Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AlignedCodon	33	18	11	0.00%	Show methods

Class AlignedCodon

Class AlignedCodon	Line # 33	Total Statements 18	Complexity 11	TOTAL Coverage 0.00%
AlignedCodon(int,int,int)   AlignedCodon(int,int,int)	5050	1.01	1.01	0.0 0.00%
AlignedCodon(int,int,int,String,int)   AlignedCodon(int,int,int,String,int)	5555	5.05	1.01	0.0 0.00%
getBaseColumn(int) : int   getBaseColumn(int) : int	7272	3.03	5.05	0.0 0.00%
equals(Object) : boolean   equals(Object) : boolean	8787	6.06	3.03	0.0 0.00%
toString() : String   toString() : String	106106	3.03	1.01	0.0 0.00%

 

Contributing tests

Source view

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		/**
24		* Holds the aligned column positions (base 0) for one codon in a nucleotide
25		* sequence, and (optionally) its peptide translation. The object is immutable
26		* once created.
27		*
28		* Example: in "G-AT-C-GA" the aligned codons are (0, 2, 3) and (5, 7, 8).
29		*
30		* @author gmcarstairs
31		*
32		*/
		0% Uncovered Elements: 33 (33) Complexity: 11 Complexity Density: 0.61
33		public final class AlignedCodon
34		{
35		// base 1 aligned sequence position (base 0)
36		public final int pos1;
37
38		// base 2 aligned sequence position (base 0)
39		public final int pos2;
40
41		// base 3 aligned sequence position (base 0)
42		public final int pos3;
43
44		// peptide aligned sequence position (base 0)
45		public final int peptideCol;
46
47		// peptide coded for by this codon
48		public final String product;
49
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
50	0	public AlignedCodon(int i, int j, int k)...
51		{
52	0	this(i, j, k, null, 0);
53		}
54
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2
55	0	public AlignedCodon(int i, int j, int k, String prod, int prodCol)...
56		{
57	0	pos1 = i;
58	0	pos2 = j;
59	0	pos3 = k;
60	0	product = prod;
61	0	peptideCol = prodCol;
62		}
63
64		/**
65		* Returns the column position for the given base (1, 2, 3).
66		*
67		* @param base
68		* @return
69		* @throws IllegalArgumentException
70		* if an argument value other than 1, 2 or 3 is supplied
71		*/
		0% Uncovered Elements: 9 (9) Complexity: 5 Complexity Density: 1.67
72	0	public int getBaseColumn(int base)...
73		{
74	0	if (base < 1 || base > 3)
75		{
76	0	throw new IllegalArgumentException(Integer.toString(base));
77		}
78	0	return base == 1 ? pos1 : (base == 2 ? pos2 : pos3);
79		}
80
81		/**
82		* Two aligned codons are equal if all their base positions are the same. We
83		* don't care about the protein product. This test is required for correct
84		* alignment of translated gapped dna alignments (the same codon positions in
85		* different sequences occupy the same column in the translated alignment).
86		*/
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
87	0	@Override...
88		public boolean equals(Object o)
89		{
90		/*
91		* Equality with null value required for consistency with
92		* Dna.compareCodonPos
93		*/
94	0	if (o == null)
95		{
96	0	return true;
97		}
98	0	if (!(o instanceof AlignedCodon))
99		{
100	0	return false;
101		}
102	0	AlignedCodon ac = (AlignedCodon) o;
103	0	return (pos1 == ac.pos1 && pos2 == ac.pos2 && pos3 == ac.pos3);
104		}
105
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
106	0	@Override...
107		public String toString()
108		{
109	0	StringBuilder sb = new StringBuilder();
110	0	sb.append("[").append(pos1).append(", ").append(pos2).append(", ")
111		.append(pos3).append("]");
112	0	return sb.toString();
113		}
114		}