-<?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>
- <class name="jalview.datamodel.UniprotFile">
- <map-to xml="uniprot"/>
- <field name="UniprotEntries" type="jalview.datamodel.UniprotEntry" collection="vector">
- <bind-xml name="entry"/>
- </field>
- </class>
-
- <class name="jalview.datamodel.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">
- <bind-xml name="sequence"/>
- </field>
- <field name="feature" type="jalview.datamodel.SequenceFeature" collection="vector"/>
- <field name="dbReference" type="jalview.datamodel.PDBEntry" collection="vector"/>
-
- </class>
- <class name="jalview.datamodel.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">
- <field name="name" type="string" collection="vector">
- <bind-xml name="name"/>
- </field>
- </class>
- -->
-
- <class name="jalview.datamodel.SequenceFeature">
- <field name="type">
- <bind-xml node="attribute"/>
- </field>
- <field name="description">
- <bind-xml node="attribute"/>
- </field>
- <field name="status">
- <bind-xml node="attribute"/>
- </field>
- <field name="position">
- <bind-xml name="position" node="attribute" location="location/position"/>
- </field>
- <field name="begin">
- <bind-xml name="position" node="attribute" location="location/begin"/>
- </field>
- <field name="end">
- <bind-xml name="position" node="attribute" location="location/end"/>
- </field>
- </class>
-
- <class name="jalview.datamodel.UniprotSequence">
- <field name="content" type="string">
- <bind-xml name="sequence" node="text"/>
- </field>
- </class>
-
- <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">
- <bind-xml name="property">
- <class name="org.exolab.castor.mapping.MapItem">
- <field name="key">
- <bind-xml name="type" node="attribute"/>
- </field>
- <field name="value">
- <bind-xml node="attribute"/>
- </field>
- </class>
- </bind-xml>
- </field>
- </class>
-
-</mapping>
+<?xml version="1.0"?>\r
+<!--\r
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)\r
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview 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 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ * The Jalview Authors are detailed in the 'AUTHORS' file.\r
+-->\r
+<mapping>\r
+ <class name="jalview.datamodel.UniprotFile">\r
+ <map-to xml="uniprot"/> \r
+ <field name="UniprotEntries" type="jalview.datamodel.UniprotEntry" collection="vector">\r
+ <bind-xml name="entry"/>\r
+ </field> \r
+ </class>\r
+ \r
+ <class name="jalview.datamodel.UniprotEntry">\r
+ <field name="name" type="string" collection="vector"/>\r
+ <field name="accession" type="string" collection="vector"/>\r
+ <field name="protein" type="jalview.datamodel.UniprotProteinName"/>\r
+ <field name="UniprotSequence" type="jalview.datamodel.UniprotSequence">\r
+ <bind-xml name="sequence"/> \r
+ </field>\r
+ <field name="feature" type="jalview.datamodel.SequenceFeature" collection="vector"/>\r
+ <field name="dbReference" type="jalview.datamodel.PDBEntry" collection="vector"/>\r
+ \r
+ </class>\r
+ <class name="jalview.datamodel.UniprotProteinName">\r
+ <field name="name" collection="vector" type="string">\r
+ <bind-xml name="fullName" location="recommendedName" node="element"/>\r
+ </field>\r
+ </class>\r
+ <!-- uniprot protein name is now a collection of collections - the INCLUDES and CONTAINS entries of the uniprot\r
+ record. This means this doesn't exist anymore...\r
+ <class name="jalview.datamodel.UniprotProteinName">\r
+ <field name="name" type="string" collection="vector">\r
+ <bind-xml name="name"/>\r
+ </field> \r
+ </class>\r
+ -->\r
+ \r
+ <class name="jalview.datamodel.SequenceFeature">\r
+ <field name="type">\r
+ <bind-xml node="attribute"/>\r
+ </field>\r
+ <field name="description">\r
+ <bind-xml node="attribute"/>\r
+ </field>\r
+ <field name="status">\r
+ <bind-xml node="attribute"/>\r
+ </field>\r
+ <field name="position">\r
+ <bind-xml name="position" node="attribute" location="location/position"/>\r
+ </field>\r
+ <field name="begin">\r
+ <bind-xml name="position" node="attribute" location="location/begin"/>\r
+ </field>\r
+ <field name="end">\r
+ <bind-xml name="position" node="attribute" location="location/end"/>\r
+ </field>\r
+ </class>\r
+ \r
+ <class name="jalview.datamodel.UniprotSequence">\r
+ <field name="content" type="string">\r
+ <bind-xml name="sequence" node="text"/>\r
+ </field>\r
+ </class>\r
+ \r
+ <class name="jalview.datamodel.PDBEntry">\r
+ <field name="type"><bind-xml node="attribute"/></field>\r
+ <field name="id"><bind-xml node="attribute"/></field>\r
+ <field name="property" collection="hashtable">\r
+ <bind-xml name="property">\r
+ <class name="org.exolab.castor.mapping.MapItem">\r
+ <field name="key">\r
+ <bind-xml name="type" node="attribute"/>\r
+ </field>\r
+ <field name="value">\r
+ <bind-xml node="attribute"/>\r
+ </field>\r
+ </class>\r
+ </bind-xml>\r
+ </field>\r
+ </class>\r
+\r
+</mapping>\r
git://source.jalview.org / jalviewjs.git / blobdiff