1 |
|
|
2 |
|
|
3 |
|
|
4 |
|
|
5 |
|
|
6 |
|
|
7 |
|
|
8 |
|
|
9 |
|
|
10 |
|
|
11 |
|
|
12 |
|
|
13 |
|
|
14 |
|
|
15 |
|
|
16 |
|
|
17 |
|
|
18 |
|
|
19 |
|
|
20 |
|
|
21 |
|
package jalview.math; |
22 |
|
|
23 |
|
import jalview.util.Format; |
24 |
|
import jalview.util.MessageManager; |
25 |
|
|
26 |
|
import java.io.PrintStream; |
27 |
|
import java.lang.Math; |
28 |
|
import java.util.Arrays; |
29 |
|
|
30 |
|
|
31 |
|
|
32 |
|
|
|
|
| 40.9% |
Uncovered Elements: 482 (816) |
Complexity: 190 |
Complexity Density: 0.38 |
|
33 |
|
public class Matrix implements MatrixI |
34 |
|
{ |
35 |
|
|
36 |
|
|
37 |
|
|
38 |
|
private static final int MAX_ITER = 45; |
39 |
|
|
40 |
|
|
41 |
|
|
42 |
|
|
43 |
|
|
44 |
|
final protected int rows; |
45 |
|
|
46 |
|
|
47 |
|
|
48 |
|
|
49 |
|
final protected int cols; |
50 |
|
|
51 |
|
|
52 |
|
|
53 |
|
|
54 |
|
private double[][] value; |
55 |
|
|
56 |
|
protected double[] d; |
57 |
|
|
58 |
|
protected double[] e; |
59 |
|
|
60 |
|
|
61 |
|
|
62 |
|
|
63 |
|
@param |
64 |
|
@param |
65 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
66 |
22 |
protected Matrix(int rowCount, int colCount)... |
67 |
|
{ |
68 |
22 |
rows = rowCount; |
69 |
22 |
cols = colCount; |
70 |
|
} |
71 |
|
|
72 |
|
|
73 |
|
|
74 |
|
|
75 |
|
|
76 |
|
|
77 |
|
|
78 |
|
|
79 |
|
|
80 |
|
|
81 |
|
|
82 |
|
|
83 |
|
|
84 |
|
|
85 |
|
|
86 |
|
|
87 |
|
@param |
88 |
|
|
89 |
|
|
|
|
| 84.6% |
Uncovered Elements: 2 (13) |
Complexity: 3 |
Complexity Density: 0.33 |
|
90 |
82 |
public Matrix(double[][] values)... |
91 |
|
{ |
92 |
82 |
this.rows = values.length; |
93 |
82 |
this.cols = this.rows == 0 ? 0 : values[0].length; |
94 |
|
|
95 |
|
|
96 |
|
|
97 |
|
|
98 |
82 |
this.value = new double[rows][]; |
99 |
82 |
int i = 0; |
100 |
82 |
for (double[] row : values) |
101 |
|
{ |
102 |
1350 |
if (row != null) |
103 |
|
{ |
104 |
1350 |
value[i] = new double[row.length]; |
105 |
1350 |
System.arraycopy(row, 0, value[i], 0, row.length); |
106 |
|
} |
107 |
1350 |
i++; |
108 |
|
} |
109 |
|
} |
110 |
|
|
|
|
| 0% |
Uncovered Elements: 16 (16) |
Complexity: 3 |
Complexity Density: 0.25 |
|
111 |
0 |
public Matrix(float[][] values)... |
112 |
|
{ |
113 |
0 |
this.rows = values.length; |
114 |
0 |
this.cols = this.rows == 0 ? 0 : values[0].length; |
115 |
|
|
116 |
|
|
117 |
|
|
118 |
|
|
119 |
0 |
this.value = new double[rows][]; |
120 |
0 |
int i = 0; |
121 |
0 |
for (float[] row : values) |
122 |
|
{ |
123 |
0 |
if (row != null) |
124 |
|
{ |
125 |
0 |
value[i] = new double[row.length]; |
126 |
0 |
int j = 0; |
127 |
0 |
for (float oldValue : row) |
128 |
|
{ |
129 |
0 |
value[i][j] = oldValue; |
130 |
0 |
j++; |
131 |
|
} |
132 |
|
} |
133 |
0 |
i++; |
134 |
|
} |
135 |
|
} |
136 |
|
|
|
|
| 0% |
Uncovered Elements: 9 (9) |
Complexity: 3 |
Complexity Density: 0.6 |
|
137 |
0 |
@Override... |
138 |
|
public MatrixI transpose() |
139 |
|
{ |
140 |
0 |
double[][] out = new double[cols][rows]; |
141 |
|
|
142 |
0 |
for (int i = 0; i < cols; i++) |
143 |
|
{ |
144 |
0 |
for (int j = 0; j < rows; j++) |
145 |
|
{ |
146 |
0 |
out[i][j] = value[j][i]; |
147 |
|
} |
148 |
|
} |
149 |
|
|
150 |
0 |
return new Matrix(out); |
151 |
|
} |
152 |
|
|
153 |
|
|
154 |
|
|
155 |
|
|
156 |
|
@param |
157 |
|
|
158 |
|
@param |
159 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 3 |
Complexity Density: 0.75 |
|
160 |
0 |
@Override... |
161 |
|
public void print(PrintStream ps, String format) |
162 |
|
{ |
163 |
0 |
for (int i = 0; i < rows; i++) |
164 |
|
{ |
165 |
0 |
for (int j = 0; j < cols; j++) |
166 |
|
{ |
167 |
0 |
Format.print(ps, format, getValue(i, j)); |
168 |
|
} |
169 |
|
|
170 |
0 |
ps.println(); |
171 |
|
} |
172 |
|
} |
173 |
|
|
|
|
| 94.7% |
Uncovered Elements: 1 (19) |
Complexity: 7 |
Complexity Density: 0.78 |
|
174 |
10 |
@Override... |
175 |
|
public MatrixI preMultiply(MatrixI in) |
176 |
|
{ |
177 |
10 |
if (in.width() != rows) |
178 |
|
{ |
179 |
2 |
throw new IllegalArgumentException("Can't pre-multiply " + this.rows |
180 |
|
+ " rows by " + in.width() + " columns"); |
181 |
|
} |
182 |
8 |
double[][] tmp = new double[in.height()][this.cols]; |
183 |
|
|
184 |
22 |
for (int i = 0; i < in.height(); i++) |
185 |
|
{ |
186 |
48 |
for (int j = 0; j < this.cols; j++) |
187 |
|
{ |
188 |
|
|
189 |
|
|
190 |
|
|
191 |
|
|
192 |
86 |
for (int k = 0; k < in.width(); k++) |
193 |
|
{ |
194 |
52 |
if (!Double.isNaN(in.getValue(i, k)) |
195 |
|
&& !Double.isNaN(this.value[k][j])) |
196 |
|
{ |
197 |
52 |
tmp[i][j] += (in.getValue(i, k) * this.value[k][j]); |
198 |
|
} |
199 |
|
} |
200 |
|
} |
201 |
|
} |
202 |
|
|
203 |
8 |
return new Matrix(tmp); |
