| 1 | /* |
|---|
| 2 | * seqstat.c Adachi, J. 1995.03.18 |
|---|
| 3 | * Copyright (C) 1993-1995 J. Adachi & M. Hasegawa, All rights reserved. |
|---|
| 4 | */ |
|---|
| 5 | |
|---|
| 6 | #define STGRAPH 0 |
|---|
| 7 | #define RRTEST 0 |
|---|
| 8 | #define RRTESTNUM 1000 /* 100000 */ |
|---|
| 9 | |
|---|
| 10 | #include "protst.h" |
|---|
| 11 | |
|---|
| 12 | |
|---|
| 13 | void |
|---|
| 14 | seqinsdel(seqchar, numspc, numsite, insdel, numnoinsdel) |
|---|
| 15 | cmatrix seqchar; |
|---|
| 16 | int numspc, numsite; |
|---|
| 17 | ivector insdel; |
|---|
| 18 | int *numnoinsdel; |
|---|
| 19 | { |
|---|
| 20 | int i, k, ninsdel; |
|---|
| 21 | |
|---|
| 22 | ninsdel = 0; |
|---|
| 23 | for (k = 0; k < numsite; k++) { |
|---|
| 24 | insdel[k] = FALSE; |
|---|
| 25 | for (i = 0; i < numspc; i++) { |
|---|
| 26 | if (seqchar[i][k] == Tpmradix) { |
|---|
| 27 | insdel[k] = TRUE; |
|---|
| 28 | ninsdel++; |
|---|
| 29 | break; |
|---|
| 30 | } |
|---|
| 31 | } |
|---|
| 32 | } |
|---|
| 33 | *numnoinsdel = numsite - ninsdel; |
|---|
| 34 | } /* seqinsdel */ |
|---|
| 35 | |
|---|
| 36 | |
|---|
| 37 | #if RRTEST |
|---|
| 38 | void |
|---|
| 39 | rrtest(seqchar, numspc, numsite, insdel, numnoinsdel) |
|---|
| 40 | cmatrix seqchar; |
|---|
| 41 | int numspc, numsite; |
|---|
| 42 | ivector insdel; |
|---|
| 43 | int numnoinsdel; |
|---|
| 44 | { |
|---|
| 45 | int i, j, k, dif, nsite, nsp1, comdiff; |
|---|
| 46 | double coefrand; |
|---|
| 47 | cvector seqchi, seqchj; |
|---|
| 48 | ivector diff; |
|---|
| 49 | imatrix hist; |
|---|
| 50 | |
|---|
| 51 | nsp1 = numspc - 1; |
|---|
| 52 | coefrand = (double)numsite / ((double)RANDOM_MAX + 1.0); |
|---|
| 53 | diff = new_ivector(numspc); |
|---|
| 54 | hist = new_imatrix(numspc, numsite); |
|---|
| 55 | for (i = 0; i < numspc; i++) { |
|---|
| 56 | for (j = 0; j < numsite; j++) hist[i][j] = 0; |
|---|
| 57 | } |
|---|
| 58 | seqchi = seqchar[numspc - 1]; |
|---|
| 59 | |
|---|
| 60 | /* putchar('\n'); */ |
|---|
| 61 | for (i = 0; i < RRTESTNUM; i++) { |
|---|
| 62 | for (j = 0; j < nsp1; j++) { |
|---|
| 63 | seqchj = seqchar[j]; |
|---|
| 64 | for (k = 0, dif = 0; k < numsite; k++) { |
|---|
| 65 | nsite = (int)( coefrand * (double)rand() ); /* RANDOM */ |
|---|
| 66 | if (!insdel[nsite]) { |
|---|
| 67 | if (seqchi[nsite] != seqchj[nsite]) dif++; |
|---|
| 68 | } |
|---|
| 69 | } |
|---|
| 70 | diff[j] = dif; |
|---|
| 71 | hist[j][dif]++; |
|---|
| 72 | } |
|---|
| 73 | diff[numspc - 1] = 0; |
|---|
| 74 | /* |
|---|
| 75 | printf("%5d", i+1); |
|---|
| 76 | for (j = 0; j < nsp1; j++) printf(" %4d",diff[j]); putchar('\n'); |
|---|
| 77 | */ |
|---|
| 78 | } |
|---|
| 79 | |
|---|
| 80 | putchar('\n'); |
|---|
| 81 | for (i = 0; i < nsp1 - 1; i++) { |
