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|
/*
* modelcodon.cpp
*
* Created on: May 24, 2013
* Author: minh
*/
#include "modelcodon.h"
#include <string>
const double MIN_OMEGA_KAPPA = 0.001;
const double MAX_OMEGA_KAPPA = 50.0;
/* Empirical codon model restricted (Kosiol et al. 2007), source: http://www.ebi.ac.uk/goldman/ECM/ */
string model_ECMrest1 =
"11.192024 \
1.315610 0.010896 \
5.427076 4.756288 24.748755 \
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string model_ECMrest = model_ECMrest1 +
"0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.091041 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.432410 0.000000 0.000000 0.000000 0.702411 0.000000 0.000000 0.000000 2.985093 0.000000 0.000000 0.000000 0.874000 0.000000 20.518100 4.120953 \
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\
0.022103 0.021383 0.016387 0.015425 0.011880 0.011131 0.009750 0.008956 0.015965 0.015782 0.006025 0.007029 0.011880 0.014467 0.017386 0.007600 0.028839 0.010007 0.010100 0.010642 0.011843 0.011097 0.011703 0.016076 0.020211 0.008311 0.014148 0.004800 0.007837 0.025576 0.023441 0.013551 0.020102 0.013424 0.020201 0.015528 0.012142 0.023006 0.020171 0.030001 0.026344 0.010142 0.011679 0.010372 0.008195 0.019047 0.018938 0.010901 0.022747 0.019005 0.028307 0.015908 0.018853 0.028198 0.024532 0.033223 0.031878 0.016852 0.022982 0.015796 0.010191 \
\
TTT TTC TTA TTG TCT TCC TCA TCG TAT TAC TGT TGC TGG CTT CTC CTA CTG CCT CCC CCA \
CCG CAT CAC CAA CAG CGT CGC CGA CGG ATT ATC ATA ATG ACT ACC ACA ACG AAT AAC AAA \
AAG AGT AGC AGA AGG GTT GTC GTA GTG GCT GCC GCA GCG GAT GAC GAA GAG GGT GGC GGA \
GGG";
/* Empirical codon model unrestricted (Kosiol et al. 2007), source: http://www.ebi.ac.uk/goldman/ECM/ */
string model_ECMunrest1 =
"16.011531 \
2.395822 0.151858 \
1.204356 0.675537 18.541946 \
0.773935 0.052602 0.249707 0.274990 \
0.030074 0.656004 0.011609 0.158873 23.655090 \
0.278090 0.056677 1.184813 0.611887 35.921779 15.982573 \
0.034137 0.198277 0.010188 0.694091 11.510965 35.359077 17.424222 \
4.317981 0.503397 0.798582 0.337279 0.688169 0.047115 0.341791 0.058136 \
0.481042 4.483501 0.033529 0.177833 0.069588 0.524116 0.070809 0.213967 24.177765 \
0.733587 0.076912 0.645571 0.395942 1.811753 0.343463 0.751980 0.143447 0.822999 0.054860 \
0.045951 0.561620 0.040012 0.240632 0.138244 1.323765 0.121937 0.493179 0.068342 0.628438 56.838378 \
0.786871 1.183337 0.271072 0.632947 0.069758 0.081312 0.195833 0.410046 1.140051 1.421996 0.264556 0.210115 \
2.016257 0.207692 12.035723 11.161511 0.277929 0.000186 0.000289 0.000000 0.485469 0.000299 0.543240 0.000674 0.010122 \
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0.483563 0.000234 0.008892 0.035630 3.994417 0.771771 1.825878 0.250545 0.370309 0.000419 1.899865 0.011733 0.035860 0.879741 0.000417 0.004077 0.000772 1.272426 0.073021 0.346978 0.013526 0.420580 0.000091 0.272950 0.040907 0.324227 0.000000 0.001871 0.000000 0.536332 0.000253 0.001795 0.451134 2.359362 0.120121 0.324162 0.108501 0.643160 0.001329 0.216244 0.268662 2.323091 0.005328 0.013852 0.045374 2.600428 0.131929 0.662578 0.152215 \
0.000093 0.512203 0.000000 0.001654 0.111968 3.452570 0.084218 1.978448 0.000058 0.380788 0.000466 1.514097 0.044178 0.000132 1.191514 0.000136 0.103766 0.022062 1.394892 0.013077 0.971148 0.000562 0.696016 0.018814 0.634927 0.000236 1.610248 0.000416 0.020471 0.000040 0.536362 0.000000 0.169264 0.038559 2.159328 0.019665 0.498504 0.000045 0.565968 0.005500 0.373948 0.000485 2.214735 0.000000 0.001768 0.046583 2.620833 0.028569 0.682579 9.612709 \
0.109975 0.016535 1.041312 0.019406 1.931350 0.558500 4.380679 0.505677 0.176829 0.034737 0.806554 0.297371 0.031466 0.002374 0.000357 0.741135 0.000351 0.335924 0.069754 1.236457 0.087384 0.039265 0.004982 1.274118 0.002219 0.000589 0.000068 0.286547 0.000123 0.002262 0.000589 0.983926 0.517896 0.381796 0.077341 2.735831 0.318574 0.084620 0.041435 0.923644 0.004382 0.126382 0.063353 0.461729 0.004420 0.718719 0.092405 3.415722 0.415718 24.400553 6.746560 \
0.005884 0.074851 0.000000 0.220908 0.103323 1.262618 0.150589 4.658653 0.027035 0.106187 0.028567 0.586111 0.446015 0.000066 0.000893 0.000000 1.524024 0.014101 0.417565 0.017824 1.950083 0.080124 0.190037 0.001165 1.544626 0.001531 0.083744 0.000624 3.409178 0.000081 0.004629 0.000078 0.837302 0.023862 0.728891 0.049848 2.866325 0.003771 0.068501 0.000482 0.759132 0.006402 0.200205 0.000000 0.187832 0.054049 0.968351 0.081861 2.211488 5.140068 19.373137 11.561124 \
0.064397 0.000000 0.042112 0.038557 1.120532 0.003717 0.348448 0.117533 0.223763 0.015452 0.099985 0.000135 0.028249 0.129492 0.000000 0.012366 0.000491 0.661776 0.000769 0.147873 0.031560 0.746792 0.046739 0.706782 0.130873 0.162525 0.000000 0.007070 0.000368 0.066966 0.000042 0.001171 0.059065 0.928969 0.000559 0.092988 0.042595 3.529593 0.371685 0.604859 0.188097 1.702817 0.012481 0.030474 0.015763 0.153418 0.007112 0.078381 0.011491 0.396521 0.015140 0.189090 0.043198 \