204 |
|
} |
205 |
|
|
206 |
|
|
207 |
|
|
208 |
|
@param |
209 |
|
|
210 |
|
@return |
211 |
|
|
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 3 |
Complexity Density: 0.5 |
|
212 |
0 |
public double[] vectorPostMultiply(double[] in)... |
213 |
|
{ |
214 |
0 |
double[] out = new double[in.length]; |
215 |
|
|
216 |
0 |
for (int i = 0; i < in.length; i++) |
217 |
|
{ |
218 |
0 |
out[i] = 0.0; |
219 |
|
|
220 |
0 |
for (int k = 0; k < in.length; k++) |
221 |
|
{ |
222 |
0 |
out[i] += (value[i][k] * in[k]); |
223 |
|
} |
224 |
|
} |
225 |
|
|
226 |
0 |
return out; |
227 |
|
} |
228 |
|
|
|
|
| 60% |
Uncovered Elements: 2 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
229 |
6 |
@Override... |
230 |
|
public MatrixI postMultiply(MatrixI in) |
231 |
|
{ |
232 |
6 |
if (in.height() != this.cols) |
233 |
|
{ |
234 |
0 |
throw new IllegalArgumentException("Can't post-multiply " + this.cols |
235 |
|
+ " columns by " + in.height() + " rows"); |
236 |
|
} |
237 |
6 |
return in.preMultiply(this); |
238 |
|
} |
239 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (15) |
Complexity: 4 |
Complexity Density: 0.44 |
|
240 |
10 |
@Override... |
241 |
|
public MatrixI copy() |
242 |
|
{ |
243 |
10 |
double[][] newmat = new double[rows][cols]; |
244 |
|
|
245 |
62 |
for (int i = 0; i < rows; i++) |
246 |
|
{ |
247 |
52 |
System.arraycopy(value[i], 0, newmat[i], 0, value[i].length); |
248 |
|
} |
249 |
|
|
250 |
10 |
Matrix m = new Matrix(newmat); |
251 |
10 |
if (this.d != null) |
252 |
|
{ |
253 |
2 |
m.d = Arrays.copyOf(this.d, this.d.length); |
254 |
|
} |
255 |
10 |
if (this.e != null) |
256 |
|
{ |
257 |
2 |
m.e = Arrays.copyOf(this.e, this.e.length); |
258 |
|
} |
259 |
|
|
260 |
10 |
return m; |
261 |
|
} |
262 |
|
|
263 |
|
|
264 |
|
|
265 |
|
|
|
|
| 98% |
Uncovered Elements: 2 (102) |
Complexity: 18 |
Complexity Density: 0.26 |
|
266 |
9 |
@Override... |
267 |
|
public void tred() |
268 |
|
{ |
269 |
9 |
int n = rows; |
270 |
9 |
int k; |
271 |
9 |
int j; |
272 |
9 |
int i; |
273 |
|
|
274 |
9 |
double scale; |
275 |
9 |
double hh; |
276 |
9 |
double h; |
277 |
9 |
double g; |
278 |
9 |
double f; |
279 |
|
|
280 |
9 |
this.d = new double[rows]; |
281 |
9 |
this.e = new double[rows]; |
282 |
|
|
283 |
87 |
for (i = n; i >= 2; i--) |
284 |
|
{ |
285 |
78 |
final int l = i - 1; |
286 |
78 |
h = 0.0; |
287 |
78 |
scale = 0.0; |
288 |
|
|
289 |
78 |
if (l > 1) |
290 |
|
{ |
291 |
465 |
for (k = 1; k <= l; k++) |
292 |
|
{ |
293 |
396 |
double v = Math.abs(getValue(i - 1, k - 1)); |
294 |
396 |
scale += v; |
295 |
|
} |
296 |
|
|
297 |
69 |
if (scale == 0.0) |
298 |
|
{ |
299 |
0 |
e[i - 1] = getValue(i - 1, l - 1); |
300 |
|
} |
301 |
|
else |
302 |
|
{ |
303 |
465 |
for (k = 1; k <= l; k++) |
304 |
|
{ |
305 |
396 |
double v = divideValue(i - 1, k - 1, scale); |
306 |
396 |
h += v * v; |
307 |
|
} |
308 |
|
|
309 |
69 |
f = getValue(i - 1, l - 1); |
310 |
|
|
311 |
69 |
if (f > 0) |
312 |
|
{ |
313 |
26 |
g = -1.0 * Math.sqrt(h); |
314 |
|
} |
315 |
|
else |
316 |
|
{ |
317 |
43 |
g = Math.sqrt(h); |
318 |
|
} |
319 |
|
|
320 |
69 |
e[i - 1] = scale * g; |
321 |
69 |
h -= (f * g); |
322 |
69 |
setValue(i - 1, l - 1, f - g); |
323 |
69 |
f = 0.0; |
324 |
|
|
325 |
465 |
for (j = 1; j <= l; j++) |
326 |
|
{ |
327 |
396 |
double val = getValue(i - 1, j - 1) / h; |
328 |
396 |
setValue(j - 1, i - 1, val); |
329 |
396 |
g = 0.0; |
330 |
|
|
331 |
2007 |
for (k = 1; k <= j; k++) |
332 |
|
{ |
333 |
1611 |
g += (getValue(j - 1, k - 1) * getValue(i - 1, k - 1)); |
334 |
|
} |
335 |
|
|
336 |
1611 |
for (k = j + 1; k <= l; k++) |
337 |
|
{ |
338 |
1215 |
g += (getValue(k - 1, j - 1) * getValue(i - 1, k - 1)); |
339 |
|
} |
340 |
|
|
341 |
396 |
e[j - 1] = g / h; |
342 |
396 |
f += (e[j - 1] * getValue(i - 1, j - 1)); |
343 |
|
} |
344 |
|
|
345 |
69 |
hh = f / (h + h); |
346 |
|
|
347 |
465 |
for (j = 1; j <= l; j++) |
348 |
|
{ |
349 |
396 |
f = getValue(i - 1, j - 1); |
350 |
396 |
g = e[j - 1] - (hh * f); |
351 |
396 |
e[j - 1] = g; |
352 |
|
|
353 |
2007 |
for (k = 1; k <= j; k++) |
354 |
|
{ |
355 |
1611 |
double val = (f * e[k - 1]) + (g * getValue(i - 1, k - 1)); |
356 |
1611 |
addValue(j - 1, k - 1, -val); |
357 |
|
} |
358 |
|
} |
359 |
|
} |
360 |
|
} |
361 |
|
else |
362 |
|
{ |
363 |
9 |
e[i - 1] = getValue(i - 1, l - 1); |
364 |
|
} |
365 |
|
|
366 |
78 |
d[i - 1] = h; |
367 |
|
} |
368 |
|
|
369 |
9 |
d[0] = 0.0; |
370 |
9 |
e[0] = 0.0; |
371 |
|
|
372 |
96 |
for (i = 1; i <= n; i++) |
373 |
|
{ |
374 |
87 |
final int l = i - 1; |
375 |
|
|
376 |
87 |
if (d[i - 1] != 0.0) |
377 |
|
{ |
378 |
465 |
for (j = 1; j <= l; j++) |
379 |
|
{ |
380 |
