1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.datamodel

File GeneLociI.java

 

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GeneLociI 28 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.datamodel;
22   
23    import jalview.util.MapList;
24   
25    /**
26    * An interface to model one or more contiguous regions on one chromosome
27    */
 
28    public interface GeneLociI
29    {
30    /**
31    * Answers the species identifier
32    *
33    * @return
34    */
35    String getSpeciesId();
36   
37    /**
38    * Answers the reference assembly identifier
39    *
40    * @return
41    */
42    String getAssemblyId();
43   
44    /**
45    * Answers the chromosome identifier e.g. "2", "Y", "II"
46    *
47    * @return
48    */
49    String getChromosomeId();
50   
51    /**
52    * Answers the mapping from sequence to chromosome loci. For a reverse strand
53    * mapping, the chromosomal ranges will have start > end.
54    *
55    * @return
56    */
57    MapList getMapping();
58    }