0.000000 0.055366 0.000062 0.006808 0.000254 1.023142 0.007428 0.670108 0.010037 0.184704 0.000000 0.071612 0.066384 0.000066 0.135255 0.001359 0.015686 0.000096 0.976175 0.003672 0.644235 0.100928 0.975727 0.121389 0.928319 0.000236 0.915505 0.009981 0.150527 0.000000 0.032447 0.000000 0.011379 0.000158 1.013424 0.003354 0.095207 0.167041 2.729647 0.053168 0.426684 0.000388 2.005334 0.000718 0.008986 0.004101 0.119062 0.006776 0.041280 0.018617 0.802516 0.027912 0.702594 14.214694 \
0.084945 0.006464 0.287373 0.005472 0.330481 0.085680 1.265487 0.002179 0.257122 0.043721 0.028878 0.003641 0.009966 0.039560 0.002679 0.313495 0.000140 0.184749 0.105112 0.890822 0.005410 0.452442 0.106069 3.081614 0.536567 0.034978 0.025678 0.440217 0.000858 0.038612 0.009174 0.361403 0.033994 0.251423 0.109664 1.164866 0.003464 0.975582 0.193544 2.258321 0.308851 0.832592 0.308372 0.668173 0.004420 0.276499 0.042565 0.469281 0.055025 0.502355 0.140546 0.905488 0.227527 2.738552 0.892903 \
0.010974 0.034428 0.000000 0.159955 0.042380 0.283432 0.001061 1.029128 0.042815 0.136432 0.014439 0.013216 0.137634 0.004220 0.010061 0.000136 0.176300 0.034437 0.294294 0.001791 0.990330 0.159217 0.566034 0.343314 3.036767 0.007891 0.528692 0.001040 2.171984 0.003312 0.031984 0.000078 0.262465 0.033581 0.360196 0.000838 1.447392 0.149578 0.372719 0.159248 1.563846 0.129098 0.822643 0.000410 1.195790 0.049842 0.245019 0.053017 0.362328 0.106257 0.938586 0.157605 1.251589 1.091224 3.195698 12.984714 \
0.164659 0.000141 0.000741 0.003881 0.976185 0.001951 0.011673 0.007109 0.130940 0.000120 0.420899 0.045044 0.039313 0.169777 0.000060 0.000272 0.000175 0.418802 0.000288 0.002508 0.001312 0.388156 0.000091 0.042812 0.003377 0.241197 0.004656 0.042005 0.011768 0.069995 0.000000 0.000156 0.027479 0.380374 0.000112 0.000534 0.000374 1.322234 0.005905 0.048730 0.021649 2.382451 0.326035 0.037657 0.047437 0.164143 0.016776 0.072521 0.024883 1.572808 0.086923 0.585071 0.083552 0.629243 0.035120 0.089148 0.030223 \
0.000000 0.172889 0.000000 0.000191 0.000085 0.880032 0.000289 0.356038 0.000058 0.127388 0.007608 0.309374 0.105305 0.000000 0.240505 0.000000 0.047268 0.000096 0.636916 0.000090 0.395771 0.000843 0.566759 0.016193 0.336277 0.021435 0.676049 0.008942 0.703728 0.000283 0.055425 0.000000 0.018603 0.000000 0.518903 0.000000 0.006459 0.001122 1.110726 0.002863 0.176224 0.054025 2.392606 0.000821 0.012227 0.002050 0.201477 0.001557 0.051048 0.022214 1.797671 0.027973 1.398079 0.037461 1.228004 0.030585 0.239725 13.935950";
string model_ECMunrest = model_ECMunrest1 +
"0.113991 0.018315 0.201112 0.001082 0.012121 0.001951 1.720919 0.001720 0.082323 0.029826 0.197641 0.061497 0.073682 0.000330 0.000060 0.165784 0.000070 0.003549 0.000384 0.556204 0.000164 0.097554 0.004982 0.551493 0.000289 0.015310 0.000753 0.247245 0.010419 0.000283 0.000084 0.194319 0.037724 0.002449 0.000112 0.466770 0.000187 0.909861 0.280400 0.713961 0.001760 1.179053 0.298738 0.938439 0.165587 0.080337 0.009773 0.324696 0.016839 0.658541 0.036022 1.693998 0.046588 0.375097 0.067431 0.639125 0.053748 21.171295 5.214689 \
0.018773 0.032039 0.000000 0.175861 0.002797 0.002974 0.003376 2.163175 0.007948 0.014314 0.105884 0.183952 0.381671 0.000066 0.000119 0.000000 0.185038 0.001918 0.001441 0.001254 0.703092 0.084060 0.053714 0.003029 0.634203 0.043222 0.097165 0.143481 0.590833 0.000081 0.000295 0.000078 0.410199 0.000553 0.000447 0.000610 0.716441 0.194964 0.293884 0.001158 0.744000 0.684968 1.149846 0.069567 1.558784 0.032177 0.064227 0.074536 0.276276 0.238907 0.496552 0.672077 1.526141 0.235747 0.403521 0.136937 0.968146 13.981617 18.675227 25.640860 \
\
0.021414 0.021349 0.016195 0.015717 0.011798 0.010761 0.010366 0.008721 0.017237 0.016697 0.006441 0.007415 0.012744 0.015167 0.016798 0.007359 0.028497 0.010425 0.010408 0.011165 0.012199 0.010671 0.011040 0.017168 0.020730 0.008491 0.014604 0.004809 0.008158 0.024759 0.023762 0.012814 0.021180 0.012656 0.017882 0.013120 0.010682 0.022276 0.020321 0.031090 0.026699 0.010310 0.013701 0.009746 0.006788 0.019020 0.018419 0.010921 0.022626 0.018907 0.026817 0.016516 0.018288 0.028590 0.025285 0.034527 0.030606 0.016883 0.023659 0.016386 0.010223 \
\
TTT TTC TTA TTG TCT TCC TCA TCG TAT TAC TGT TGC TGG CTT CTC CTA CTG CCT CCC CCA \
CCG CAT CAC CAA CAG CGT CGC CGA CGG ATT ATC ATA ATG ACT ACC ACA ACG AAT AAC AAA \
AAG AGT AGC AGA AGG GTT GTC GTA GTG GCT GCC GCA GCG GAT GAC GAA GAG GGT GGC GGA \
GGG";
/* empirical codon model of Schneider, Cannarozzi, Gonnet 2005
*/
string model_ECM_Schneider05 =
"15594\
787 609\
717 391 22864\
476 0 89 133\
0 444 39 51 15656\
77 11 2230 662 15154 11009\
99 0 0 2501 21330 19335 36566\
2355 360 127 41 400 18 28 0\
300 1911 76 49 0 260 23 70 25720\
378 30 81 96 1004 0 238 90 1025 0\
60 275 46 53 37 766 83 157 0 623 29318\
102 74 24 357 16 23 83 277 110 80 186 164\
1304 0 4065 4641 278 0 0 0 138 18 147 21 9\