396 |
g = 0.0; |
381 |
|
|
382 |
3222 |
for (k = 1; k <= l; k++) |
383 |
|
{ |
384 |
2826 |
g += (getValue(i - 1, k - 1) * getValue(k - 1, j - 1)); |
385 |
|
} |
386 |
|
|
387 |
3222 |
for (k = 1; k <= l; k++) |
388 |
|
{ |
389 |
2826 |
addValue(k - 1, j - 1, -(g * getValue(k - 1, i - 1))); |
390 |
|
} |
391 |
|
} |
392 |
|
} |
393 |
|
|
394 |
87 |
d[i - 1] = getValue(i - 1, i - 1); |
395 |
87 |
setValue(i - 1, i - 1, 1.0); |
396 |
|
|
397 |
492 |
for (j = 1; j <= l; j++) |
398 |
|
{ |
399 |
405 |
setValue(j - 1, i - 1, 0.0); |
400 |
405 |
setValue(i - 1, j - 1, 0.0); |
401 |
|
} |
402 |
|
} |
403 |
|
} |
404 |
|
|
405 |
|
|
406 |
|
|
407 |
|
|
408 |
|
@param |
409 |
|
@param |
410 |
|
@param |
411 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
412 |
3005 |
protected double addValue(int i, int j, double f)... |
413 |
|
{ |
414 |
3005 |
double v = value[i][j] + f; |
415 |
3005 |
value[i][j] = v; |
416 |
3005 |
return v; |
417 |
|
} |
418 |
|
|
419 |
|
|
420 |
|
|
421 |
|
|
422 |
|
|
423 |
|
@param |
424 |
|
@param |
425 |
|
@param |
426 |
|
@return |
427 |
|
|
|
|
| 75% |
Uncovered Elements: 2 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
|
428 |
250 |
protected double divideValue(int i, int j, double divisor)... |
429 |
|
{ |
430 |
250 |
if (divisor == 0d) |
431 |
|
{ |
432 |
0 |
return getValue(i, j); |
433 |
|
} |
434 |
250 |
double v = value[i][j]; |
435 |
250 |
v = v / divisor; |
436 |
250 |
value[i][j] = v; |
437 |
250 |
return v; |
438 |
|
} |
439 |
|
|
440 |
|
|
441 |
|
|
442 |
|
|
|
|
| 97.5% |
Uncovered Elements: 2 (80) |
Complexity: 11 |
Complexity Density: 0.18 |
|
443 |
3 |
@Override... |
444 |
|
public void tqli() throws Exception |
445 |
|
{ |
446 |
3 |
int n = rows; |
447 |
|
|
448 |
3 |
int m; |
449 |
3 |
int l; |
450 |
3 |
int iter; |
451 |
3 |
int i; |
452 |
3 |
int k; |
453 |
3 |
double s; |
454 |
3 |
double r; |
455 |
3 |
double p; |
456 |
|
|
457 |
3 |
double g; |
458 |
3 |
double f; |
459 |
3 |
double dd; |
460 |
3 |
double c; |
461 |
3 |
double b; |
462 |
|
|
463 |
27 |
for (i = 2; i <= n; i++) |
464 |
|
{ |
465 |
24 |
e[i - 2] = e[i - 1]; |
466 |
|
} |
467 |
|
|
468 |
3 |
e[n - 1] = 0.0; |
469 |
|
|
470 |
30 |
for (l = 1; l <= n; l++) |
471 |
|
{ |
472 |
27 |
iter = 0; |
473 |
|
|
474 |
27 |
do |
475 |
|
{ |
476 |
371 |
for (m = l; m <= (n - 1); m++) |
477 |
|
{ |
478 |
325 |
dd = Math.abs(d[m - 1]) + Math.abs(d[m]); |
479 |
|
|
480 |
325 |
if ((Math.abs(e[m - 1]) + dd) == dd) |
481 |
|
{ |
482 |
27 |
break; |
483 |
|
} |
484 |
|
} |
485 |
|
|
486 |
73 |
if (m != l) |
487 |
|
{ |
488 |
46 |
iter++; |
489 |
|
|
490 |
46 |
if (iter == MAX_ITER) |
491 |
|
{ |
492 |
0 |
throw new Exception(MessageManager.formatMessage( |
493 |
|
"exception.matrix_too_many_iteration", new String[] |
494 |
|
{ "tqli", Integer.valueOf(MAX_ITER).toString() })); |
495 |
|
} |
496 |
|
else |
497 |
|
{ |
498 |
|
|
499 |
|
} |
500 |
|
|
501 |
46 |
g = (d[l] - d[l - 1]) / (2.0 * e[l - 1]); |
502 |
46 |
r = Math.sqrt((g * g) + 1.0); |
503 |
46 |
g = d[m - 1] - d[l - 1] + (e[l - 1] / (g + sign(r, g))); |
504 |
46 |
c = 1.0; |
505 |
46 |
s = c; |
506 |
46 |
p = 0.0; |
507 |
|
|
508 |
344 |
for (i = m - 1; i >= l; i--) |
509 |
|
{ |
510 |
298 |
f = s * e[i - 1]; |
511 |
298 |
b = c * e[i - 1]; |
512 |
|
|
513 |
298 |
if (Math.abs(f) >= Math.abs(g)) |
514 |
|
{ |
515 |
34 |
c = g / f; |
516 |
34 |
r = Math.sqrt((c * c) + 1.0); |
517 |
34 |
e[i] = f * r; |
518 |
34 |
s = 1.0 / r; |
519 |
34 |
c *= s; |
520 |
|
} |
521 |
|
else |
522 |
|
{ |
523 |
264 |
s = f / g; |
524 |
264 |
r = Math.sqrt((s * s) + 1.0); |
525 |
264 |
e[i] = g * r; |
526 |
264 |
c = 1.0 / r; |
527 |
264 |
s *= c; |
528 |
|
} |
529 |
|
|
530 |
298 |
g = d[i] - p; |
531 |
298 |
r = ((d[i - 1] - g) * s) + (2.0 * c * b); |
532 |
298 |
p = s * r; |
533 |
298 |
d[i] = g + p; |
534 |
298 |
g = (c * r) - b; |
535 |
|
|
536 |
4228 |
for (k = 1; k <= n; k++) |
537 |
|
{ |
538 |
3930 |
f = getValue(k - 1, i); |
539 |
3930 |
setValue(k - 1, i, (s * getValue(k - 1, i - 1)) + (c * f)); |
540 |
3930 |
setValue(k - 1, i - 1, |
541 |
|
(c * getValue(k - 1, i - 1)) - (s * f)); |
542 |
|
} |
543 |
|
} |
544 |
|
|
545 |
46 |
d[l - 1] = d[l - 1] - p; |
546 |
46 |
e[l - 1] = g; |
547 |
46 |
e[m - 1] = 0.0; |
548 |
|
} |
549 |
73 |
} while (m != l); |
550 |
|
} |
551 |
|
} |
552 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
553 |
71178 |
@Override... |
554 |
|
public double getValue(int i, int j) |
555 |
|
{ |
556 |
71178 |
return value[i][j]; |
557 |
|
} |
558 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
559 |
19083 |
@Override... |
560 |
|
public void setValue(int i, int j, double val) |
