Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
GeneticCodeI	23	0	0	-1.0 -	Show methods

Class GeneticCodeI

Class GeneticCodeI	Line # 23	Total Statements 0	Complexity 0	TOTAL Coverage -1.0 -

 

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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.analysis;
22
		- Uncovered Elements: 0 (0) Complexity: 0 Complexity Density: -
23		public interface GeneticCodeI
24		{
25		/**
26		* Answers the single letter amino acid code (e.g. "D") for the given codon
27		* (e.g. "GAC"), or "*" for a stop codon, or null for an unknown input. The
28		* codon is not case-sensitive, the return value is upper case.
29		* <p>
30		* If the codon includes any of the standard ambiguity codes
31		* <ul>
32		* <li>if all possible translations are the same, returns that value</li>
33		* <li>else returns null</li>
34		* </ul>
35		*
36		* @param codon
37		* @return
38		*/
39		String translate(String codon);
40
41		/**
42		* Answers the single letter amino acid code (e.g. "D") for the given codon
43		* (e.g. "GAC"), or "*" for a stop codon, or null for an unknown input. The
44		* codon is not case-sensitive, the return value is upper case. If the codon
45		* includes any of the standard ambiguity codes, this method returns null.
46		*
47		* @param codon
48		* @return
49		*/
50		String translateCanonical(String codon);
51
52		/**
53		* Answers a unique identifier for the genetic code (using the numbering
54		* system as on NCBI)
55		*
56		* @return
57		*/
58		String getId();
59
60		/**
61		* Answers a display name suitable for use in menus, reports etc
62		*
63		* @return
64		*/
65		String getName();
66		}