Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
CodonComparator	35	16	15	0.00%	Show methods

Class CodonComparator

Class CodonComparator	Line # 35	Total Statements 16	Complexity 15	TOTAL Coverage 0.00%
compare(AlignedCodon,AlignedCodon) : int   compare(AlignedCodon,AlignedCodon) : int	3838	16.016	15.015	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.analysis;
22
23		import jalview.datamodel.AlignedCodon;
24
25		import java.util.Comparator;
26
27		/**
28		* Implements rules for comparing two aligned codons, i.e. determining whether
29		* they should occupy the same position in a translated protein alignment, or
30		* one or the other should 'follow' (by preceded by a gap).
31		*
32		* @author gmcarstairs
33		*
34		*/
		0% Uncovered Elements: 31 (31) Complexity: 15 Complexity Density: 0.94
35		public final class CodonComparator implements Comparator<AlignedCodon>
36		{
37
		0% Uncovered Elements: 30 (30) Complexity: 15 Complexity Density: 0.94
38	0	@Override...
39		public int compare(AlignedCodon ac1, AlignedCodon ac2)
40		{
41	0	if (ac1 == null || ac2 == null || ac1.equals(ac2))
42		{
43	0	return 0;
44		}
45
46		/**
47		* <pre>
48		* Case 1: if one starts before the other, and doesn't end after it, then it
49		* precedes. We ignore the middle base position here.
50		* A--GT
51		* -CT-G
52		* </pre>
53		*/
54	0	if (ac1.pos1 < ac2.pos1 && ac1.pos3 <= ac2.pos3)
55		{
56	0	return -1;
57		}
58	0	if (ac2.pos1 < ac1.pos1 && ac2.pos3 <= ac1.pos3)
59		{
60	0	return 1;
61		}
62
63		/**
64		* <pre>
65		* Case 2: if one ends after the other, and doesn't start before it, then it
66		* follows. We ignore the middle base position here.
67		* -TG-A
68		* G-TC
69		* </pre>
70		*/
71	0	if (ac1.pos3 > ac2.pos3 && ac1.pos1 >= ac2.pos1)
72		{
73	0	return 1;
74		}
75	0	if (ac2.pos3 > ac1.pos3 && ac2.pos1 >= ac1.pos1)
76		{
77	0	return -1;
78		}
79
80		/*
81		* Case 3: if start and end match, compare middle base positions.
82		*/
83	0	if (ac1.pos1 == ac2.pos1 && ac1.pos3 == ac2.pos3)
84		{
85	0	return Integer.compare(ac1.pos2, ac2.pos2);
86		}
87
88		/*
89		* That just leaves the 'enclosing' case - one codon starts after but ends
90		* before the other. If the middle bases don't match, use their comparison
91		* (majority vote).
92		*/
93	0	int compareMiddles = Integer.compare(ac1.pos2, ac2.pos2);
94	0	if (compareMiddles != 0)
95		{
96	0	return compareMiddles;
97		}
98
99		/**
100		* <pre>
101		* Finally just leaves overlap with matching middle base, e.g.
102		* -A-A-A
103		* G--GG
104		* In this case the choice is arbitrary whether to compare based on
105		* first or last base position. We pick the first. Note this preserves
106		* symmetricality of the comparison.
107		* </pre>
108		*/
109	0	return Integer.compare(ac1.pos1, ac2.pos1);
110		}
111		}