Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
BinarySequence	33	36	22	0.00%	Show methods
BinarySequence.InvalidSequenceTypeException	35	1	1	0.00%	Show methods

Class BinarySequence

Class BinarySequence	Line # 33	Total Statements 36	Complexity 22	TOTAL Coverage 0.00%
BinarySequence(String,boolean)   BinarySequence(String,boolean)	5757	2.02	1.01	0.0 0.00%
initMatrixGetNoRes() : int   initMatrixGetNoRes() : int	6868	3.03	2.02	0.0 0.00%
getSymbolmatrix() : int[]   getSymbolmatrix() : int[]	7878	1.01	2.02	0.0 0.00%
encode() : void   encode() : void	8787	10.010	4.04	0.0 0.00%
matrixEncode(ScoreMatrix) : void   matrixEncode(ScoreMatrix) : void	117117	3.03	4.04	0.0 0.00%
matrixEncode(int[],float[][]) : void   matrixEncode(int[],float[][]) : void	131131	10.010	5.05	0.0 0.00%
toBinaryString() : String   toBinaryString() : String	166166	6.06	3.03	0.0 0.00%
getDBinary() : double[]   getDBinary() : double[]	188188	1.01	1.01	0.0 0.00%

 

Class BinarySequence.InvalidSequenceTypeException

Class BinarySequence.InvalidSequenceTypeException	Line # 35	Total Statements 1	Complexity 1	TOTAL Coverage 0.00%
InvalidSequenceTypeException(String)   InvalidSequenceTypeException(String)	3838	1.01	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		import jalview.analysis.scoremodels.ScoreMatrix;
24		import jalview.schemes.ResidueProperties;
25
26		/**
27		* Encode a sequence as a numeric vector using either classic residue binary
28		* encoding or convolved with residue substitution matrix.
29		*
30		* @author $author$
31		* @version $Revision$
32		*/
		0% Uncovered Elements: 68 (68) Complexity: 22 Complexity Density: 0.61
33		public class BinarySequence extends Sequence
34		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 1
35		public class InvalidSequenceTypeException extends Exception
36		{
37
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
38	0	public InvalidSequenceTypeException(String string)...
39		{
40	0	super(string);
41		}
42
43		}
44
45		int[] binary;
46
47		double[] dbinary;
48
49		boolean isNa = false;
50
51		/**
52		* Creates a new BinarySequence object.
53		*
54		* @param s
55		* DOCUMENT ME!
56		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
57	0	public BinarySequence(String s, boolean isNa)...
58		{
59	0	super("", s, 0, s.length());
60	0	this.isNa = isNa;
61		}
62
63		/**
64		* clear the dbinary matrix
65		*
66		* @return nores - dimension of sequence symbol encoding for this sequence
67		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
68	0	private int initMatrixGetNoRes()...
69		{
70	0	int nores = (isNa) ? ResidueProperties.maxNucleotideIndex
71		: ResidueProperties.maxProteinIndex;
72
73	0	dbinary = new double[getLength() * nores];
74
75	0	return nores;
76		}
77
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
78	0	private int[] getSymbolmatrix()...
79		{
80	0	return (isNa) ? ResidueProperties.nucleotideIndex
81		: ResidueProperties.aaIndex;
82		}
83
84		/**
85		* DOCUMENT ME!
86		*/
		0% Uncovered Elements: 14 (14) Complexity: 4 Complexity Density: 0.4
87	0	public void encode()...
88		{
89	0	int nores = initMatrixGetNoRes();
90	0	final int[] sindex = getSymbolmatrix();
91	0	for (int i = 0; i < getLength(); i++)
92		{
93	0	int aanum = nores - 1;
94
95	0	try
96		{
97	0	aanum = sindex[getCharAt(i)];
98		} catch (NullPointerException e)
99		{
100	0	aanum = nores - 1;
101		}
102
103	0	if (aanum >= nores)
104		{
105	0	aanum = nores - 1;
106		}
107
108	0	dbinary[(i * nores) + aanum] = 1.0;
109		}
110		}
111
112		/**
113		* ancode using substitution matrix given in matrix
114		*
115		* @param smtrx
116		*/
		0% Uncovered Elements: 9 (9) Complexity: 4 Complexity Density: 1.33
117	0	public void matrixEncode(final ScoreMatrix smtrx)...
118		throws InvalidSequenceTypeException
119		{
120	0	if (isNa != smtrx.isDNA())
121		{
122	0	throw new InvalidSequenceTypeException(
123		"matrix " + smtrx.getClass().getCanonicalName()
124		+ " is not a valid matrix for "
125	0	+ (isNa ? "nucleotide" : "protein") + "sequences");
126		}
127	0	matrixEncode(smtrx.isDNA() ? ResidueProperties.nucleotideIndex
128		: ResidueProperties.aaIndex, smtrx.getMatrix());
129		}
130
		0% Uncovered Elements: 16 (16) Complexity: 5 Complexity Density: 0.5
131	0	private void matrixEncode(final int[] aaIndex, final float[][] matrix)...
132		{
133	0	int nores = initMatrixGetNoRes();
134
135	0	for (int i = 0, iSize = getLength(); i < iSize; i++)
136		{
137	0	int aanum = nores - 1;
138
139	0	try
140		{
141	0	aanum = aaIndex[getCharAt(i)];
142		} catch (NullPointerException e)
143		{
144	0	aanum = nores - 1;
145		}
146
147	0	if (aanum >= nores)
148		{
149	0	aanum = nores - 1;
150		}
151
152		// Do the blosum^H^H^H^H^H score matrix summation thing
153
154	0	for (int j = 0; j < nores; j++)
155		{
156	0	dbinary[(i * nores) + j] = matrix[aanum][j];
157		}
158		}
159		}
160
161		/**
162		* DOCUMENT ME!
163		*
164		* @return DOCUMENT ME!
165		*/
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
166	0	public String toBinaryString()...
167		{
168	0	String out = "";
169
170	0	for (int i = 0; i < binary.length; i++)
171		{
172	0	out += (Integer.valueOf(binary[i])).toString();
173
174	0	if (i < (binary.length - 1))
175		{
176	0	out += " ";
177		}
178		}
179
180	0	return out;
181		}
182
183		/**
184		* DOCUMENT ME!
185		*
186		* @return DOCUMENT ME!
187		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
188	0	public double[] getDBinary()...
189		{
190	0	return dbinary;
191		}
192
193		}