0 1293 3595 2691 0 214 0 0 1 128 9 152 9 15530\
112 106 26307 6745 0 0 154 340 68 0 59 0 36 10903 8429\
186 136 4180 13314 20 34 0 0 39 14 17 9 51 7205 7138 16270\
97 0 7 72 2744 0 0 0 43 3 101 12 0 937 34 0 0\
0 82 18 3 65 2535 0 0 0 47 0 49 0 0 706 0 0 16327\
0 12 99 87 0 0 2829 131 7 0 11 0 14 0 0 1474 137 15604 10490\
26 3 11 109 0 0 244 5851 4 22 44 31 68 0 0 0 935 15588 21512 27394\
172 22 80 27 315 22 76 0 2184 0 475 6 63 676 55 0 43 756 38 56 173\
36 166 5 20 43 211 53 112 137 1624 21 276 20 0 390 96 40 0 617 97 246 30148\
35 18 93 63 143 90 403 0 122 56 70 60 38 168 38 1166 51 126 99 1405 296 1995 1176\
11 13 50 95 55 80 109 288 42 58 43 35 97 77 92 46 290 88 161 235 1234 1086 1057 15317\
70 7 49 98 326 11 1 0 362 0 1302 0 14 685 0 0 0 712 0 0 0 4390 0 646 232\
0 56 40 0 0 177 0 105 4 139 0 908 40 1 486 0 34 0 404 8 121 0 2689 217 355 42123\
8 0 0 25 0 0 163 53 68 0 51 53 130 0 45 966 0 0 23 393 0 133 261 3956 0 40836 19396\
10 8 2 45 0 50 31 385 0 17 50 109 576 21 0 7 340 0 0 57 1276 191 317 0 2408 25507 19595 39593\
437 29 201 399 72 30 0 18 64 1 90 1 10 1848 131 185 283 68 10 24 0 84 4 0 20 27 0 64 0\
23 356 111 27 15 35 6 15 7 42 10 62 7 133 1745 0 351 0 55 0 29 0 36 24 7 17 20 0 15 16920\
157 33 3243 833 0 54 209 88 29 1 14 16 14 134 176 3786 421 49 13 97 79 51 4 93 20 43 3 5 0 15113 13126\
126 89 536 1607 75 39 153 229 32 21 29 22 45 346 369 726 1104 34 27 55 92 61 20 96 116 29 23 0 50 781 495 2443\
82 23 67 79 2679 170 489 362 61 17 194 41 0 233 0 0 25 990 52 0 15 212 6 166 30 318 42 0 0 1552 0 0 262\
7 74 3 39 279 2315 113 0 21 33 10 153 9 0 186 0 44 76 817 0 0 15 171 37 61 14 118 71 33 0 1028 0 176 16316\
23 11 295 92 567 81 3129 578 12 0 75 22 19 4 0 288 46 64 0 1015 88 93 27 341 96 39 0 0 26 0 0 2434 714 16829 10306\
51 5 49 306 0 682 232 6944 52 9 134 0 44 55 28 0 181 0 170 0 1953 0 35 0 307 0 116 322 172 166 134 0 1616 20814 19942 34110\
41 0 48 36 289 32 139 78 316 0 191 0 11 110 0 22 0 115 34 55 46 1623 55 311 168 429 0 45 27 202 0 50 68 1425 16 237 182\
8 34 4 22 87 277 79 40 0 196 4 116 7 0 64 19 7 14 98 17 47 9 1196 148 142 0 264 0 58 0 145 21 42 122 984 165 67 17900\
4 6 59 28 54 24 133 53 16 8 20 15 9 30 17 100 0 26 18 91 39 169 94 1364 137 334 337 908 410 16 0 292 80 114 54 650 0 580 305\
6 0 4 39 26 24 52 70 11 11 13 16 24 7 3 0 36 14 14 28 105 84 110 33 727 353 569 299 1249 20 21 22 189 27 85 94 795 298 269 12057\
49 0 0 47 938 51 528 366 157 0 981 105 27 71 0 26 4 178 0 76 37 605 0 198 84 1145 0 0 44 345 0 91 78 2941 0 402 387 4830 0 245 146\
10 34 33 0 312 983 214 697 10 79 169 792 19 23 68 0 21 15 213 25 88 41 454 133 123 0 740 72 22 0 228 27 67 421 2248 343 618 178 3430 158 131 21641\
10 2 87 13 54 26 79 12 0 20 52 7 23 32 0 9 13 5 17 0 45 118 55 623 32 6203 2803 22415 6405 0 0 415 93 11 31 743 0 178 142 4144 390 638 339\
12 0 51 36 33 12 4 72 31 0 36 20 264 0 20 0 22 17 0 39 5 62 95 60 271 2885 5913 6064 18118 29 15 106 258 40 59 49 927 145 139 572 3644 544 444 25118\
446 0 175 236 218 61 96 0 80 0 108 60 20 1661 28 0 11 258 0 0 65 68 1 82 28 96 15 0 3 6623 53 389 259 1227 72 65 141 100 20 37 3 233 69 31 0\
6 460 73 35 15 199 49 0 7 69 28 105 4 18 1603 120 42 0 199 36 69 15 75 29 25 18 52 0 36 79 6084 158 190 148 1080 1 0 21 86 13 11 16 170 5 38 17102\
83 13 3202 251 70 2 396 0 18 2 52 24 6 131 5 2164 7 0 63 394 0 23 36 276 31 0 0 86 0 125 0 11512 626 0 20 1694 36 55 26 153 16 31 87 249 0 15228 10722\
60 42 0 1017 46 19 85 271 9 17 54 16 27 0 24 16 827 27 21 58 154 23 18 10 62 12 20 0 58 743 928 1567 1219 155 66 206 995 12 12 10 54 28 10 0 106 10663 9288 21679\
89 10 43 68 2454 180 301 0 54 11 203 32 0 183 8 14 31 1111 63 28 0 111 5 60 52 121 0 0 62 233 32 42 108 3490 0 0 0 252 38 43 31 628 101 47 0 2567 0 14 37\
1 78 42 24 250 2338 201 324 11 28 22 197 15 30 160 0 31 79 965 7 145 0 119 22 88 29 133 26 0 0 217 0 115 0 2888 0 36 25 224 13 45 0 608 24 51 0 2241 0 80 12825\
39 0 293 82 303 127 3185 250 19 1 87 27 17 29 0 300 46 91 19 1186 101 70 20 307 61 38 0 72 23 73 0 484 282 0 0 3718 0 149 28 216 48 268 106 108 88 0 0 3240 591 14816 8169\
19 59 0 480 450 354 0 9766 0 68 96 134 32 16 40 0 261 0 206 0 4882 109 45 182 246 0 94 0 379 0 77 315 392 0 193 0 7718 81 161 62 171 178 258 49 171 0 0 0 2849 13866 14245 22755\
14 0 0 16 138 0 52 20 122 0 41 0 3 21 0 5 0 44 7 28 37 378 0 132 54 66 8 0 13 36 0 19 8 149 2 83 0 1636 4 56 44 488 30 27 19 187 0 24 5 384 0 59 20\
0 13 16 0 1 115 35 76 0 76 9 24 1 10 20 0 3 8 72 6 40 22 311 76 72 1 57 0 11 0 20 0 9 54 124 0 77 33 1249 58 35 38 395 22 11 0 141 19 0 0 322 39 182 13482\
8 2 32 46 42 14 118 53 16 9 13 0 5 13 6 52 0 29 17 71 35 123 28 1246 112 69 0 24 0 0 5 95 22 38 36 196 0 187 74 626 0 114 82 213 0 62 24 367 16 64 41 636 0 1758 1114\
3 4 20 18 36 42 43 84 16 6 3 11 13 7 12 0 27 19 40 51 81 69 71 66 739 0 44 0 104 21 1 17 63 52 35 76 199 106 80 0 429 101 86 0 162 4 26 38 161 70 91 118 916 1216 1466 11181\
32 0 44 0 293 18 60 85 62 0 515 0 0 50 0 9 9 161 16 29 0 266 0 0 43 688 0 117 0 46 0 0 23 349 91 46 0 829 98 44 32 3432 6 0 0 557 0 0 21 1264 0 171 0 1058 0 28 30\