561 |
|
{ |
562 |
19083 |
value[i][j] = val; |
563 |
|
} |
564 |
|
|
565 |
|
|
566 |
|
|
567 |
|
|
|
|
| 0% |
Uncovered Elements: 100 (100) |
Complexity: 18 |
Complexity Density: 0.27 |
|
568 |
0 |
public void tred2()... |
569 |
|
{ |
570 |
0 |
int n = rows; |
571 |
0 |
int l; |
572 |
0 |
int k; |
573 |
0 |
int j; |
574 |
0 |
int i; |
575 |
|
|
576 |
0 |
double scale; |
577 |
0 |
double hh; |
578 |
0 |
double h; |
579 |
0 |
double g; |
580 |
0 |
double f; |
581 |
|
|
582 |
0 |
this.d = new double[rows]; |
583 |
0 |
this.e = new double[rows]; |
584 |
|
|
585 |
0 |
for (i = n - 1; i >= 1; i--) |
586 |
|
{ |
587 |
0 |
l = i - 1; |
588 |
0 |
h = 0.0; |
589 |
0 |
scale = 0.0; |
590 |
|
|
591 |
0 |
if (l > 0) |
592 |
|
{ |
593 |
0 |
for (k = 0; k < l; k++) |
594 |
|
{ |
595 |
0 |
scale += Math.abs(value[i][k]); |
596 |
|
} |
597 |
|
|
598 |
0 |
if (scale == 0.0) |
599 |
|
{ |
600 |
0 |
e[i] = value[i][l]; |
601 |
|
} |
602 |
|
else |
603 |
|
{ |
604 |
0 |
for (k = 0; k < l; k++) |
605 |
|
{ |
606 |
0 |
value[i][k] /= scale; |
607 |
0 |
h += (value[i][k] * value[i][k]); |
608 |
|
} |
609 |
|
|
610 |
0 |
f = value[i][l]; |
611 |
|
|
612 |
0 |
if (f > 0) |
613 |
|
{ |
614 |
0 |
g = -1.0 * Math.sqrt(h); |
615 |
|
} |
616 |
|
else |
617 |
|
{ |
618 |
0 |
g = Math.sqrt(h); |
619 |
|
} |
620 |
|
|
621 |
0 |
e[i] = scale * g; |
622 |
0 |
h -= (f * g); |
623 |
0 |
value[i][l] = f - g; |
624 |
0 |
f = 0.0; |
625 |
|
|
626 |
0 |
for (j = 0; j < l; j++) |
627 |
|
{ |
628 |
0 |
value[j][i] = value[i][j] / h; |
629 |
0 |
g = 0.0; |
630 |
|
|
631 |
0 |
for (k = 0; k < j; k++) |
632 |
|
{ |
633 |
0 |
g += (value[j][k] * value[i][k]); |
634 |
|
} |
635 |
|
|
636 |
0 |
for (k = j; k < l; k++) |
637 |
|
{ |
638 |
0 |
g += (value[k][j] * value[i][k]); |
639 |
|
} |
640 |
|
|
641 |
0 |
e[j] = g / h; |
642 |
0 |
f += (e[j] * value[i][j]); |
643 |
|
} |
644 |
|
|
645 |
0 |
hh = f / (h + h); |
646 |
|
|
647 |
0 |
for (j = 0; j < l; j++) |
648 |
|
{ |
649 |
0 |
f = value[i][j]; |
650 |
0 |
g = e[j] - (hh * f); |
651 |
0 |
e[j] = g; |
652 |
|
|
653 |
0 |
for (k = 0; k < j; k++) |
654 |
|
{ |
655 |
0 |
value[j][k] -= ((f * e[k]) + (g * value[i][k])); |
656 |
|
} |
657 |
|
} |
658 |
|
} |
659 |
|
} |
660 |
|
else |
661 |
|
{ |
662 |
0 |
e[i] = value[i][l]; |
663 |
|
} |
664 |
|
|
665 |
0 |
d[i] = h; |
666 |
|
} |
667 |
|
|
668 |
0 |
d[0] = 0.0; |
669 |
0 |
e[0] = 0.0; |
670 |
|
|
671 |
0 |
for (i = 0; i < n; i++) |
672 |
|
{ |
673 |
0 |
l = i - 1; |
674 |
|
|
675 |
0 |
if (d[i] != 0.0) |
676 |
|
{ |
677 |
0 |
for (j = 0; j < l; j++) |
678 |
|
{ |
679 |
0 |
g = 0.0; |
680 |
|
|
681 |
0 |
for (k = 0; k < l; k++) |
682 |
|
{ |
683 |
0 |
g += (value[i][k] * value[k][j]); |
684 |
|
} |
685 |
|
|
686 |
0 |
for (k = 0; k < l; k++) |
687 |
|
{ |
688 |
0 |
value[k][j] -= (g * value[k][i]); |
689 |
|
} |
690 |
|
} |
691 |
|
} |
692 |
|
|
693 |
0 |
d[i] = value[i][i]; |
694 |
0 |
value[i][i] = 1.0; |
695 |
|
|
696 |
0 |
for (j = 0; j < l; j++) |
697 |
|
{ |
698 |
0 |
value[j][i] = 0.0; |
699 |
0 |
value[i][j] = 0.0; |
700 |
|
} |
701 |
|
} |
702 |
|
} |
703 |
|
|
704 |
|
|
705 |
|
|
706 |
|
|
|
|
| 0% |
Uncovered Elements: 81 (81) |
Complexity: 11 |
Complexity Density: 0.18 |
|
707 |
0 |
public void tqli2() throws Exception... |
708 |
|
{ |
709 |
0 |
int n = rows; |
710 |
|
|
711 |
0 |
int m; |
712 |
0 |
int l; |
713 |
0 |
int iter; |
714 |
0 |
int i; |
715 |
0 |
int k; |
716 |
0 |
double s; |
717 |
0 |
double r; |
718 |
0 |
double p; |
719 |
0 |
; |
720 |
|
|
721 |
0 |
double g; |
722 |
0 |
double f; |
723 |
0 |
double dd; |
724 |
0 |
double c; |
725 |
0 |
double b; |
726 |
|
|
727 |
0 |
for (i = 2; i <= n; i++) |
728 |
|
{ |
729 |
0 |
e[i - 2] = e[i - 1]; |
730 |
|
} |
731 |
|
|
732 |
0 |
e[n - 1] = 0.0; |
733 |
|
|
734 |
0 |
for (l = 1; l <= n; l++) |
735 |
|
{ |
736 |
0 |
iter = 0; |
737 |
|
|
738 |
0 |
do |
739 |
|
{ |
740 |
0 |
for (m = l; m <= (n - 1); m++) |
741 |
|
{ |
742 |
0 |
dd = Math.abs(d[m - 1]) + Math.abs(d[m]); |
743 |
|
|
744 |
0 |
if ((Math.abs(e[m - 1]) + dd) == dd) |
745 |
|
{ |
746 |
0 |
break; |
747 |
|
} |
748 |
|
} |
749 |
|
|
750 |
0 |
if (m != l) |
751 |
|
{ |
752 |
0 |
iter++; |
753 |
|
|
754 |
0 |
if (iter == MAX_ITER) |
755 |
|
{ |
756 |
0 |
throw new Exception(MessageManager.formatMessage( |
757 |
|
"exception.matrix_too_many_iteration", new String[] |
758 |
|
{ "tqli2", Integer.valueOf(MAX_ITER).toString() })); |
759 |
|
} |
760 |
|
else |
761 |
|
{ |
762 |
|
|
763 |
|
} |
764 |
|
|
765 |
0 |
g = (d[l] - d[l - 1]) / (2.0 * e[l - 1]); |
766 |
0 |
r = Math.sqrt((g * g) + 1.0); |
767 |
0 |
g = d[m - 1] - d[l - 1] + (e[l - 1] / (g + sign(r, g))); |
768 |
0 |
c = 1.0; |
