3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 <!-- see https://www.uniprot.org/docs/uniprot.xsd for latest Uniprot XML schema -->
22 <class name="jalview.datamodel.xdb.uniprot.UniprotFile">
23 <map-to xml="uniprot"/>
24 <field name="UniprotEntries" type="jalview.datamodel.xdb.uniprot.UniprotEntry" collection="vector">
25 <bind-xml name="entry"/>
29 <class name="jalview.datamodel.xdb.uniprot.UniprotEntry">
30 <field name="name" type="string" collection="vector"/>
31 <field name="accession" type="string" collection="vector"/>
32 <field name="protein" type="jalview.datamodel.xdb.uniprot.UniprotProteinName"/>
33 <field name="UniprotSequence" type="jalview.datamodel.xdb.uniprot.UniprotSequence">
34 <bind-xml name="sequence"/>
36 <field name="feature" type="jalview.datamodel.xdb.uniprot.UniprotFeature" collection="vector"/>
37 <field name="dbReference" type="jalview.datamodel.PDBEntry" collection="vector"/>
40 <class name="jalview.datamodel.xdb.uniprot.UniprotProteinName">
41 <field name="name" collection="vector" type="string">
42 <bind-xml name="fullName" location="recommendedName" node="element"/>
45 <!-- uniprot protein name is now a collection of collections - the INCLUDES and CONTAINS entries of the uniprot
46 record. This means this doesn't exist anymore...
47 <class name="jalview.datamodel.xdb.uniprot.UniprotProteinName">
48 <field name="name" type="string" collection="vector">
49 <bind-xml name="name"/>
54 <class name="jalview.datamodel.xdb.uniprot.UniprotFeature">
56 <bind-xml node="attribute"/>
58 <field name="description">
59 <bind-xml node="attribute"/>
62 <bind-xml node="attribute"/>
64 <field name="position">
65 <bind-xml name="position" node="attribute" location="location/position"/>
68 <bind-xml name="position" node="attribute" location="location/begin"/>
71 <bind-xml name="position" node="attribute" location="location/end"/>
73 <field name="variation" collection="vector" type="string">
74 <bind-xml name="variation"/>
76 <field name="original">
77 <bind-xml name="original"/>
81 <class name="jalview.datamodel.xdb.uniprot.UniprotSequence">
82 <field name="content" type="string">
83 <bind-xml name="sequence" node="text"/>
87 <class name="jalview.datamodel.PDBEntry">
88 <field name="type"><bind-xml node="attribute"/></field>
89 <field name="id"><bind-xml node="attribute"/></field>
90 <field name="props" collection="hashtable">
91 <bind-xml name="property">
92 <class name="org.exolab.castor.mapping.MapItem">
94 <bind-xml name="type" node="attribute"/>
97 <bind-xml node="attribute"/>