9 23 0 15 52 224 28 240 0 38 38 372 7 14 38 0 6 14 114 31 129 12 165 15 40 1 452 0 78 10 42 18 16 50 250 6 62 91 589 13 28 0 2627 25 0 15 383 0 0 72 1050 0 357 0 795 0 50 17792\
15 1 23 0 80 59 198 0 9 0 34 0 4 13 12 70 0 16 11 78 26 26 16 225 8 0 0 176 0 16 0 85 31 3 12 214 51 121 31 137 11 151 134 1071 0 0 0 629 0 133 44 1071 0 50 86 798 0 13656 9267\
2 11 9 122 10 49 162 532 14 3 42 39 214 0 1 0 39 9 55 36 251 29 31 53 148 0 0 0 515 0 22 14 116 77 0 84 405 67 171 13 144 398 328 0 1567 0 0 86 380 35 151 360 2466 88 32 0 749 11092 11188 21307\
0.019065 0.019572 0.008521 0.014125 0.017115 0.015966 0.013340 0.004325 0.013196 0.015988 0.010982 0.011900 0.012462 0.015017 0.017340 0.008031 0.037328 0.017599 0.014989 0.017755 0.005879 0.011592 0.014372 0.013669 0.033679 0.005419 0.008712 0.006185 0.008488 0.017469 0.019956 0.009364 0.021871 0.014391 0.015964 0.016870 0.005890 0.018236 0.020614 0.028227 0.031883 0.013622 0.019058 0.013502 0.011845 0.013592 0.013760 0.008372 0.026506 0.019952 0.021260 0.017896 0.005964 0.025167 0.024586 0.031093 0.038868 0.011549 0.017608 0.018437 0.013269\
TTT TTC TTA TTG TCT TCC TCA TCG TAT TAC TGT TGC TGG CTT CTC CTA CTG CCT CCC CCA \
CCG CAT CAC CAA CAG CGT CGC CGA CGG ATT ATC ATA ATG ACT ACC ACA ACG AAT AAC AAA \
AAG AGT AGC AGA AGG GTT GTC GTA GTG GCT GCC GCA GCG GAT GAC GAA GAG GGT GGC GGA \
GGG";
ModelCodon::ModelCodon(const char *model_name, string model_params, StateFreqType freq, string freq_params,
PhyloTree *tree) : ModelMarkov(tree)
{
half_matrix = false;
omega = kappa = kappa2 = 1.0;
fix_omega = fix_kappa = false;
fix_kappa2 = true;
codon_freq_style = CF_TARGET_CODON;
codon_kappa_style = CK_ONE_KAPPA;
ntfreq = new double[12];
empirical_rates = NULL;
int nrates = getNumRateEntries();
delete [] rates;
rates = new double[nrates];
empirical_rates = new double [nrates];
rate_attr = NULL;
computeRateAttributes();
init(model_name, model_params, freq, freq_params);
}
ModelCodon::~ModelCodon() {
if (rate_attr) {
delete [] rate_attr;
rate_attr = NULL;
}
if (empirical_rates) {
delete [] empirical_rates;
empirical_rates = NULL;
}
if (ntfreq) {
delete [] ntfreq;
ntfreq = NULL;
}
}
void ModelCodon::startCheckpoint() {
checkpoint->startStruct("ModelCodon");
}
void ModelCodon::saveCheckpoint() {
startCheckpoint();
// CKP_ARRAY_SAVE(12, ntfreq);
CKP_SAVE(omega);
// CKP_SAVE(fix_omega);
// int codon_kappa_style = this->codon_kappa_style;
// CKP_SAVE(codon_kappa_style);
CKP_SAVE(kappa);
// CKP_SAVE(fix_kappa);
CKP_SAVE(kappa2);
// CKP_SAVE(fix_kappa2);
// int codon_freq_style = this->codon_freq_style;
// CKP_SAVE(codon_freq_style);
endCheckpoint();
ModelMarkov::saveCheckpoint();
}
void ModelCodon::restoreCheckpoint() {
ModelMarkov::restoreCheckpoint();
startCheckpoint();
// CKP_ARRAY_RESTORE(12, ntfreq);
CKP_RESTORE(omega);
// CKP_RESTORE(fix_omega);
// int codon_kappa_style;
// CKP_RESTORE(codon_kappa_style);
// this->codon_kappa_style = (CodonKappaStyle)codon_kappa_style;
CKP_RESTORE(kappa);
// CKP_RESTORE(fix_kappa);
CKP_RESTORE(kappa2);
// CKP_RESTORE(fix_kappa2);
// int codon_freq_style;
// CKP_RESTORE(codon_freq_style);
// this->codon_freq_style = (CodonFreqStyle)codon_freq_style;
endCheckpoint();
decomposeRateMatrix();
if (phylo_tree)
phylo_tree->clearAllPartialLH();
}
StateFreqType ModelCodon::initCodon(const char *model_name, StateFreqType freq, bool reset_params) {
string name_upper = model_name;
for (string::iterator it = name_upper.begin(); it != name_upper.end(); it++)
(*it) = toupper(*it);
if (name_upper == "MG") {
return initMG94(true, freq, CK_ONE_KAPPA);
} else if (name_upper == "MGK") {
return initMG94(false, freq, CK_ONE_KAPPA);
} else if (name_upper == "MG1KTS" || name_upper == "MGKAP2") {
return initMG94(false, freq, CK_ONE_KAPPA_TS);
} else if (name_upper == "MG1KTV" || name_upper == "MGKAP3") {
return initMG94(false, freq, CK_ONE_KAPPA_TV);
} else if (name_upper == "MG2K" || name_upper == "MGKAP4") {
return initMG94(false, freq, CK_TWO_KAPPA);
} else if (name_upper == "GY") {
return initGY94(false, CK_ONE_KAPPA);
} else if (name_upper == "GY0K" || name_upper == "GYKAP1") {
return initGY94(true, CK_ONE_KAPPA);
} else if (name_upper == "GY1KTS" || name_upper == "GYKAP2") {
return initGY94(false, CK_ONE_KAPPA_TS);
} else if (name_upper == "GY1KTV" || name_upper == "GYKAP3") {
return initGY94(false, CK_ONE_KAPPA_TV);
} else if (name_upper == "GY2K" || name_upper == "GYKAP4") {
return initGY94(false, CK_TWO_KAPPA);
} else if (name_upper == "ECM" || name_upper == "KOSI07" || name_upper == "ECMK07") {
if (!phylo_tree->aln->isStandardGeneticCode())
outError("For ECMK07 a standard genetic code must be used");
readCodonModel(model_ECMunrest, reset_params);
return FREQ_USER_DEFINED;
} else if (name_upper == "ECMREST") {
if (!phylo_tree->aln->isStandardGeneticCode())
outError("For ECMREST a standard genetic code must be used");
readCodonModel(model_ECMrest, reset_params);
