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.
20 <mapping xmlns="http://castor.exolab.org/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
21 xsi:schemaLocation="http://castor.exolab.org/ ../schemas/castor-mapping.xsd">
23 History: Originally created from EMBL_common_V1.0
24 Updated on 24th April 2007 for WsDBFetch Service move to EMBL_Services_V1.1.xsd
25 Updated May 2016 for EMBL XML 1.2 JAL-2113 JAL-2114
26 see ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_5/ENA.embl.xsd
27 see http://www.ebi.ac.uk/ena/submit/data-formats
29 <class name="jalview.datamodel.xdb.embl.EmblFile">
31 <field name="text" type="string">
32 <bind-xml node="text"/>
34 <field name="entries" type="jalview.datamodel.xdb.embl.EmblEntry" collection="vector">
35 <bind-xml name="entry"/>
37 <field name="errors" type="jalview.datamodel.xdb.embl.EmblError" collection="vector">
38 <bind-xml name="Error"/>
41 <class name="jalview.datamodel.xdb.embl.EmblEntry">
42 <field name="accession" type="string">
43 <bind-xml name="accession" node="attribute"/>
46 in EMBL XML 1.2 sequence/@version became entry/version
47 entry/@version became entry/@entryVersion
49 <field name="sequenceVersion" type="string">
50 <bind-xml name="version" node="attribute"/>
52 <field name="entryVersion" type="string">
53 <bind-xml name="entryVersion" node="attribute"/>
55 <field name="dataClass" type="string">
56 <bind-xml name="dataClass" node="attribute"/>
58 <field name="taxonomicDivision" type="string">
59 <bind-xml name="taxonomicDivision" node="attribute"/>
61 <field name="moleculeType" type="string">
62 <bind-xml name="moleculeType" node="attribute"/>
64 <field name="sequenceLength" type="string">
65 <bind-xml name="sequenceLength" node="attribute"/>
67 <field name="topology" type="string">
68 <bind-xml name="topology" node="attribute" location="type"/>
70 <field name="firstPublicDate" type="string">
71 <bind-xml name="firstPublic" node="attribute"/>
73 <field name="firstPublicRelease" type="string">
74 <bind-xml name="firstPublicRelease" node="attribute"/>
76 <field name="lastUpdatedDate" type="string">
77 <bind-xml name="lastUpdated" node="attribute"/>
79 <field name="lastUpdatedRelease" type="string">
80 <bind-xml name="lastUpdatedRelease" node="attribute"/>
82 <field name="description" type="string">
83 <bind-xml name="description" node="element"/>
85 <field name="keywords" type="string" collection="vector">
86 <bind-xml name="keyword" node="element"/>
88 <field name="features" type="jalview.datamodel.xdb.embl.EmblFeature" collection="vector">
89 <bind-xml name="feature"/>
91 <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">
92 <bind-xml name="xref" />
94 <field name="sequence" type="jalview.datamodel.xdb.embl.EmblSequence">
95 <bind-xml name="sequence"/>
98 <class name="jalview.datamodel.xdb.embl.EmblSequence">
99 <field name="sequence" type="string">
100 <bind-xml node="text"/>
103 <class name="jalview.datamodel.xdb.embl.EmblFeature" verify-constructable="false">
104 <field name="name" type="string">
105 <bind-xml name="name" node="attribute"/>
107 <field name="location" type="string">
108 <bind-xml name="location" node="attribute"/>
110 <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">
111 <bind-xml name="xref" node="element"/>
113 <field name="qualifiers" type="jalview.datamodel.xdb.embl.Qualifier" collection="vector">
114 <bind-xml name="qualifier"/>
117 <class name="jalview.datamodel.DBRefEntry" verify-constructable="false">
118 <field name="accessionId" type="java.lang.String">
119 <bind-xml name="id" node="attribute"/>
121 <field name="source" type="java.lang.String">
122 <bind-xml name="db" node="attribute"/>
124 <field name="version" type="string">
125 <bind-xml name="secondaryId" node="attribute"/>
128 <class name="jalview.datamodel.xdb.embl.Qualifier" verify-constructable="false">
130 <bind-xml name="name" node="attribute"/>
132 <field name="evidence" type="string" collection="array">
133 <bind-xml name="evidence" node="element"/>
135 <field name="values" type="string" collection="array">
136 <bind-xml name="value" node="element"/>