1 /*
2  * Jalview - A Sequence Alignment Editor and Viewer (2.11.1.4)
3  * Copyright (C) 2021 The Jalview Authors
4  *
5  * This file is part of Jalview.
6  *
7  * Jalview is free software: you can redistribute it and/or
8  * modify it under the terms of the GNU General Public License
9  * as published by the Free Software Foundation, either version 3
10  * 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
18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
19  * The Jalview Authors are detailed in the 'AUTHORS' file.
20  */
21 package jalview.io.packed;
22 
23 /**
24  * API for a data provider that can be used with
25  * jalview.io.packed.ParsePackedSet
26  *
27  * @author JimP
28  *
29  */
30 public interface DataProvider
31 {
32   /**
33    * class of data expected to be provided by datasource
34    *
35    * @author JimP
36    *
37    */
38   public enum JvDataType
39   {
40     /**
41      * any alignment flatfile recognisable by jalview.io.IdentifyFile
42      */
43     ALIGNMENT,
44     /**
45      * a jalview annotation file
46      */
47     ANNOTATION,
48     /**
49      * a GFF or Jalview features file
50      */
51     FEATURES,
52     /**
53      * a tree representation understood by the NewickFile parser
54      */
55     TREE,
56     /**
57      * any file that provides data that should be associated with a specified
58      * sequence.
59      */
60     SEQASSOCATED;
61   }
62 
63   /**
64    * data to be parsed according to its type. Each call to getDataSource should
65    * return a new instance of the same data stream initialised to the beginning
66    * of the chunk of data that is to be parsed.
67    *
68    * @return
69    */
getDataSource()70   jalview.io.FileParse getDataSource();
71 
72   /**
73    * association context for data. Either null or a specific sequence.
74    *
75    * @return
76    */
getSequenceTarget()77   Object getSequenceTarget();
78 
79   /**
80    * type of data
81    *
82    * @return
83    */
getType()84   DataProvider.JvDataType getType();
85 }
86