return FREQ_USER_DEFINED;
} else if (name_upper == "SCHN05" || name_upper == "ECMS05") {
if (!phylo_tree->aln->isStandardGeneticCode())
outError("For ECMS05 a standard genetic code must be used");
readCodonModel(model_ECM_Schneider05, reset_params);
return FREQ_USER_DEFINED;
} else {
//cout << "User-specified model "<< model_name << endl;
//readParameters(model_name);
//name += " (user-defined)";
readCodonModelFile(model_name, reset_params);
return FREQ_USER_DEFINED;
}
return FREQ_UNKNOWN;
}
void ModelCodon::init(const char *model_name, string model_params, StateFreqType freq, string freq_params)
{
int i, j;
for (i = 0; i < 12; i++)
ntfreq[i] = 0.25;
// initialize empirical_rates
for (i = 0; i < num_states; i++) {
double *this_emp_rate = &empirical_rates[i*num_states];
int *this_rate_attr = &rate_attr[i*num_states];
if (phylo_tree->aln->isStopCodon(i)) {
memset(this_emp_rate, 0, num_states*sizeof(double));
continue;
}
for (j = 0; j < num_states; j++) {
int attr = this_rate_attr[j];
if (attr & (CA_STOP_CODON+CA_MULTI_NT)) { // stop codon or multiple nt substitutions
this_emp_rate[j] = 0.0;
} else {
this_emp_rate[j] = 1.0;
}
}
}
ignore_state_freq = false;
StateFreqType def_freq = FREQ_UNKNOWN;
name = full_name = model_name;
size_t pos;
if ((pos=name.find('_')) == string::npos) {
def_freq = initCodon(model_name, freq, true);
} else {
def_freq = initCodon(name.substr(0, pos).c_str(), freq, false);
if (def_freq != FREQ_USER_DEFINED)
outError("Invalid model " + name + ": first component must be an empirical model"); // first model must be empirical
def_freq = initCodon(name.substr(pos+1).c_str(), freq, false);
if (def_freq == FREQ_USER_DEFINED) // second model must be parametric
outError("Invalid model " + name + ": second component must be a mechanistic model");
// adjust the constraint
if (codon_freq_style==CF_TARGET_CODON)
def_freq = FREQ_USER_DEFINED;
}
num_params = (!fix_omega) + (!fix_kappa) + (!fix_kappa2);
if (freq_params != "") {
readStateFreq(freq_params);
}
if (model_params != "") {
readRates(model_params);
}
// if (freq == FREQ_UNKNOWN || def_freq == FREQ_EQUAL) freq = def_freq;
if (freq == FREQ_UNKNOWN) freq = def_freq;
if (freq == FREQ_CODON_1x4 || freq == FREQ_CODON_3x4 || freq == FREQ_CODON_3x4C) {
//ntfreq = new double[12];
phylo_tree->aln->computeCodonFreq(freq, state_freq, ntfreq);
}
ModelMarkov::init(freq);
}
StateFreqType ModelCodon::initMG94(bool fix_kappa, StateFreqType freq, CodonKappaStyle kappa_style) {
/* Muse-Gaut 1994 model with 1 parameters: omega */
fix_omega = false;
this->fix_kappa = fix_kappa;
if (fix_kappa)
kappa = 1.0;
fix_kappa2 = true;
codon_freq_style = CF_TARGET_NT;
this->codon_kappa_style = kappa_style;
if (kappa_style == CK_TWO_KAPPA)
fix_kappa2 = false;
if (freq == FREQ_UNKNOWN || freq == FREQ_USER_DEFINED)
freq = FREQ_CODON_3x4;
switch (freq) {
case FREQ_CODON_1x4:
case FREQ_CODON_3x4:
case FREQ_CODON_3x4C:
phylo_tree->aln->computeCodonFreq(freq, state_freq, ntfreq);
break;
case FREQ_EMPIRICAL:
case FREQ_ESTIMATE:
case FREQ_USER_DEFINED:
outError("Invalid state frequency type for MG model, please use +F1X4 or +F3X4 or +F3X4C");
break;
default:
break;
}
// ignote state_freq because ntfreq is already used
ignore_state_freq = true;
combineRateNTFreq();
return FREQ_CODON_3x4;
}
StateFreqType ModelCodon::initGY94(bool fix_kappa, CodonKappaStyle kappa_style) {
fix_omega = false;
this->fix_kappa = fix_kappa;
if (fix_kappa)
kappa = 1.0;
fix_kappa2 = true;
codon_freq_style = CF_TARGET_CODON;
this->codon_kappa_style = kappa_style;
if (kappa_style == CK_TWO_KAPPA)
fix_kappa2 = false;
return FREQ_EMPIRICAL;
}
void ModelCodon::computeRateAttributes() {
char symbols_protein[] = "ARNDCQEGHILKMFPSTWYVX"; // X for unknown AA
int i, j, ts, tv;
int nrates = getNumRateEntries();
if (!rate_attr) {
rate_attr = new int[nrates];
memset(rate_attr, 0, sizeof(int)*nrates);
}
char aa_cost_change[400];
memset(aa_cost_change, 10, sizeof(char)*400);
for (i = 0; i < num_states; i++) {
int *rate_attr_row = &rate_attr[i*num_states];
if (phylo_tree->aln->isStopCodon(i)) {
for (j = 0; j < num_states; j++)
rate_attr_row[j] = CA_STOP_CODON;
continue;
}
for (j = 0; j < num_states; j++) {
if (j == i || phylo_tree->aln->isStopCodon(j)) {
rate_attr_row[j] = CA_STOP_CODON;
continue;
}
int nuc1, nuc2;
int attr = 0;
ts = tv = 0;
int codoni = phylo_tree->aln->codon_table[i];
int codonj = phylo_tree->aln->codon_table[j];
if (phylo_tree->aln->genetic_code[codoni] == phylo_tree->aln->genetic_code[codonj])
attr |= CA_SYNONYMOUS;
else
attr |= CA_NONSYNONYMOUS;
int nt_changes = ((codoni/16) != (codonj/16)) + (((codoni%16)/4) != ((codonj%16)/4)) + ((codoni%4) != (codonj%4));
int aa1 = strchr(symbols_protein, phylo_tree->aln->genetic_code[codoni]) - symbols_protein;
int aa2 = strchr(symbols_protein, phylo_tree->aln->genetic_code[codonj]) - symbols_protein;
ASSERT(aa1 >= 0 && aa1 < 20 && aa2 >= 0 && aa2 < 20);
if (nt_changes < aa_cost_change[aa1*20+aa2]) {