769 |
0 |
s = c; |
770 |
0 |
p = 0.0; |
771 |
|
|
772 |
0 |
for (i = m - 1; i >= l; i--) |
773 |
|
{ |
774 |
0 |
f = s * e[i - 1]; |
775 |
0 |
b = c * e[i - 1]; |
776 |
|
|
777 |
0 |
if (Math.abs(f) >= Math.abs(g)) |
778 |
|
{ |
779 |
0 |
c = g / f; |
780 |
0 |
r = Math.sqrt((c * c) + 1.0); |
781 |
0 |
e[i] = f * r; |
782 |
0 |
s = 1.0 / r; |
783 |
0 |
c *= s; |
784 |
|
} |
785 |
|
else |
786 |
|
{ |
787 |
0 |
s = f / g; |
788 |
0 |
r = Math.sqrt((s * s) + 1.0); |
789 |
0 |
e[i] = g * r; |
790 |
0 |
c = 1.0 / r; |
791 |
0 |
s *= c; |
792 |
|
} |
793 |
|
|
794 |
0 |
g = d[i] - p; |
795 |
0 |
r = ((d[i - 1] - g) * s) + (2.0 * c * b); |
796 |
0 |
p = s * r; |
797 |
0 |
d[i] = g + p; |
798 |
0 |
g = (c * r) - b; |
799 |
|
|
800 |
0 |
for (k = 1; k <= n; k++) |
801 |
|
{ |
802 |
0 |
f = value[k - 1][i]; |
803 |
0 |
value[k - 1][i] = (s * value[k - 1][i - 1]) + (c * f); |
804 |
0 |
value[k - 1][i - 1] = (c * value[k - 1][i - 1]) - (s * f); |
805 |
|
} |
806 |
|
} |
807 |
|
|
808 |
0 |
d[l - 1] = d[l - 1] - p; |
809 |
0 |
e[l - 1] = g; |
810 |
0 |
e[m - 1] = 0.0; |
811 |
|
} |
812 |
0 |
} while (m != l); |
813 |
|
} |
814 |
|
} |
815 |
|
|
816 |
|
|
817 |
|
|
818 |
|
|
819 |
|
@param |
820 |
|
@param |
821 |
|
|
822 |
|
@return |
823 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
824 |
46 |
static double sign(double a, double b)... |
825 |
|
{ |
826 |
46 |
if (b < 0) |
827 |
|
{ |
828 |
12 |
return -Math.abs(a); |
829 |
|
} |
830 |
|
else |
831 |
|
{ |
832 |
34 |
return Math.abs(a); |
833 |
|
} |
834 |
|
} |
835 |
|
|
836 |
|
|
837 |
|
|
838 |
|
|
839 |
|
@return |
840 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
841 |
0 |
@Override... |
842 |
|
public double[][] asArray() |
843 |
|
{ |
844 |
0 |
return value; |
845 |
|
} |
846 |
|
|
847 |
|
|
848 |
|
|
849 |
|
|
850 |
|
@param |
851 |
|
|
852 |
|
@return |
853 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
854 |
0 |
@Override... |
855 |
|
public double[] getColumn(int col) |
856 |
|
{ |
857 |
0 |
double[] out = new double[rows]; |
858 |
|
|
859 |
0 |
for (int i = 0; i < rows; i++) |
860 |
|
{ |
861 |
0 |
out[i] = value[i][col]; |
862 |
|
} |
863 |
|
|
864 |
0 |
return out; |
865 |
|
} |
866 |
|
|
867 |
|
|
868 |
|
|
869 |
|
|
870 |
|
@param |
871 |
|
|
872 |
|
@param |
873 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
874 |
0 |
@Override... |
875 |
|
public void printD(PrintStream ps, String format) |
876 |
|
{ |
877 |
0 |
for (int j = 0; j < d.length; j++) |
878 |
|
{ |
879 |
0 |
Format.print(ps, format, d[j]); |
880 |
|
} |
881 |
|
} |
882 |
|
|
883 |
|
|
884 |
|
|
885 |
|
|
886 |
|
@param |
887 |
|
|
888 |
|
@param |
889 |
|
|
890 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
891 |
0 |
@Override... |
892 |
|
public void printE(PrintStream ps, String format) |
893 |
|
{ |
894 |
0 |
for (int j = 0; j < rows; j++) |
895 |
|
{ |
896 |
0 |
Format.print(ps, format, e[j]); |
897 |
|
} |
898 |
|
} |
899 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
900 |
72 |
@Override... |
901 |
|
public double[] getD() |
902 |
|
{ |
903 |
72 |
return d; |
904 |
|
} |
905 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
906 |
27 |
@Override... |
907 |
|
public double[] getE() |
908 |
|
{ |
909 |
27 |
return e; |
910 |
|
} |
911 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
912 |
346 |
@Override... |
913 |
|
public int height() |
914 |
|
{ |
915 |
346 |
return rows; |
916 |
|
} |
917 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
918 |
2450 |
@Override... |
919 |
|
public int width() |
920 |
|
{ |
921 |
2450 |
return cols; |
922 |
|
} |
923 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
924 |
26 |
@Override... |
925 |
|
public double[] getRow(int i) |
926 |
|
{ |
927 |
26 |
double[] row = new double[cols]; |
928 |
26 |
System.arraycopy(value[i], 0, row, 0, cols); |
929 |
26 |
return row; |
930 |
|
} |
931 |
|
|
932 |
|
|
933 |
|
|
934 |
|
|
935 |
|
|
936 |
|
@return |
937 |
|
|
|
|
| 87.5% |
Uncovered Elements: 3 (24) |
Complexity: 6 |
Complexity Density: 0.43 |
|
938 |
13 |
double[] findMinMax()... |
939 |
|
{ |
940 |
13 |
if (value == null) |
941 |
|
{ |
942 |
0 |
return null; |
943 |
|
} |
944 |
13 |
double min = Double.MAX_VALUE; |
945 |
13 |
double max = -Double.MAX_VALUE; |
946 |
13 |
boolean empty = true; |
947 |
13 |
for (double[] row : value) |
948 |
|
{ |
949 |
1023 |
if (row != null) |
950 |
|
{ |
951 |
1023 |
for (double x : row) |
952 |
|
{ |
953 |
1000054 |
empty = false; |
954 |
1000054 |
if (x > max) |
955 |
|
{ |
956 |
45 |
max = x; |
957 |
|
} |
958 |
1000054 |
if (x < min) |
959 |
|
{ |
960 |
36 |
min = x; |
961 |
|
} |
962 |
|
} |
963 |
|
