Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
CigarCigar	23	8	5	0.00%	Show methods

Class CigarCigar

Class CigarCigar	Line # 23	Total Statements 8	Complexity 5	TOTAL Coverage 0.00%
CigarCigar(SeqCigar)   CigarCigar(SeqCigar)	3333	2.02	1.01	0.0 0.00%
getSequenceString(char) : String   getSequenceString(char) : String	4646	6.06	4.04	0.0 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
		0% Uncovered Elements: 16 (16) Complexity: 5 Complexity Density: 0.62
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		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
33	0	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		*/
		0% Uncovered Elements: 12 (12) Complexity: 4 Complexity Density: 0.67
46	0	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		}