aa_cost_change[aa1*20+aa2] = aa_cost_change[aa2*20+aa1] = nt_changes;
}
if ((nuc1=codoni/16) != (nuc2=codonj/16)) {
if (abs(nuc1-nuc2)==2) { // transition
attr |= CA_TRANSITION_1NT;
ts++;
} else { // transversion
attr |= CA_TRANSVERSION_1NT;
tv++;
}
}
if ((nuc1=(codoni%16)/4) != (nuc2=(codonj%16)/4)) {
if (abs(nuc1-nuc2)==2) { // transition
attr |= CA_TRANSITION_2NT;
ts++;
} else { // transversion
attr |= CA_TRANSVERSION_2NT;
tv++;
}
}
if ((nuc1=codoni%4) != (nuc2=codonj%4)) {
if (abs(nuc1-nuc2)==2) { // transition
attr |= CA_TRANSITION_3NT;
ts++;
} else { // transversion
attr |= CA_TRANSVERSION_3NT;
tv++;
}
}
if (ts+tv>1)
attr |= CA_MULTI_NT;
else if (ts==1)
attr |= CA_TRANSITION;
else if (tv==1)
attr |= CA_TRANSVERSION;
rate_attr_row[j] = attr;
}
}
if (verbose_mode >= VB_MAX) {
// make cost matrix fulfill triangular inequality
for (int k = 0; k < 20; k++)
for (i = 0; i < 20; i++)
for (j = 0; j < 20; j++)
if (aa_cost_change[i*20+j] > aa_cost_change[i*20+k] + aa_cost_change[k*20+j])
aa_cost_change[i*20+j] = aa_cost_change[i*20+k] + aa_cost_change[k*20+j];
cout << "cost matrix by number of nt changes for TNT use" << endl;
cout << "smatrix =1 (aa_nt_changes)";
for (i = 0; i < 19; i++)
for (j = i+1; j < 20; j++)
cout << " " << symbols_protein[i] << "/" << symbols_protein[j] << " " << (int)aa_cost_change[i*20+j];
cout << ";" << endl;
cout << 20 << endl;
for (i = 0; i < 20; i++) {
aa_cost_change[i*20+i] = 0;
for (j = 0; j < 20; j++)
cout << (int)aa_cost_change[i*20+j] << " ";
cout << endl;
}
}
}
void ModelCodon::combineRateNTFreq() {
int i, j;
for (i = 0; i < num_states; i++) {
if (phylo_tree->aln->isStopCodon(i))
continue;
double *this_rate = &empirical_rates[i*num_states];
for (j = 0; j < num_states; j++) {
if (this_rate[j] == 0.0)
continue;
int codoni = phylo_tree->aln->codon_table[i];
int codonj = phylo_tree->aln->codon_table[j];
int nuc1, nuc2;
if ((nuc1=codoni/16) != (nuc2=codonj/16)) {
this_rate[j] *= ntfreq[nuc2];
}
if ((nuc1=(codoni%16)/4) != (nuc2=(codonj%16)/4)) {
this_rate[j] *= ntfreq[nuc2+4];
}
if ((nuc1=codoni%4) != (nuc2=codonj%4)) {
this_rate[j] *= ntfreq[nuc2+8];
}
}
}
}
void ModelCodon::readCodonModel(istream &in, bool reset_params) {
int nrates = getNumRateEntries();
int i, j;
int nscodons = phylo_tree->aln->getNumNonstopCodons();
double * q = new double[nscodons*nscodons];
double *f = new double[nscodons];
for (i = 1; i < nscodons; i++) {
for (j = 0; j < i; j++) {
in >> q[i*nscodons+j];
//q[j*num_states+i] = q[i*num_states+j];
if (verbose_mode >= VB_MAX) cout << " " << q[i*nscodons+j];
}
if (verbose_mode >= VB_MAX) cout << endl;
}
for (i = 0; i < nscodons; i++)
in >> f[i];
StrVector codons;
codons.resize(nscodons);
IntVector state_map;
state_map.resize(nscodons);
for (i = 0; i < nscodons; i++) {
in >> codons[i];
if (codons[i].length() != 3)
outError("Input model has wrong codon format ", codons[i]);
int nt1 = phylo_tree->aln->convertState(codons[i][0], SEQ_DNA);
int nt2 = phylo_tree->aln->convertState(codons[i][1], SEQ_DNA);
int nt3 = phylo_tree->aln->convertState(codons[i][2], SEQ_DNA);
if (nt1 > 3 || nt2 > 3 || nt3 > 3)
outError("Wrong codon triplet ", codons[i]);
state_map[i] = phylo_tree->aln->non_stop_codon[nt1*16+nt2*4+nt3];
if (phylo_tree->aln->isStopCodon(state_map[i]) || state_map[i] == STATE_INVALID)
outError("Stop codon encountered");
if (verbose_mode >= VB_MAX)
cout << " " << codons[i] << " " << state_map[i];
}
if (verbose_mode >= VB_MAX) cout << endl;
//int row = 0, col = 1;
// since rates for codons is stored in lower-triangle, special treatment is needed
memset(empirical_rates, 0, nrates*sizeof(double));
memset(rates, 0, nrates*sizeof(double));
for (i = 1; i < nscodons; i++) {
for (j = 0; j < i; j++) {
int row = state_map[i], col = state_map[j];
if (row < col) {
int tmp = row;
row = col;
col = tmp;
}
// int id = col*(2*num_states-col-1)/2 + (row-col-1);
double qentry = q[i*nscodons+j];
int id = row*num_states+col;
ASSERT(id < nrates && id >= 0);
empirical_rates[id] = rates[id] = qentry;
id = col*num_states+row;
ASSERT(id < nrates && id >= 0);
empirical_rates[id] = rates[id] = qentry;
}
}
memset(state_freq, 0, num_states*sizeof(double));
for (i = 0; i < num_states; i++)
state_freq[i] = MIN_FREQUENCY;
for (i = 0; i < nscodons; i++)
state_freq[state_map[i]] = f[i]-(num_states-nscodons)*MIN_FREQUENCY/nscodons;
if (reset_params) {
fix_omega = fix_kappa = fix_kappa2 = true;
omega = kappa = kappa2 = 1.0;
}
delete [] f;
delete [] q;
}
void ModelCodon::readCodonModel(string &str, bool reset_params) {
try {
istringstream in(str);
readCodonModel(in, reset_params);
}
catch (const char *str) {
outError(str);
}
}
void ModelCodon::readCodonModelFile(const char *filename, bool reset_params) {
try {
ifstream in;
// set the failbit and badbit
in.exceptions(ios::failbit | ios::badbit);
in.open(filename);
// remove the failbit
in.exceptions(ios::badbit);
readCodonModel(in, reset_params);
in.clear();
// set the failbit again
in.exceptions(ios::failbit | ios::badbit);