|---|
| 82 | for (j = i + 1; j < nsp1; j++) { |
|---|
| 83 | comdiff = 0; |
|---|
| 84 | for (k = 0; k < numsite; k++) { |
|---|
| 85 | if (hist[i][k] <= hist[j][k]) { |
|---|
| 86 | dif = hist[i][k]; |
|---|
| 87 | } else { |
|---|
| 88 | dif = hist[j][k]; |
|---|
| 89 | } |
|---|
| 90 | comdiff += dif; |
|---|
| 91 | } |
|---|
| 92 | printf("%3d %3d %8d %9.5f\n", |
|---|
| 93 | i+1, j+1, comdiff, (double)comdiff/RRTESTNUM); |
|---|
| 94 | } |
|---|
| 95 | } |
|---|
| 96 | |
|---|
| 97 | printf("\n%5s", "diff"); |
|---|
| 98 | for (i = 0; i < nsp1; i++) printf(" %4d",i+1); putchar('\n'); |
|---|
| 99 | for (j = 0; j < numsite; j++) { |
|---|
| 100 | printf("%5d", j); |
|---|
| 101 | for (i = 0; i < nsp1; i++) printf(" %4d",hist[i][j]); putchar('\n'); |
|---|
| 102 | } |
|---|
| 103 | |
|---|
| 104 | free_ivector(diff); |
|---|
| 105 | free_imatrix(hist); |
|---|
| 106 | exit(1); |
|---|
| 107 | } /* rrtest */ |
|---|
| 108 | #endif /*RRTEST*/ |
|---|
| 109 | |
|---|
| 110 | |
|---|
| 111 | void |
|---|
| 112 | seqdiff(seqchar, numspc, numsite, insdel, numnoinsdel) |
|---|
| 113 | cmatrix seqchar; |
|---|
| 114 | int numspc, numsite; |
|---|
| 115 | ivector insdel; |
|---|
| 116 | int numnoinsdel; |
|---|
| 117 | { |
|---|
| 118 | int i, j, k, x, y, z, dif1, dif2, maxk, numk; |
|---|
| 119 | cvector seqchi, seqchj; |
|---|
| 120 | imatrix diff; |
|---|
| 121 | #if STGRAPH |
|---|
| 122 | double v, s, vsd2, ssd2; |
|---|
| 123 | #endif |
|---|
| 124 | |
|---|
| 125 | diff = new_imatrix(numspc, numspc); |
|---|
| 126 | for (i = 0; i < numspc-1; i++) { |
|---|
| 127 | seqchi = seqchar[i]; |
|---|
| 128 | for (j = i+1; j < numspc; j++) { |
|---|
| 129 | seqchj = seqchar[j]; |
|---|
| 130 | /* for (k=0;k<numsite;k++) printf("%2d",seqchj[k]); putchar('\n'); */ |
|---|
| 131 | for (k = 0, dif1 = 0, dif2 = 0; k < numsite; k++) { |
|---|
| 132 | if (!insdel[k]) { |
|---|
| 133 | if ((x = seqchi[k]) != (y = seqchj[k])) { |
|---|
| 134 | #ifndef NUC |
|---|
| 135 | dif1++; |
|---|
| 136 | #else |
|---|
| 137 | z = x + y; |
|---|
| 138 | if ((z == 1) || (z == 5)) |
|---|
| 139 | dif1++; |
|---|
| 140 | else |
|---|
| 141 | dif2++; |
|---|
| 142 | #endif /* NUC */ |
|---|
| 143 | } |
|---|
| 144 | } |
|---|
| 145 | } |
|---|
| 146 | #ifndef NUC |
|---|
| 147 | diff[i][j] = dif1; |
|---|
| 148 | diff[j][i] = dif1; |
|---|
| 149 | #else |
|---|
| 150 | diff[i][j] = dif1; |
|---|
| 151 | diff[j][i] = dif2; |
|---|
| 152 | #endif /* NUC */ |
|---|
| 153 | } |
|---|
| 154 | diff[i][i] = 0; |
|---|
| 155 | } |
|---|
| 156 | diff[numspc-1][numspc-1] = 0; |
|---|
| 157 | |
|---|
| 158 | if (!Align_optn) { |
|---|
| 159 | if (numnoinsdel != numsite) |
|---|
| 160 | printf("\nexcluding ins/del sites: %d\n", numnoinsdel); |
