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

File CigarCigar.java

 

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../../img/srcFileCovDistChart0.png
60% of files have more coverage

Code metrics

6
8
2
1
64
27
5
0.62
4
2
2.5

Classes

Class
Line #
Actions
CigarCigar 23 8 5
0.00%
 

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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    public class CigarCigar extends CigarSimple
24    {
25    SeqCigar refCigar;
26   
27    /**
28    * Apply CIGAR operations to the result of another cigar
29    *
30    * @param cigar
31    * Cigar
32    */
 
33  0 toggle CigarCigar(SeqCigar cigar)
34    {
35  0 super();
36  0 refCigar = cigar;
37    }
38   
39    /**
40    *
41    * @return String formed by applying CIGAR operations to the reference object
42    * @param GapChar
43    * char
44    * @todo Implement this jalview.datamodel.Cigar method
45    */
 
46  0 toggle public String getSequenceString(char GapChar)
47    {
48  0 if (length == 0)
49    {
50  0 return "";
51    }
52  0 String refString = refCigar.getSequenceString(GapChar);
53  0 if (refString != null)
54    {
55  0 return (length == 0) ? ""
56    : (String) getSequenceAndDeletions(refString, GapChar)[0];
57    }
58    else
59    {
60  0 return null;
61    }
62    }
63   
64    }