name="value" node="element"/>\r
- </field>\r
- </class>\r
- <class name="jalview.datamodel.xdb.embl.EmblFeatureLocations">\r
- <map-to xml="location"/>\r
- <field name="locationType" type="string">\r
- <bind-xml name="type" node="attribute"/>\r
- </field>\r
- <field name="locationComplement" type="boolean">\r
- <bind-xml name="complement" node="attribute"/>\r
- </field>\r
- <field name="locElements" type="jalview.datamodel.xdb.embl.EmblFeatureLocElement" collection="vector">\r
- <bind-xml name="locationElement"/>\r
- </field>\r
- </class>\r
- <class name="jalview.datamodel.xdb.embl.EmblFeatureLocElement">\r
- <map-to xml="locationElement"/>\r
- <field name="type" type="string">\r
- <bind-xml name="type" node="attribute"/>\r
- </field>\r
- <field name="accession" type="string">\r
- <bind-xml name="accession" node="attribute"/> \r
- </field>\r
- <field name="version" type="string">\r
- <bind-xml name="version" node="attribute"/>\r
- </field>\r
- <field name="complement" type="boolean">\r
- <bind-xml name="complement"/>\r
- </field>\r
- <field name="basePositions" type="jalview.datamodel.xdb.embl.BasePosition" collection="array">\r
- <bind-xml name="basePosition" node="element"/>\r
- </field>\r
- </class>\r
- <class name="jalview.datamodel.xdb.embl.BasePosition">\r
- <map-to xml="basePosition"/>\r
- <field name="type">\r
- <bind-xml name="type" node="attribute"/>\r
- </field>\r
- <field name="pos">\r
- <bind-xml node="text"/>\r
- </field>\r
- </class>\r
-</mapping>\r
+<?xml version="1.0"?>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
+<mapping xmlns="http://castor.exolab.org/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://castor.exolab.org/ ../schemas/castor-mapping.xsd">
+<!--
+ 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="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">
+ <field name="accession" type="string">
+ <bind-xml name="accession" node="attribute"/>
+ </field>
+ <!--
+ 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="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="firstPublicDate" type="string">
+ <bind-xml name="firstPublic" node="attribute"/>
+ </field>
+ <field name="firstPublicRelease" type="string">
+ <bind-xml name="firstPublicRelease" node="attribute"/>
+ </field>
+ <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">
+ <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="xref" />
+ </field>
+ <field name="sequence" type="jalview.datamodel.xdb.embl.EmblSequence">
+ <bind-xml name="sequence"/>
+ </field>
+ </class>
+ <class name="jalview.datamodel.xdb.embl.EmblSequence">
+ <field name="sequence" type="string">
+ <bind-xml node="text"/>
+ </field>
+ </class>
+ <class name="jalview.datamodel.xdb.embl.EmblFeature" verify-constructable="false">
+ <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="xref" node="element"/>
+ </field>
+ <field name="qualifiers" type="jalview.datamodel.xdb.embl.Qualifier" collection="vector">
+ <bind-xml name="qualifier"/>
+ </field>
+ </class>
+ <class name="jalview.datamodel.DBRefEntry" verify-constructable="false">
+ <field name="accessionId" type="java.lang.String">
+ <bind-xml name="id" node="attribute"/>
+ </field>
+ <field name="source" type="java.lang.String">
+ <bind-xml name="db" node="attribute"/>
+ </field>
+ <field name="version" type="string">
+ <bind-xml name="secondaryId" node="attribute"/>
+ </field>
+ </class>
+ <class name="jalview.datamodel.xdb.embl.Qualifier" verify-constructable="false">
+ <field name="name">
+ <bind-xml name="name" node="attribute"/>
+ </field>
+ <field name="evidence" type="string" collection="array">
+ <bind-xml name="evidence" node="element"/>
+ </field>
+ <field name="values" type="string" collection="array">
+ <bind-xml name="value" node="element"/>
+ </field>
+ </class>
+</mapping>
git://source.jalview.org / jalview.git / blobdiff