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="entries" type="jalview.datamodel.xdb.embl.EmblEntry" collection="vector">
32 <bind-xml name="entry"/>
34 <field name="errors" type="jalview.datamodel.xdb.embl.EmblError" collection="vector">
35 <bind-xml name="Error"/>
38 <class name="jalview.datamodel.xdb.embl.EmblEntry">
39 <field name="accession" type="string">
40 <bind-xml name="accession" node="attribute"/>
42 <field name="lastUpdated" type="string">
43 <bind-xml name="lastUpdated" node="attribute"/>
46 in EMBL XML 1.2 sequence/@version becomes entry/version
47 entry/@version becomes 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="moleculeType" type="string">
56 <bind-xml name="moleculeType" node="attribute"/>
58 <field name="sequenceLength" type="string">
59 <bind-xml name="sequenceLength" node="attribute"/>
61 <field name="topology" type="string">
62 <bind-xml name="topology" node="attribute" location="type"/>
64 <field name="rCreated" type="string">
65 <bind-xml name="releaseCreated" node="attribute"/>
67 <field name="rLastUpdated" type="string">
68 <bind-xml name="releaseLastUpdated" node="attribute"/>
70 <field name="desc" type="string">
71 <bind-xml name="description" node="element"/>
73 <field name="keywords" type="string" collection="vector">
74 <bind-xml name="keyword" node="element"/>
76 <field name="features" type="jalview.datamodel.xdb.embl.EmblFeature" collection="vector">
77 <bind-xml name="feature"/>
79 <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">
80 <bind-xml name="xref" />
82 <field name="sequence" type="jalview.datamodel.xdb.embl.EmblSequence">
83 <bind-xml name="sequence"/>
86 <class name="jalview.datamodel.xdb.embl.EmblSequence">
87 <field name="sequence" type="string">
88 <bind-xml node="text"/>
91 <class name="jalview.datamodel.xdb.embl.EmblFeature" verify-constructable="false">
92 <field name="name" type="string">
93 <bind-xml name="name" node="attribute"/>
95 <field name="location" type="string">
96 <bind-xml name="location" node="attribute"/>
98 <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">
99 <bind-xml name="xref" node="element"/>
101 <field name="qualifiers" type="jalview.datamodel.xdb.embl.Qualifier" collection="vector">
102 <bind-xml name="qualifier"/>
105 <class name="jalview.datamodel.DBRefEntry" verify-constructable="false">
106 <field name="accessionId" type="java.lang.String">
107 <bind-xml name="id" node="attribute"/>
109 <field name="source" type="java.lang.String">
110 <bind-xml name="db" node="attribute"/>
112 <field name="version" type="string">
113 <bind-xml name="secondaryId" node="attribute"/>
116 <class name="jalview.datamodel.xdb.embl.Qualifier" verify-constructable="false">
118 <bind-xml name="name" node="attribute"/>
120 <field name="evidence" type="string" collection="array">
121 <bind-xml name="evidence" node="element"/>
123 <field name="values" type="string" collection="array">
124 <bind-xml name="value" node="element"/>
127 <class name="jalview.datamodel.xdb.embl.EmblFeatureLocations">
128 <field name="locationType" type="string">
129 <bind-xml name="type" node="attribute"/>
131 <field name="locationComplement" type="boolean">
132 <bind-xml name="complement" node="attribute"/>
134 <field name="locElements" type="jalview.datamodel.xdb.embl.EmblFeatureLocElement" collection="vector">
135 <bind-xml name="locationElement"/>
138 <class name="jalview.datamodel.xdb.embl.EmblFeatureLocElement">
139 <field name="type" type="string">
140 <bind-xml name="type" node="attribute"/>
142 <field name="accession" type="string">
143 <bind-xml name="accession" node="attribute"/>
145 <field name="version" type="string">
146 <bind-xml name="version" node="attribute"/>
148 <field name="complement" type="boolean">
149 <bind-xml name="complement"/>
151 <field name="basePositions" type="jalview.datamodel.xdb.embl.BasePosition" collection="array">
152 <bind-xml name="basePosition" node="element"/>
155 <class name="jalview.datamodel.xdb.embl.BasePosition">
157 <bind-xml name="type" node="attribute"/>
160 <bind-xml node="text"/>