Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SparseMatrix	33	56	27	0.00%	Show methods

Class SparseMatrix

Class SparseMatrix	Line # 33	Total Statements 56	Complexity 27	TOTAL Coverage 0.00%
SparseMatrix(double[][])   SparseMatrix(double[][])	4646	9.09	5.05	0.0 0.00%
getValue(int,int) : double   getValue(int,int) : double	7373	1.01	1.01	0.0 0.00%
setValue(int,int,double) : void   setValue(int,int,double) : void	8282	3.03	2.02	0.0 0.00%
getColumn(int) : double[]   getColumn(int) : double[]	9595	5.05	2.02	0.0 0.00%
copy() : MatrixI   copy() : MatrixI	108108	4.04	2.02	0.0 0.00%
transpose() : MatrixI   transpose() : MatrixI	119119	6.06	3.03	0.0 0.00%
preMultiply(MatrixI) : MatrixI   preMultiply(MatrixI) : MatrixI	153153	18.018	8.08	0.0 0.00%
divideValue(int,int,double) : double   divideValue(int,int,double) : double	203203	4.04	2.02	0.0 0.00%
addValue(int,int,double) : double   addValue(int,int,double) : double	214214	2.02	1.01	0.0 0.00%
getFillRatio() : float   getFillRatio() : float	227227	4.04	1.01	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.math;
22
23		import jalview.ext.android.SparseDoubleArray;
24
25		/**
26		* A variant of Matrix intended for use for sparse (mostly zero) matrices. This
27		* class uses a SparseDoubleArray to hold each row of the matrix. The sparse
28		* array only stores non-zero values. This gives a smaller memory footprint, and
29		* fewer matrix calculation operations, for mostly zero matrices.
30		*
31		* @author gmcarstairs
32		*/
		0% Uncovered Elements: 98 (98) Complexity: 27 Complexity Density: 0.48
33		public class SparseMatrix extends Matrix
34		{
35		/*
36		* we choose columns for the sparse arrays as this allows
37		* optimisation of the preMultiply() method used in PCA.run()
38		*/
39		SparseDoubleArray[] sparseColumns;
40
41		/**
42		* Constructor given data in [row][column] order
43		*
44		* @param v
45		*/
		0% Uncovered Elements: 17 (17) Complexity: 5 Complexity Density: 0.56
46	0	public SparseMatrix(double[][] v)...
47		{
48	0	super(v.length, v.length > 0 ? v[0].length : 0);
49
50	0	sparseColumns = new SparseDoubleArray[cols];
51
52		/*
53		* transpose v[row][col] into [col][row] order
54		*/
55	0	for (int col = 0; col < cols; col++)
56		{
57	0	SparseDoubleArray sparseColumn = new SparseDoubleArray();
58	0	sparseColumns[col] = sparseColumn;
59	0	for (int row = 0; row < rows; row++)
60		{
61	0	double value = v[row][col];
62	0	if (value != 0d)
63		{
64	0	sparseColumn.put(row, value);
65		}
66		}
67		}
68		}
69
70		/**
71		* Answers the value at row i, column j
72		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
73	0	@Override...
74		public double getValue(int i, int j)
75		{
76	0	return sparseColumns[j].get(i);
77		}
78
79		/**
80		* Sets the value at row i, column j to val
81		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
82	0	@Override...
83		public void setValue(int i, int j, double val)
84		{
85	0	if (val == 0d)
86		{
87	0	sparseColumns[j].delete(i);
88		}
89		else
90		{
91	0	sparseColumns[j].put(i, val);
92		}
93		}
94
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
95	0	@Override...
96		public double[] getColumn(int i)
97		{
98	0	double[] col = new double[height()];
99
100	0	SparseDoubleArray vals = sparseColumns[i];
101	0	for (int nonZero = 0; nonZero < vals.size(); nonZero++)
102		{
103	0	col[vals.keyAt(nonZero)] = vals.valueAt(nonZero);
104		}
105	0	return col;
106		}
107
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
108	0	@Override...
