<?xml version="1.0"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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/>.
+ * 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>
- <class name="jalview.datamodel.UniprotFile">
+ <class name="jalview.datamodel.xdb.uniprot.UniprotFile">
<map-to xml="uniprot"/>
- <field name="UniprotEntries" type="jalview.datamodel.UniprotEntry" collection="vector">
+ <field name="UniprotEntries" type="jalview.datamodel.xdb.uniprot.UniprotEntry" collection="vector">
<bind-xml name="entry"/>
</field>
</class>
- <class name="jalview.datamodel.UniprotEntry">
+ <class name="jalview.datamodel.xdb.uniprot.UniprotEntry">
<field name="name" type="string" collection="vector"/>
<field name="accession" type="string" collection="vector"/>
- <field name="protein" type="jalview.datamodel.UniprotProteinName"/>
- <field name="UniprotSequence" type="jalview.datamodel.UniprotSequence">
+ <field name="protein" type="jalview.datamodel.xdb.uniprot.UniprotProteinName"/>
+ <field name="UniprotSequence" type="jalview.datamodel.xdb.uniprot.UniprotSequence">
<bind-xml name="sequence"/>
</field>
- <field name="feature" type="jalview.datamodel.SequenceFeature" collection="vector"/>
+ <field name="feature" type="jalview.datamodel.xdb.uniprot.UniprotFeature" collection="vector"/>
<field name="dbReference" type="jalview.datamodel.PDBEntry" collection="vector"/>
</class>
- <class name="jalview.datamodel.UniprotProteinName">
+ <class name="jalview.datamodel.xdb.uniprot.UniprotProteinName">
<field name="name" collection="vector" type="string">
<bind-xml name="fullName" location="recommendedName" node="element"/>
</field>
</class>
<!-- uniprot protein name is now a collection of collections - the INCLUDES and CONTAINS entries of the uniprot
record. This means this doesn't exist anymore...
- <class name="jalview.datamodel.UniprotProteinName">
+ <class name="jalview.datamodel.xdb.uniprot.UniprotProteinName">
<field name="name" type="string" collection="vector">
<bind-xml name="name"/>
</field>
</class>
-->
- <class name="jalview.datamodel.SequenceFeature">
+ <class name="jalview.datamodel.xdb.uniprot.UniprotFeature">
<field name="type">
<bind-xml node="attribute"/>
</field>
</field>
</class>
- <class name="jalview.datamodel.UniprotSequence">
+ <class name="jalview.datamodel.xdb.uniprot.UniprotSequence">
<field name="content" type="string">
<bind-xml name="sequence" node="text"/>
</field>
<class name="jalview.datamodel.PDBEntry">
<field name="type"><bind-xml node="attribute"/></field>
<field name="id"><bind-xml node="attribute"/></field>
- <field name="property" collection="hashtable">
+ <field name="props" collection="hashtable">
<bind-xml name="property">
<class name="org.exolab.castor.mapping.MapItem">
<field name="key">