} |
964 |
|
} |
965 |
13 |
return empty ? null : new double[] { min, max }; |
966 |
|
} |
967 |
|
|
968 |
|
|
969 |
|
@inheritDoc |
970 |
|
|
|
|
| 75% |
Uncovered Elements: 5 (20) |
Complexity: 5 |
Complexity Density: 0.42 |
|
971 |
10 |
@Override... |
972 |
|
public void reverseRange(boolean maxToZero) |
973 |
|
{ |
974 |
10 |
if (value == null) |
975 |
|
{ |
976 |
0 |
return; |
977 |
|
} |
978 |
10 |
double[] minMax = findMinMax(); |
979 |
10 |
if (minMax == null) |
980 |
|
{ |
981 |
0 |
return; |
982 |
|
} |
983 |
10 |
double subtractFrom = maxToZero ? minMax[1] : minMax[0] + minMax[1]; |
984 |
|
|
985 |
10 |
for (double[] row : value) |
986 |
|
{ |
987 |
20 |
if (row != null) |
988 |
|
{ |
989 |
20 |
int j = 0; |
990 |
20 |
for (double x : row) |
991 |
|
{ |
992 |
48 |
row[j] = subtractFrom - x; |
993 |
48 |
j++; |
994 |
|
} |
995 |
|
} |
996 |
|
} |
997 |
|
} |
998 |
|
|
999 |
|
|
1000 |
|
|
1001 |
|
|
1002 |
|
@param |
1003 |
|
|
|
|
| 87.5% |
Uncovered Elements: 1 (8) |
Complexity: 3 |
Complexity Density: 0.75 |
|
1004 |
1 |
@Override... |
1005 |
|
public void multiply(double by) |
1006 |
|
{ |
1007 |
1 |
for (double[] row : value) |
1008 |
|
{ |
1009 |
2 |
if (row != null) |
1010 |
|
{ |
1011 |
8 |
for (int i = 0; i < row.length; i++) |
1012 |
|
{ |
1013 |
6 |
row[i] *= by; |
1014 |
|
} |
1015 |
|
} |
1016 |
|
} |
1017 |
|
} |
1018 |
|
|
1019 |
|
|
1020 |
|
|
1021 |
|
|
1022 |
|
@param |
1023 |
|
|
1024 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 3 |
Complexity Density: 0.75 |
|
1025 |
0 |
@Override... |
1026 |
|
public void add(double d) |
1027 |
|
{ |
1028 |
0 |
for (double[] row : value) |
1029 |
|
{ |
1030 |
0 |
if (row != null) |
1031 |
|
{ |
1032 |
0 |
for (int i = 0; i < row.length; i++) |
1033 |
|
{ |
1034 |
0 |
row[i] += d; |
1035 |
|
} |
1036 |
|
} |
1037 |
|
} |
1038 |
|
} |
1039 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1040 |
2 |
@Override... |
1041 |
|
public void setD(double[] v) |
1042 |
|
{ |
1043 |
2 |
d = v; |
1044 |
|
} |
1045 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1046 |
2 |
@Override... |
1047 |
|
public void setE(double[] v) |
1048 |
|
{ |
1049 |
2 |
e = v; |
1050 |
|
} |
1051 |
|
|
|
|
| 0% |
Uncovered Elements: 9 (9) |
Complexity: 3 |
Complexity Density: 0.6 |
|
1052 |
0 |
public double getTotal()... |
1053 |
|
{ |
1054 |
0 |
double d = 0d; |
1055 |
0 |
for (int i = 0; i < this.height(); i++) |
1056 |
|
{ |
1057 |
0 |
for (int j = 0; j < this.width(); j++) |
1058 |
|
{ |
1059 |
0 |
d += value[i][j]; |
1060 |
|
} |
1061 |
|
} |
1062 |
0 |
return d; |
1063 |
|
} |
1064 |
|
|
1065 |
|
|
1066 |
|
@inheritDoc |
1067 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (16) |
Complexity: 7 |
Complexity Density: 0.88 |
|
1068 |
12 |
@Override... |
1069 |
|
public boolean equals(MatrixI m2, double delta) |
1070 |
|
{ |
1071 |
12 |
if (m2 == null || this.height() != m2.height() |
1072 |
|
|| this.width() != m2.width()) |
1073 |
|
{ |
1074 |
2 |
return false; |
1075 |
|
} |
1076 |
27 |
for (int i = 0; i < this.height(); i++) |
1077 |
|
{ |
1078 |
66 |
for (int j = 0; j < this.width(); j++) |
1079 |
|
{ |
1080 |
49 |
double diff = this.getValue(i, j) - m2.getValue(i, j); |
1081 |
49 |
if (Math.abs(diff) > delta) |
1082 |
|
{ |
1083 |
3 |
return false; |
1084 |
|
} |
1085 |
|
} |
1086 |
|
} |
1087 |
7 |
return true; |
1088 |
|
} |
1089 |
|
|
1090 |
|
|
1091 |
|
|
1092 |
|
|
1093 |
|
@return |
1094 |
|
|
|
|
| 0% |
Uncovered Elements: 13 (13) |
Complexity: 4 |
Complexity Density: 0.57 |
|
1095 |
0 |
@Override... |
1096 |
|
public MatrixI absolute() |
1097 |
|
{ |
1098 |
0 |
MatrixI copy = this.copy(); |
1099 |
0 |
for (int i = 0; i < copy.width(); i++) |
1100 |
|
{ |
1101 |
0 |
double[] row = copy.getRow(i); |
1102 |
0 |
if (row != null) |
1103 |
|
{ |
1104 |
0 |
for (int j = 0; j < row.length; j++) |
1105 |
|
{ |
1106 |
0 |
row[j] = Math.abs(row[j]); |
1107 |
|
} |
1108 |
|
} |
1109 |
|
} |
1110 |
0 |
return copy; |
1111 |
|
} |
1112 |
|
|
1113 |
|
|
1114 |
|
|
1115 |
|
|
1116 |
|
@return |
1117 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
|
1118 |
0 |
@Override... |
1119 |
|
public double[] meanRow() |
1120 |
|
{ |
1121 |
0 |
double[] mean = new double[rows]; |
1122 |
0 |
int i = 0; |
1123 |
0 |
for (double[] row : value) |
1124 |
|
{ |
1125 |
0 |
if (row != null) |
1126 |
|
{ |
1127 |
0 |
mean[i++] = MiscMath.mean(row); |
1128 |
|
} |
1129 |
|
} |
1130 |
0 |
return mean; |
1131 |
|
} |
1132 |
|
|
1133 |
|
|
1134 |
|
|
1135 |
|
|
1136 |
|
@return |
1137 |
|
|
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 3 |
Complexity Density: 0.5 |
|
1138 |
0 |
@Override... |
1139 |
|