|---|
| 161 | numk = Maxelement; |
|---|
| 162 | for (k = 0; maxk = k + numk, k < numspc; k += numk) { |
|---|
| 163 | if (maxk > numspc) maxk = numspc; |
|---|
| 164 | if (Tpmradix == NUMAMI) |
|---|
| 165 | printf("\n%4s%6s", "Diff",""); |
|---|
| 166 | else |
|---|
| 167 | printf("\n%4s%-6s", " ","Ts"); |
|---|
| 168 | for (j = k; j < maxk; j++) printf("%4d", j + 1); |
|---|
| 169 | putchar('\n'); |
|---|
| 170 | if (Tpmradix == NUMAMI) |
|---|
| 171 | printf("%4s%6s", "",""); |
|---|
| 172 | else |
|---|
| 173 | printf("%-4s%6s", "Tv",""); |
|---|
| 174 | for (j = k; j < maxk; j++) printf("%4.3s", Identif[j]); |
|---|
| 175 | putchar('\n'); |
|---|
| 176 | for (i = 0; i < numspc; i++) { |
|---|
| 177 | printf("%-4d%-6.6s", i + 1, Identif[i]); |
|---|
| 178 | for (j = k; j < maxk; j++) { |
|---|
| 179 | if (i != j) |
|---|
| 180 | printf("%4d", diff[i][j]); |
|---|
| 181 | else |
|---|
| 182 | printf("%4.3s", Identif[i]); |
|---|
| 183 | } |
|---|
| 184 | putchar('\n'); |
|---|
| 185 | } |
|---|
| 186 | } |
|---|
| 187 | } /* Align_optn */ |
|---|
| 188 | |
|---|
| 189 | #if STGRAPH |
|---|
| 190 | putchar('\n'); |
|---|
| 191 | for (i = 0; i < numspc - 1; i++) { |
|---|
| 192 | for (j = i + 1; j < numspc; j++) { |
|---|
| 193 | v = (double)diff[j][i]; |
|---|
| 194 | s = (double)diff[i][j]; |
|---|
| 195 | vsd2 = 2 * sqrt(v * (1 - v/numsite)) / numsite; |
|---|
| 196 | ssd2 = 2 * sqrt(s * (1 - s/numsite)) / numsite; |
|---|
| 197 | printf("%9.5f%9.5f%9.5f%9.5f%9.5f%9.5f\n", |
|---|
| 198 | v/numsite, v/numsite - vsd2, v/numsite + vsd2, |
|---|
| 199 | s/numsite, s/numsite - ssd2, s/numsite + ssd2); |
|---|
| 200 | } |
|---|
| 201 | } |
|---|
| 202 | #endif /* STGRAPH */ |
|---|
| 203 | |
|---|
| 204 | free_imatrix(diff); |
|---|
| 205 | |
|---|
| 206 | #if RRTEST |
|---|
| 207 | rrtest(seqchar, numspc, numsite, insdel, numnoinsdel); |
|---|
| 208 | #endif /* RRTEST */ |
|---|
| 209 | |
|---|
| 210 | } /* seqdiff */ |
|---|
| 211 | |
|---|
| 212 | |
|---|
| 213 | void |
|---|
| 214 | seqfreq(seqchar, numspc, numsite, insdel, numnoinsdel) |
|---|
| 215 | cmatrix seqchar; |
|---|
| 216 | int numspc, numsite; |
|---|
| 217 | ivector insdel; |
|---|
| 218 | int numnoinsdel; |
|---|
| 219 | { |
|---|
| 220 | int i, j, k, l, numfreq, numk, maxk; |
|---|
| 221 | double temp, bias, skew, nid1, nid2; |
|---|
| 222 | cvector seqchi; |
|---|
| 223 | imatrix freqs; |
|---|
| 224 | ivector freq; |
|---|
| 225 | ivector freqall; |
|---|
| 226 | |
|---|
| 227 | nid1 = 1.0 / numnoinsdel; |
|---|
| 228 | nid2 = 1.0 / (numnoinsdel * numnoinsdel); |
|---|
| 229 | freqs = new_imatrix(numspc, Tpmradix + 1); |
|---|
| 230 | freqall = new_ivector(Tpmradix + 1); |
|---|