109		public MatrixI copy()
110		{
111	0	double[][] vals = new double[height()][width()];
112	0	for (int i = 0; i < height(); i++)
113		{
114	0	vals[i] = getRow(i);
115		}
116	0	return new SparseMatrix(vals);
117		}
118
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
119	0	@Override...
120		public MatrixI transpose()
121		{
122	0	double[][] out = new double[cols][rows];
123
124		/*
125		* for each column...
126		*/
127	0	for (int i = 0; i < cols; i++)
128		{
129		/*
130		* put non-zero values into the corresponding row
131		* of the transposed matrix
132		*/
133	0	SparseDoubleArray vals = sparseColumns[i];
134	0	for (int nonZero = 0; nonZero < vals.size(); nonZero++)
135		{
136	0	out[i][vals.keyAt(nonZero)] = vals.valueAt(nonZero);
137		}
138		}
139
140	0	return new SparseMatrix(out);
141		}
142
143		/**
144		* Answers a new matrix which is the product in.this. If the product contains
145		* less than 20% non-zero values, it is returned as a SparseMatrix, else as a
146		* Matrix.
147		* <p>
148		* This method is optimised for the sparse arrays which store column values
149		* for a SparseMatrix. Note that postMultiply is not so optimised. That would
150		* require redundantly also storing sparse arrays for the rows, which has not
151		* been done. Currently only preMultiply is used in Jalview.
152		*/
		0% Uncovered Elements: 30 (30) Complexity: 8 Complexity Density: 0.44
153	0	@Override...
154		public MatrixI preMultiply(MatrixI in)
155		{
156	0	if (in.width() != rows)
157		{
158	0	throw new IllegalArgumentException("Can't pre-multiply " + this.rows
159		+ " rows by " + in.width() + " columns");
160		}
161	0	double[][] tmp = new double[in.height()][this.cols];
162
163	0	long count = 0L;
164	0	for (int i = 0; i < in.height(); i++)
165		{
166	0	for (int j = 0; j < this.cols; j++)
167		{
168		/*
169		* result[i][j] is the vector product of
170		* in.row[i] and this.column[j]
171		* we only need to use non-zero values from the column
172		*/
173	0	SparseDoubleArray vals = sparseColumns[j];
174	0	boolean added = false;
175	0	for (int nonZero = 0; nonZero < vals.size(); nonZero++)
176		{
177	0	int myRow = vals.keyAt(nonZero);
178	0	double myValue = vals.valueAt(nonZero);
179	0	tmp[i][j] += (in.getValue(i, myRow) * myValue);
180	0	added = true;
181		}
182	0	if (added && tmp[i][j] != 0d)
183		{
184	0	count++; // non-zero entry in product
185		}
186		}
187		}
188
189		/*
190		* heuristic rule - if product is more than 80% zero
191		* then construct a SparseMatrix, else a Matrix
192		*/
193	0	if (count * 5 < in.height() * cols)
194		{
195	0	return new SparseMatrix(tmp);
196		}
197		else
198		{
199	0	return new Matrix(tmp);
200		}
201		}
202
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
203	0	@Override...
204		protected double divideValue(int i, int j, double divisor)
205		{
206	0	if (divisor == 0d)
207		{
208	0	return getValue(i, j);
209		}
210	0	double v = sparseColumns[j].divide(i, divisor);
211	0	return v;
212		}
213
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
214	0	@Override...
215		protected double addValue(int i, int j, double addend)
216		{
217	0	double v = sparseColumns[j].add(i, addend);
218	0	return v;
219		}
220
221		/**
222		* Returns the fraction of the whole matrix size that is actually modelled in
223		* sparse arrays (normally, the non-zero values)
224		*
225		* @return
226		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
227	0	public float getFillRatio()...
228		{
229	0	long count = 0L;
230	0	for (SparseDoubleArray col : sparseColumns)
231		{
232	0	count += col.size();
233		}
234	0	return count / (float) (height() * width());
235		}
236		}