public double[] meanCol() |
1140 |
|
{ |
1141 |
0 |
double[] mean = new double[cols]; |
1142 |
0 |
for (int j = 0; j < cols; j++) |
1143 |
|
{ |
1144 |
0 |
double[] column = getColumn(j); |
1145 |
0 |
if (column != null) |
1146 |
|
{ |
1147 |
0 |
mean[j] = MiscMath.mean(column); |
1148 |
|
} |
1149 |
|
} |
1150 |
0 |
return mean; |
1151 |
|
} |
1152 |
|
|
1153 |
|
|
1154 |
|
|
1155 |
|
|
1156 |
|
@return |
1157 |
|
|
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 3 |
Complexity Density: 0.5 |
|
1158 |
0 |
@Override... |
1159 |
|
public double[] sumCol() |
1160 |
|
{ |
1161 |
0 |
double[] sum = new double[cols]; |
1162 |
0 |
for (int j = 0; j < cols; j++) |
1163 |
|
{ |
1164 |
0 |
double[] column = getColumn(j); |
1165 |
0 |
if (column != null) |
1166 |
|
{ |
1167 |
0 |
sum[j] = MiscMath.sum(column); |
1168 |
|
} |
1169 |
|
} |
1170 |
0 |
return sum; |
1171 |
|
} |
1172 |
|
|
1173 |
|
|
1174 |
|
|
1175 |
|
|
1176 |
|
@return |
1177 |
|
|
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 2 |
Complexity Density: 0.25 |
|
1178 |
0 |
@Override... |
1179 |
|
public double mean() |
1180 |
|
{ |
1181 |
0 |
double sum = 0; |
1182 |
0 |
int nanCount = 0; |
1183 |
0 |
for (double[] row : value) |
1184 |
|
{ |
1185 |
0 |
for (double col : row) |
1186 |
|
{ |
1187 |
0 |
if (!Double.isNaN(col)) |
1188 |
|
{ |
1189 |
0 |
sum += col; |
1190 |
|
} |
1191 |
|
else |
1192 |
|
{ |
1193 |
0 |
nanCount++; |
1194 |
|
} |
1195 |
|
} |
1196 |
|
} |
1197 |
0 |
return sum / (double) (this.rows * this.cols - nanCount); |
1198 |
|
} |
1199 |
|
|
1200 |
|
|
1201 |
|
|
1202 |
|
|
1203 |
|
|
1204 |
|
|
1205 |
|
|
1206 |
|
|
|
|
| 0% |
Uncovered Elements: 13 (13) |
Complexity: 4 |
Complexity Density: 0.57 |
|
1207 |
0 |
@Override... |
1208 |
|
public void fillDiagonal() |
1209 |
|
{ |
1210 |
0 |
int n = this.rows; |
1211 |
0 |
int m = this.cols; |
1212 |
0 |
MatrixI copy = this.transpose(); |
1213 |
|
|
1214 |
0 |
for (int i = 0; i < n; i++) |
1215 |
|
|
1216 |
|
{ |
1217 |
0 |
for (int j = 0; j < m; j++) |
1218 |
|
{ |
1219 |
0 |
if (i != j) |
1220 |
|
{ |
1221 |
0 |
this.addValue(i, j, copy.getValue(i, j)); |
1222 |
|
} |
1223 |
|
} |
1224 |
|
} |
1225 |
|
} |
1226 |
|
|
1227 |
|
|
1228 |
|
|
1229 |
|
|
1230 |
|
@return |
1231 |
|
|
|
|
| 0% |
Uncovered Elements: 12 (12) |
Complexity: 4 |
Complexity Density: 0.67 |
|
1232 |
0 |
@Override... |
1233 |
|
public int countNaN() |
1234 |
|
{ |
1235 |
0 |
int NaN = 0; |
1236 |
0 |
for (int i = 0; i < this.rows; i++) |
1237 |
|
{ |
1238 |
0 |
for (int j = 0; j < this.cols; j++) |
1239 |
|
{ |
1240 |
0 |
if (Double.isNaN(this.getValue(i, j))) |
1241 |
|
{ |
1242 |
0 |
NaN++; |
1243 |
|
} |
1244 |
|
} |
1245 |
|
} |
1246 |
0 |
return NaN; |
1247 |
|
} |
1248 |
|
|
1249 |
|
|
1250 |
|
|
1251 |
|
|
1252 |
|
|
1253 |
|
@param |
1254 |
|
|
1255 |
|
|
1256 |
|
@return |
1257 |
|
|
|
|
| 0% |
Uncovered Elements: 13 (13) |
Complexity: 5 |
Complexity Density: 0.71 |
|
1258 |
0 |
@Override... |
1259 |
|
public MatrixI add(MatrixI m) |
1260 |
|
{ |
1261 |
0 |
if (m.width() != cols || m.height() != rows) |
1262 |
|
{ |
1263 |
0 |
throw new IllegalArgumentException( |
1264 |
|
"Can't add a " + m.height() + "x" + m.width() + " to a " |
1265 |
|
+ this.rows + "x" + this.cols + " matrix"); |
1266 |
|
} |
1267 |
0 |
double[][] tmp = new double[this.rows][this.cols]; |
1268 |
0 |
for (int i = 0; i < this.rows; i++) |
1269 |
|
{ |
1270 |
0 |
for (int j = 0; j < this.cols; j++) |
1271 |
|
{ |
1272 |
0 |
tmp[i][j] = this.getValue(i, j) + m.getValue(i, j); |
1273 |
|
} |
1274 |
|
} |
1275 |
0 |
return new Matrix(tmp); |
1276 |
|
} |
1277 |
|
|
1278 |
|
|
1279 |
|
|
1280 |
|
|
1281 |
|
|
1282 |
|
@param |
1283 |
|
|
1284 |
|
|
1285 |
|
@return |
1286 |
|
|
|
|
| 0% |
Uncovered Elements: 13 (13) |
Complexity: 5 |
Complexity Density: 0.71 |
|
1287 |
0 |
@Override... |
1288 |
|
public MatrixI subtract(MatrixI m) |
1289 |
|
{ |
1290 |
0 |
if (m.width() != cols || m.height() != rows) |
1291 |
|
{ |
1292 |
0 |
throw new IllegalArgumentException("Can't subtract a " + m.height() |
1293 |
|
+ "x" + m.width() + " from a " + this.rows + "x" + this.cols |
1294 |
|
+ " matrix"); |
1295 |
|
} |
1296 |
0 |
double[][] tmp = new double[this.rows][this.cols]; |
1297 |
0 |
for (int i = 0; i < this.rows; i++) |
1298 |
|
{ |
1299 |
0 |
for (int j = 0; j < this.cols; j++) |
1300 |
|
{ |
1301 |
0 |
tmp[i][j] = this.getValue(i, j) - m.getValue(i, j); |
1302 |
|
} |
1303 |
|
} |
1304 |
0 |
return new Matrix(tmp); |
1305 |
|
} |
1306 |
|
|
1307 |
|
|
1308 |
|
|
1309 |
|
|
1310 |
|
|
1311 |
|
@param |
1312 |
|
|
1313 |
|
|
1314 |
|
@return |
1315 |
|
|
|
|
| 0% |
Uncovered Elements: 13 (13) |