in.close();
}
catch (const char *str) {
outError(str);
}
catch (...) {
outError(ERR_READ_INPUT, filename);
}
}
void ModelCodon::decomposeRateMatrix() {
computeCodonRateMatrix();
ModelMarkov::decomposeRateMatrix();
}
void ModelCodon::computeCodonRateMatrix() {
// if (num_params == 0)
// return; // do nothing for empirical codon model
switch (codon_kappa_style) {
case CK_ONE_KAPPA:
computeCodonRateMatrix_1KAPPA();
break;
case CK_ONE_KAPPA_TS:
computeCodonRateMatrix_1KAPPATS();
break;
case CK_ONE_KAPPA_TV:
computeCodonRateMatrix_1KAPPATV();
break;
case CK_TWO_KAPPA:
computeCodonRateMatrix_2KAPPA();
break;
}
}
void ModelCodon::computeCodonRateMatrix_1KAPPA() {
int nrates = getNumRateEntries();
memcpy(rates, empirical_rates, nrates*sizeof(double));
if (omega == 1.0 && kappa == 1.0)
return; // do nothing
int i, j;
double omega_kappa = omega*kappa;
for (i = 0; i < num_states; i++) {
double *this_rate = &rates[i*num_states];
int *this_rate_attr = &rate_attr[i*num_states];
if (phylo_tree->aln->isStopCodon(i)) {
continue;
}
for (j = 0; j < num_states; j++) {
if (this_rate[j] == 0.0) continue;
int attr = this_rate_attr[j];
if (attr & CA_SYNONYMOUS) { // synonymous
if (attr & CA_TRANSITION) // transition
this_rate[j] *= kappa;
} else if (attr & CA_NONSYNONYMOUS) { // non-synomyous
if (attr & CA_TRANSITION) // transition
this_rate[j] *= omega_kappa;
else // transversion
this_rate[j] *= omega;
}
}
}
}
void ModelCodon::computeCodonRateMatrix_1KAPPATS() {
int nrates = getNumRateEntries();
memcpy(rates, empirical_rates, nrates*sizeof(double));
int i, j;
double kappa_pow[] = {1.0, kappa, kappa*kappa, kappa*kappa*kappa};
double omega_kappa_pow[] = {omega, omega*kappa, omega*kappa*kappa, omega*kappa*kappa*kappa};
for (i = 0; i < num_states; i++) {
double *this_rate = &rates[i*num_states];
int *this_rate_attr = &rate_attr[i*num_states];
if (phylo_tree->aln->isStopCodon(i)) {
continue;
}
for (j = 0; j < num_states; j++) {
int attr = this_rate_attr[j];
if (this_rate[j] == 0.0) continue;
if (attr & CA_SYNONYMOUS) { // synonymous
int num = ((attr & CA_TRANSITION_1NT) != 0) + ((attr & CA_TRANSITION_2NT) != 0) + ((attr & CA_TRANSITION_3NT) != 0);
this_rate[j] *= kappa_pow[num];
} else if (attr & CA_NONSYNONYMOUS) { // non-synomyous
int num = ((attr & CA_TRANSITION_1NT) != 0) + ((attr & CA_TRANSITION_2NT) != 0) + ((attr & CA_TRANSITION_3NT) != 0);
this_rate[j] *= omega_kappa_pow[num];
}
}
}
}
void ModelCodon::computeCodonRateMatrix_1KAPPATV() {
int nrates = getNumRateEntries();
memcpy(rates, empirical_rates, nrates*sizeof(double));
int i, j;
double kappa_pow[] = {1.0, kappa, kappa*kappa, kappa*kappa*kappa};
double omega_kappa_pow[] = {omega, omega*kappa, omega*kappa*kappa, omega*kappa*kappa*kappa};
for (i = 0; i < num_states; i++) {
double *this_rate = &rates[i*num_states];
int *this_rate_attr = &rate_attr[i*num_states];
if (phylo_tree->aln->isStopCodon(i)) {
continue;
}
for (j = 0; j < num_states; j++) {
int attr = this_rate_attr[j];
if (this_rate[j] == 0.0) continue;
if (attr & CA_SYNONYMOUS) { // synonymous
int num = ((attr & CA_TRANSVERSION_1NT) != 0) + ((attr & CA_TRANSVERSION_2NT) != 0) + ((attr & CA_TRANSVERSION_3NT) != 0);
this_rate[j] *= kappa_pow[num];
} else if (attr & CA_NONSYNONYMOUS) { // non-synomyous
int num = ((attr & CA_TRANSVERSION_1NT) != 0) + ((attr & CA_TRANSVERSION_2NT) != 0) + ((attr & CA_TRANSVERSION_3NT) != 0);
this_rate[j] *= omega_kappa_pow[num];
}
}
}
}
void ModelCodon::computeCodonRateMatrix_2KAPPA() {
int nrates = getNumRateEntries();
memcpy(rates, empirical_rates, nrates*sizeof(double));
int i, j;
double kappa_pow[] = {1.0, kappa, kappa*kappa, kappa*kappa*kappa};
double omega_kappa_pow[] = {omega, omega*kappa, omega*kappa*kappa, omega*kappa*kappa*kappa};
double kappa2_pow[] = {1.0, kappa2, kappa2*kappa2, kappa2*kappa2*kappa2};
for (i = 0; i < num_states; i++) {
double *this_rate = &rates[i*num_states];
int *this_rate_attr = &rate_attr[i*num_states];
if (phylo_tree->aln->isStopCodon(i)) {
continue;
}
for (j = 0; j < num_states; j++) {
int attr = this_rate_attr[j];
if (this_rate[j] == 0.0) continue;
if (attr & CA_SYNONYMOUS) { // synonymous
int numts = ((attr & CA_TRANSITION_1NT) != 0) + ((attr & CA_TRANSITION_2NT) != 0) + ((attr & CA_TRANSITION_3NT) != 0);
int numtv = ((attr & CA_TRANSVERSION_1NT) != 0) + ((attr & CA_TRANSVERSION_2NT) != 0) + ((attr & CA_TRANSVERSION_3NT) != 0);
this_rate[j] *= kappa_pow[numts]*kappa2_pow[numtv];
} else if (attr & CA_NONSYNONYMOUS) { // non-synomyous
int numts = ((attr & CA_TRANSITION_1NT) != 0) + ((attr & CA_TRANSITION_2NT) != 0) + ((attr & CA_TRANSITION_3NT) != 0);
int numtv = ((attr & CA_TRANSVERSION_1NT) != 0) + ((attr & CA_TRANSVERSION_2NT) != 0) + ((attr & CA_TRANSVERSION_3NT) != 0);
this_rate[j] *= omega_kappa_pow[numts]*kappa2_pow[numtv];
}
}
}
}
double ModelCodon::computeEmpiricalOmega() {
double dn = 0.0, ds = 0.0;
int i, j;
if (ignore_state_freq) {
for (i = 0; i < num_states; i++) {
