JAL-1782 refactored JAL-1766 JAL-653 tests to TestNG
[jalview.git] / resources / embl_mapping.xml
1 <?xml version="1.0"?>
2 <!--
3  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4  * Copyright (C) $$Year-Rel$$ The Jalview Authors
5  * 
6  * This file is part of Jalview.
7  * 
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.
11  *  
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.
16  * 
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.
19 -->
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">
22 <!--
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         -->
26         <class name="jalview.datamodel.xdb.embl.EmblFile">
27                 <map-to xml="EMBL_Services"/>
28                 <field name="entries" type="jalview.datamodel.xdb.embl.EmblEntry" collection="vector">
29                         <bind-xml name="entry"/>
30                 </field>
31                 
32                 <field name="errors" type="jalview.datamodel.xdb.embl.EmblError" collection="vector">
33                         <bind-xml name="Error"/>
34                 </field>
35         </class>
36         <class name="jalview.datamodel.xdb.embl.EmblEntry">
37                 <field name="accession" type="string">
38                         <bind-xml location="accession" node="attribute"/>
39                 </field>
40                 <!--  May 2015 changed from last-updated to match xml -->
41                 <field name="lastUpdated" type="string">
42                         <bind-xml location="lastUpdated" node="attribute"/>
43                 </field>
44                 <field name="version" type="string">
45                         <bind-xml location="version" node="attribute"/>
46                 </field>
47                 <field name="rCreated" type="string">
48                         <bind-xml location="releaseCreated" node="attribute"/>
49                 </field>
50                 <field name="rLastUpdated" type="string">
51                         <bind-xml location="releaseLastUpdated" node="attribute"/>
52                 </field>
53                 <field name="desc" type="string">
54                         <bind-xml name="description" node="element"/>
55                 </field>
56                 <field name="keywords" type="string" collection="vector">
57                         <bind-xml name="keyword" node="element"/>
58                 </field>
59                 <field name="features" type="jalview.datamodel.xdb.embl.EmblFeature" collection="vector">
60                         <bind-xml name="feature"/>
61                 </field>
62                 <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">
63                         <bind-xml name="dbreference" />
64                 </field>
65                 <field name="sequence" type="jalview.datamodel.xdb.embl.EmblSequence">
66                         <bind-xml name="sequence"/>
67                 </field>
68         </class>
69         <class name="jalview.datamodel.xdb.embl.EmblSequence">
70                 <field name="type" type="string">
71                         <bind-xml name="type" node="attribute" location="type"/>
72                 </field>
73                 <field name="version" type="string">
74                         <bind-xml name="version" node="attribute" location="version"/>
75                 </field>
76                 <field name="sequence" type="string">
77                         <bind-xml node="text"/>
78                 </field>
79         </class>
80         <class name="jalview.datamodel.xdb.embl.EmblFeature" verify-constructable="false">
81                 <field name="name" type="string">
82                         <bind-xml name="name" node="attribute"/>
83                 </field>
84                 <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">
85                         <bind-xml name="dbreference" node="element"/>
86                 </field>
87                 <field name="qualifiers" type="jalview.datamodel.xdb.embl.Qualifier" collection="vector">
88                         <bind-xml name="qualifier"/>
89                 </field>                                        
90                 <field name="locations" type="jalview.datamodel.xdb.embl.EmblFeatureLocations" collection="vector">
91                         <bind-xml name="location"/>
92                 </field>
93         </class>
94         <class name="jalview.datamodel.DBRefEntry" verify-constructable="false">
95                 <field name="accessionId" type="java.lang.String">
96                         <bind-xml name="primary" node="attribute"/>
97                 </field>
98                 <field name="source" type="java.lang.String"> 
99                         <bind-xml name="db" node="attribute"/>
100                 </field>
101                 <field name="version" type="string">
102                         <bind-xml name="secondary" node="attribute"/>
103                 </field>
104         </class>
105         <class  name="jalview.datamodel.xdb.embl.Qualifier" verify-constructable="false">
106                 <field name="name">
107                         <bind-xml name="name" node="attribute"/>
108                 </field>
109                 <field name="evidence" type="string" collection="array">
110                         <bind-xml name="evidence" node="element"/>
111                 </field>
112                 <field name="values" type="string" collection="array">
113                         <bind-xml name="value" node="element"/>
114                 </field>
115         </class>
116         <class name="jalview.datamodel.xdb.embl.EmblFeatureLocations">
117                 <field name="locationType" type="string">
118                         <bind-xml name="type" node="attribute"/>
119                 </field>
120                 <field name="locationComplement" type="boolean">
121                         <bind-xml name="complement" node="attribute"/>
122                 </field>
123                 <field name="locElements" type="jalview.datamodel.xdb.embl.EmblFeatureLocElement" collection="vector">
124                         <bind-xml name="locationElement"/>
125                 </field>
126         </class>
127         <class name="jalview.datamodel.xdb.embl.EmblFeatureLocElement">
128                 <field name="type" type="string">
129                         <bind-xml name="type" node="attribute"/>
130                 </field>
131                 <field name="accession" type="string">
132                         <bind-xml name="accession" node="attribute"/>                   
133                 </field>
134                 <field name="version" type="string">
135                         <bind-xml name="version" node="attribute"/>
136                 </field>
137                 <field name="complement" type="boolean">
138                         <bind-xml name="complement"/>
139                 </field>
140                 <field name="basePositions" type="jalview.datamodel.xdb.embl.BasePosition" collection="array">
141                         <bind-xml name="basePosition" node="element"/>
142                 </field>
143         </class>
144         <class name="jalview.datamodel.xdb.embl.BasePosition">
145                 <field name="type">
146                         <bind-xml name="type" node="attribute"/>
147                 </field>
148                 <field name="pos">
149                         <bind-xml node="text"/>
150                 </field>
151         </class>
152 </mapping>