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jalviewX

  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.io.packed

File DataProvider.java

 

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Classes

Class Line # Actions
DataProvider 30 0 0 0
-1.0 -
DataProvider.JvDataType 38 0 0 0
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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ 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    */
70    jalview.io.FileParse getDataSource();
71   
72    /**
73    * association context for data. Either null or a specific sequence.
74    *
75    * @return
76    */
77    Object getSequenceTarget();
78   
79    /**
80    * type of data
81    *
82    * @return
83    */
84    DataProvider.JvDataType getType();
85    }