-<?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
+<?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>
git://source.jalview.org / jalviewjs.git / blobdiff