3 Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.0.b2)
4 Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
6 This program is free software; you can redistribute it and/or
7 modify it under the terms of the GNU General Public License
8 as published by the Free Software Foundation; either version 2
9 of the License, or (at your option) any later version.
11 This program is distributed in the hope that it will be useful,
12 but WITHOUT ANY WARRANTY; without even the implied warranty of
13 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14 GNU General Public License for more details.
16 You should have received a copy of the GNU General Public License
17 along with this program; if not, write to the Free Software
18 Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
21 <class name="jalview.datamodel.UniprotFile">
22 <map-to xml="uniprot"/>
23 <field name="UniprotEntries" type="jalview.datamodel.UniprotEntry" collection="vector">
24 <bind-xml name="entry"/>
28 <class name="jalview.datamodel.UniprotEntry">
29 <field name="name" type="string" collection="vector"/>
30 <field name="accession" type="string" collection="vector"/>
31 <field name="protein" type="jalview.datamodel.UniprotProteinName"/>
32 <field name="UniprotSequence" type="jalview.datamodel.UniprotSequence">
33 <bind-xml name="sequence"/>
35 <field name="feature" type="jalview.datamodel.SequenceFeature" collection="vector"/>
36 <field name="dbReference" type="jalview.datamodel.PDBEntry" collection="vector"/>
39 <class name="jalview.datamodel.UniprotProteinName">
40 <field name="name" collection="vector" type="string">
41 <bind-xml name="fullName" location="recommendedName" node="element"/>
44 <!-- uniprot protein name is now a collection of collections - the INCLUDES and CONTAINS entries of the uniprot
45 record. This means this doesn't exist anymore...
46 <class name="jalview.datamodel.UniprotProteinName">
47 <field name="name" type="string" collection="vector">
48 <bind-xml name="name"/>
53 <class name="jalview.datamodel.SequenceFeature">
55 <bind-xml node="attribute"/>
57 <field name="description">
58 <bind-xml node="attribute"/>
61 <bind-xml node="attribute"/>
63 <field name="position">
64 <bind-xml name="position" node="attribute" location="location/position"/>
67 <bind-xml name="position" node="attribute" location="location/begin"/>
70 <bind-xml name="position" node="attribute" location="location/end"/>
74 <class name="jalview.datamodel.UniprotSequence">
75 <field name="content" type="string">
76 <bind-xml name="sequence" node="text"/>
80 <class name="jalview.datamodel.PDBEntry">
81 <field name="type"><bind-xml node="attribute"/></field>
82 <field name="id"><bind-xml node="attribute"/></field>
83 <field name="property" collection="hashtable">
84 <bind-xml name="property">
85 <class name="org.exolab.castor.mapping.MapItem">
87 <bind-xml name="type" node="attribute"/>
90 <bind-xml node="attribute"/>