| 231 | for (j = 0; j < Tpmradix + 1; j++) freqall[j] = 0; |
|---|
| 232 | for (i = 0; i < numspc; i++) { |
|---|
| 233 | seqchi = seqchar[i]; |
|---|
| 234 | freq = freqs[i]; |
|---|
| 235 | for (j = 0; j < Tpmradix + 1; j++) freq[j] = 0; |
|---|
| 236 | for (k = 0; k < numsite; k++) { |
|---|
| 237 | if (!insdel[k]) |
|---|
| 238 | freq[seqchi[k]]++; |
|---|
| 239 | } |
|---|
| 240 | for (j = 0; j < Tpmradix + 1; j++) freqall[j] += freq[j]; |
|---|
| 241 | } |
|---|
| 242 | |
|---|
| 243 | if (Tpmradix == NUMAMI) |
|---|
| 244 | numfreq = NUMAMI / 2; |
|---|
| 245 | else |
|---|
| 246 | numfreq = NUMNUC; |
|---|
| 247 | |
|---|
| 248 | if (!Align_optn) { |
|---|
| 249 | printf("\n%-10s", ""); /* Frequencies, Composition */ |
|---|
| 250 | if (Tpmradix == NUMAMI) { |
|---|
| 251 | for (j = 0; j < numfreq; j++) |
|---|
| 252 | printf("%3s%4s", Cacid1[j], Cacid3[j]); |
|---|
| 253 | } else { |
|---|
| 254 | for (j = 0; j < numfreq; j++) printf("%5s%2s", Cacid1[j], " "); |
|---|
| 255 | printf("%7.4s%7.4s%7.4s%7.4s", "A+T ", "G+C ", "Bias", "Skew"); |
|---|
| 256 | } |
|---|
| 257 | putchar('\n'); |
|---|
| 258 | for (i = 0; i < numspc; i++) { |
|---|
| 259 | freq = freqs[i]; |
|---|
| 260 | printf("%-4d%-6.6s", i + 1, Identif[i]); |
|---|
| 261 | for (j = 0; j < numfreq ; j++) { |
|---|
| 262 | if (freq[j] != 0) |
|---|
| 263 | printf("%7.3f", (double)freq[j] / numnoinsdel); |
|---|
| 264 | else |
|---|
| 265 | printf("%5.1f ", (double)freq[j] / numnoinsdel); |
|---|
| 266 | } |
|---|
| 267 | if (Tpmradix == NUMNUC) { |
|---|
| 268 | printf("%7.3f", (double)(freq[0]+freq[2]) / numnoinsdel); |
|---|
| 269 | printf("%7.3f", (double)(freq[1]+freq[3]) / numnoinsdel); |
|---|
| 270 | for (l = 0, bias = 0.0; l < Tpmradix; l++) { |
|---|
| 271 | temp = (freq[l] * nid1 - 0.25); |
|---|
| 272 | bias += temp * temp; |
|---|
| 273 | } |
|---|
| 274 | bias = bias * 4 / 3; |
|---|
| 275 | printf("%7.3f", bias); |
|---|
| 276 | skew = fabs(freq[0] - freq[2]) + fabs(freq[1] - freq[3]); |
|---|
| 277 | skew /= numnoinsdel; |
|---|
| 278 | printf("%7.3f", skew); |
|---|
| 279 | } |
|---|
| 280 | putchar('\n'); |
|---|
| 281 | } |
|---|
| 282 | printf("%4s%-6s", " ", "mean"); |
|---|
| 283 | for (j = 0; j < numfreq ; j++) { |
|---|
| 284 | if (freqall[j] != 0) |
|---|
| 285 | printf("%7.3f", (double)freqall[j] / (numspc * numnoinsdel)); |
|---|
| 286 | else |
|---|
| 287 | printf("%5.1f ", (double)freqall[j] / (numspc * numnoinsdel)); |
|---|
| 288 | } |
|---|
| 289 | if (Tpmradix == NUMNUC) { |
|---|
| 290 | printf("%7.3f", |
|---|
| 291 | (double)(freqall[0]+freqall[2])/(numspc*numnoinsdel)); |
|---|
| 292 | printf("%7.3f", |
|---|
| 293 | (double)(freqall[1]+freqall[3])/(numspc*numnoinsdel)); |
|---|
| 294 | for (l = 0, bias = 0.0; l < Tpmradix; l++) { |