Complexity: 5 |
Complexity Density: 0.71 |
|
1316 |
0 |
@Override... |
1317 |
|
public MatrixI elementwiseMultiply(MatrixI m) |
1318 |
|
{ |
1319 |
0 |
if (m.width() != cols || m.height() != rows) |
1320 |
|
{ |
1321 |
0 |
throw new IllegalArgumentException( |
1322 |
|
"Can't multiply a " + this.rows + "x" + this.cols + " by a " |
1323 |
|
+ m.height() + "x" + m.width() + " matrix"); |
1324 |
|
} |
1325 |
0 |
double[][] tmp = new double[this.rows][this.cols]; |
1326 |
0 |
for (int i = 0; i < this.rows; i++) |
1327 |
|
{ |
1328 |
0 |
for (int j = 0; j < this.cols; j++) |
1329 |
|
{ |
1330 |
0 |
tmp[i][j] = this.getValue(i, j) * m.getValue(i, j); |
1331 |
|
} |
1332 |
|
} |
1333 |
0 |
return new Matrix(tmp); |
1334 |
|
} |
1335 |
|
|
1336 |
|
|
1337 |
|
|
1338 |
|
|
1339 |
|
|
1340 |
|
@param |
1341 |
|
|
1342 |
|
|
1343 |
|
@return |
1344 |
|
|
|
|
| 0% |
Uncovered Elements: 13 (13) |
Complexity: 5 |
Complexity Density: 0.71 |
|
1345 |
0 |
@Override... |
1346 |
|
public MatrixI elementwiseDivide(MatrixI m) |
1347 |
|
{ |
1348 |
0 |
if (m.width() != cols || m.height() != rows) |
1349 |
|
{ |
1350 |
0 |
throw new IllegalArgumentException( |
1351 |
|
"Can't divide a " + this.rows + "x" + this.cols + " by a " |
1352 |
|
+ m.height() + "x" + m.width() + " matrix"); |
1353 |
|
} |
1354 |
0 |
double[][] tmp = new double[this.rows][this.cols]; |
1355 |
0 |
for (int i = 0; i < this.rows; i++) |
1356 |
|
{ |
1357 |
0 |
for (int j = 0; j < this.cols; j++) |
1358 |
|
{ |
1359 |
0 |
tmp[i][j] = this.getValue(i, j) / m.getValue(i, j); |
1360 |
|
} |
1361 |
|
} |
1362 |
0 |
return new Matrix(tmp); |
1363 |
|
} |
1364 |
|
|
1365 |
|
|
1366 |
|
|
1367 |
|
|
1368 |
|
@param |
1369 |
|
|
1370 |
|
|
1371 |
|
@return |
1372 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
1373 |
0 |
@Override... |
1374 |
|
public double rmsd(MatrixI m) |
1375 |
|
{ |
1376 |
0 |
MatrixI squaredDeviates = this.subtract(m); |
1377 |
0 |
squaredDeviates = squaredDeviates.preMultiply(squaredDeviates); |
1378 |
0 |
return Math.sqrt(squaredDeviates.mean()); |
1379 |
|
} |
1380 |
|
|
1381 |
|
|
1382 |
|
|
1383 |
|
|
1384 |
|
@return |
1385 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
|
1386 |
0 |
@Override... |
1387 |
|
public double norm() |
1388 |
|
{ |
1389 |
0 |
double result = 0; |
1390 |
0 |
for (double[] row : value) |
1391 |
|
{ |
1392 |
0 |
for (double val : row) |
1393 |
|
{ |
1394 |
0 |
result += Math.pow(val, 2); |
1395 |
|
} |
1396 |
|
} |
1397 |
0 |
return Math.sqrt(result); |
1398 |
|
} |
1399 |
|
|
1400 |
|
|
1401 |
|
|
1402 |
|
|
1403 |
|
@return |
1404 |
|
|
|
|
| 0% |
Uncovered Elements: 7 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
1405 |
0 |
@Override... |
1406 |
|
public double sum() |
1407 |
|
{ |
1408 |
0 |
double sum = 0; |
1409 |
0 |
for (double[] row : value) |
1410 |
|
{ |
1411 |
0 |
for (double val : row) |
1412 |
|
{ |
1413 |
0 |
sum += (Double.isNaN(val)) ? 0.0 : val; |
1414 |
|
} |
1415 |
|
} |
1416 |
0 |
return sum; |
1417 |
|
} |
1418 |
|
|
1419 |
|
|
1420 |
|
|
1421 |
|
|
1422 |
|
@param |
1423 |
|
|
1424 |
|
|
1425 |
|
@return |
1426 |
|
|
|
|
| 0% |
Uncovered Elements: 16 (16) |
Complexity: 4 |
Complexity Density: 0.4 |
|
1427 |
0 |
@Override... |
1428 |
|
public double[] sumProduct(double[] v) |
1429 |
|
{ |
1430 |
0 |
if (v.length != cols) |
1431 |
|
{ |
1432 |
0 |
throw new IllegalArgumentException( |
1433 |
|
"Vector and matrix do not have the same dimension! (" |
1434 |
|
+ v.length + " != " + cols + ")"); |
1435 |
|
} |
1436 |
0 |
double[] result = new double[rows]; |
1437 |
0 |
for (int i = 0; i < rows; i++) |
1438 |
|
{ |
1439 |
0 |
double[] row = value[i]; |
1440 |
0 |
double sum = 0; |
1441 |
0 |
for (int j = 0; j < row.length; j++) |
1442 |
|
{ |
1443 |
0 |
sum += row[j] * v[j]; |
1444 |
|
} |
1445 |
0 |
result[i] = sum; |
1446 |
|
} |
1447 |
0 |
return result; |
1448 |
|
} |
1449 |
|
|
1450 |
|
|
1451 |
|
|
1452 |
|
|
1453 |
|
@return |
1454 |
|
|
|
|
| 0% |
Uncovered Elements: 19 (19) |
Complexity: 5 |
Complexity Density: 0.45 |
|
1455 |
0 |
@Override... |
1456 |
|
public MatrixI mirrorCol() |
1457 |
|
{ |
1458 |
0 |
double[][] result = new double[rows][cols]; |
1459 |
0 |
for (int i = 0; i < rows; i++) |
1460 |
|
{ |
1461 |
0 |
int k = cols - 1; |
1462 |
0 |
for (int j = 0; j < cols; j++) |
1463 |
|
{ |
1464 |
0 |
result[i][k--] = this.getValue(i, j); |
1465 |
|
} |
1466 |
|
} |
1467 |
0 |
MatrixI resultMatrix = new Matrix(result); |
1468 |
0 |
if (d != null) |
1469 |
0 |
resultMatrix.setD(d); |
1470 |
0 |
if (e != null) |
1471 |
0 |
resultMatrix.setE(e); |
1472 |
|
|
1473 |
0 |
return resultMatrix; |
1474 |
|
} |
1475 |
|
} |