if (phylo_tree->aln->isStopCodon(i))
continue;
double *this_rate = &rates[i*num_states];
int *this_rate_attr = &rate_attr[i*num_states];
for (j = 0; j < num_states; j++)
if (this_rate_attr[j] & CA_NONSYNONYMOUS)
dn += state_freq[i]*this_rate[j];
else
ds += state_freq[i]*this_rate[j];
}
} else {
for (i = 0; i < num_states; i++) {
if (phylo_tree->aln->isStopCodon(i))
continue;
double *this_rate = &rates[i*num_states];
int *this_rate_attr = &rate_attr[i*num_states];
for (j = 0; j < num_states; j++)
if (this_rate_attr[j] & CA_NONSYNONYMOUS)
dn += state_freq[i]*state_freq[j]*this_rate[j];
else
ds += state_freq[i]*state_freq[j]*this_rate[j];
}
}
return (dn/ds)*(0.21/0.79);
}
bool ModelCodon::getVariables(double *variables) {
int j;
bool changed = false;
if (num_params > 0) {
j = 1;
if (!fix_omega) {
changed |= (omega != variables[j]);
omega = variables[j++];
}
if (!fix_kappa) {
changed |= (kappa != variables[j]);
kappa = variables[j++];
}
if (!fix_kappa2) {
changed |= (kappa2 != variables[j]);
kappa2 = variables[j++];
}
ASSERT(j == num_params+1);
}
if (freq_type == FREQ_ESTIMATE) {
// 2015-09-07: relax the sum of state_freq to be 1, this will be done at the end of optimization
int ndim = getNDim();
changed |= memcmpcpy(state_freq, variables+(ndim-num_states+2), (num_states-1)*sizeof(double));
// double sum = 0;
// for (i = 0; i < num_states-1; i++)
// sum += state_freq[i];
// state_freq[num_states-1] = 1.0 - sum;
// BUG FIX 2015.08.28
// int nrate = getNDim();
// if (freq_type == FREQ_ESTIMATE) nrate -= (num_states-1);
// double sum = 1.0;
//// int i, j;
// for (i = 1; i < num_states; i++)
// sum += variables[nrate+i];
// for (i = 0, j = 1; i < num_states; i++)
// if (i != highest_freq_state) {
// state_freq[i] = variables[nrate+j] / sum;
// j++;
// }
// state_freq[highest_freq_state] = 1.0/sum;
}
return changed;
}
void ModelCodon::setVariables(double *variables) {
int j;
if (num_params > 0) {
j = 1;
if (!fix_omega)
variables[j++] = omega;
if (!fix_kappa)
variables[j++] = kappa;
if (!fix_kappa2)
variables[j++] = kappa2;
ASSERT(j == num_params+1);
}
if (freq_type == FREQ_ESTIMATE) {
// 2015-09-07: relax the sum of state_freq to be 1, this will be done at the end of optimization
int ndim = getNDim();
memcpy(variables+(ndim-num_states+2), state_freq, (num_states-1)*sizeof(double));
// BUG FIX 2015.08.28
// int nrate = getNDim();
// if (freq_type == FREQ_ESTIMATE) nrate -= (num_states-1);
// int i, j;
// for (i = 0, j = 1; i < num_states; i++)
// if (i != highest_freq_state) {
// variables[nrate+j] = state_freq[i] / state_freq[highest_freq_state];
// j++;
// }
}
}
void ModelCodon::setBounds(double *lower_bound, double *upper_bound, bool *bound_check) {
int i, ndim = getNDim();
for (i = 1; i <= ndim; i++) {
//cout << variables[i] << endl;
lower_bound[i] = MIN_OMEGA_KAPPA;
upper_bound[i] = MAX_OMEGA_KAPPA;
bound_check[i] = false;
}
if (freq_type == FREQ_ESTIMATE) {
for (i = ndim-num_states+2; i <= ndim; i++) {
// lower_bound[i] = MIN_FREQUENCY/state_freq[highest_freq_state];
// upper_bound[i] = state_freq[highest_freq_state]/MIN_FREQUENCY;
lower_bound[i] = MIN_FREQUENCY;
// upper_bound[i] = 100.0;
upper_bound[i] = 1.0;
bound_check[i] = false;
}
}
}
double ModelCodon::optimizeParameters(double gradient_epsilon) {
int ndim = getNDim();
// return if nothing to be optimized
if (ndim == 0) return 0.0;
if (verbose_mode >= VB_MAX)
cout << "Optimizing " << name << " model parameters..." << endl;
double *variables = new double[ndim+1];
double *upper_bound = new double[ndim+1];
double *lower_bound = new double[ndim+1];
bool *bound_check = new bool[ndim+1];
double score;
for (int i = 0; i < num_states; i++)
if (state_freq[i] > state_freq[highest_freq_state])
highest_freq_state = i;
// by BFGS algorithm
setVariables(variables);
setBounds(lower_bound, upper_bound, bound_check);
if (phylo_tree->params->optimize_alg.find("BFGS-B") == string::npos)
score = -minimizeMultiDimen(variables, ndim, lower_bound, upper_bound, bound_check, max(gradient_epsilon, TOL_RATE));
else
score = -L_BFGS_B(ndim, variables+1, lower_bound+1, upper_bound+1, max(gradient_epsilon, TOL_RATE));
bool changed = getVariables(variables);
// BQM 2015-09-07: normalize state_freq
if (freq_type == FREQ_ESTIMATE) {
scaleStateFreq(true);
changed = true;
}
if (changed) {
decomposeRateMatrix();
phylo_tree->clearAllPartialLH();
score = phylo_tree->computeLikelihood();
}
delete [] bound_check;
delete [] lower_bound;
delete [] upper_bound;
delete [] variables;
return score;
}
void ModelCodon::writeInfo(ostream &out) {
if (name.find('_') == string::npos)
out << "Nonsynonymous/synonymous ratio (omega): " << omega << endl;
else
out << "Empirical nonsynonymous/synonymous ratio (omega_E): " << computeEmpiricalOmega() << endl;
out << "Transition/transversion ratio (kappa): " << kappa << endl;
if (codon_kappa_style == CK_TWO_KAPPA)
out << "Transition/transversion ratio 2 (kappa2): " << kappa2 << endl;
}
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