|---|
| 295 | temp = (freqall[l] * nid1 / numspc - 0.25); |
|---|
| 296 | bias += temp * temp; |
|---|
| 297 | } |
|---|
| 298 | bias = bias * 4 / 3; |
|---|
| 299 | printf("%7.3f", bias); |
|---|
| 300 | skew = fabs(freqall[0] - freqall[2]) |
|---|
| 301 | + fabs(freqall[1] - freqall[3]); |
|---|
| 302 | skew /= (numspc * numnoinsdel); |
|---|
| 303 | printf("%7.3f", skew); |
|---|
| 304 | } |
|---|
| 305 | putchar('\n'); |
|---|
| 306 | |
|---|
| 307 | if (Tpmradix == NUMAMI) { |
|---|
| 308 | printf("\n%-10s", ""); /* Frequencies, Composition */ |
|---|
| 309 | if (Tpmradix == NUMAMI) { |
|---|
| 310 | for (j = numfreq; j < Tpmradix; j++) |
|---|
| 311 | printf("%3s%4s", Cacid1[j], Cacid3[j]); |
|---|
| 312 | } else { |
|---|
| 313 | for (j = numfreq; j < Tpmradix; j++) |
|---|
| 314 | printf("%5s%2s", Cacid1[j], " "); |
|---|
| 315 | } |
|---|
| 316 | putchar('\n'); |
|---|
| 317 | for (i = 0; i < numspc; i++) { |
|---|
| 318 | freq = freqs[i]; |
|---|
| 319 | printf("%-4d%-6.6s", i + 1, Identif[i]); |
|---|
| 320 | for (j = numfreq; j < Tpmradix ; j++) { |
|---|
| 321 | if (freq[j] != 0) |
|---|
| 322 | printf("%7.3f", (double)freq[j] / numnoinsdel); |
|---|
| 323 | else |
|---|
| 324 | printf("%5.1f ", (double)freq[j] / numnoinsdel); |
|---|
| 325 | } |
|---|
| 326 | putchar('\n'); |
|---|
| 327 | } |
|---|
| 328 | printf("%4s%-6s", " ", "mean"); |
|---|
| 329 | for (j = numfreq; j < Tpmradix ; j++) { |
|---|
| 330 | if (freqall[j] != 0) |
|---|
| 331 | printf("%7.3f", (double)freqall[j] / (numspc * numnoinsdel)); |
|---|
| 332 | else |
|---|
| 333 | printf("%5.1f ", (double)freqall[j] / (numspc * numnoinsdel)); |
|---|
| 334 | } putchar('\n'); |
|---|
| 335 | } |
|---|
| 336 | } /* Align_optn */ |
|---|
| 337 | |
|---|
| 338 | if (!Align_optn) { |
|---|
| 339 | if (Maxspc > 28) putchar('\f'); |
|---|
| 340 | numk = Maxelement; |
|---|
| 341 | for (k = 0; maxk = k + numk, k < numspc; k += numk) { |
|---|
| 342 | if (maxk > numspc) maxk = numspc; |
|---|
| 343 | #if 0 |
|---|
| 344 | printf("\n%4s%6s", "Bias"," x1e5"); |
|---|
| 345 | #else |
|---|
| 346 | printf("\n%4s%6s", "Bias"," x1e3"); |
|---|
| 347 | #endif |
|---|
| 348 | for (j = k; j < maxk; j++) printf("%4d", j + 1); putchar('\n'); |
|---|
| 349 | printf("%4s%6s", "",""); |
|---|
| 350 | for (j = k; j < maxk; j++) printf("%4.3s", Identif[j]); |
|---|
| 351 | putchar('\n'); |
|---|
| 352 | for (i = 0; i < numspc; i++) { |
|---|
| 353 | printf("%-4d%-6.6s", i + 1, Identif[i]); |
|---|
| 354 | for (j = k; j < maxk; j++) { |
|---|
| 355 | if (i != j) { |
|---|
| 356 | #if 0 |
|---|
| 357 | for (l = 0, bias = 0.0; l < Tpmradix; l++) { |
|---|
| 358 | temp = (freqs[i][l] - freqs[j][l]); |
|---|
| 359 | bias += temp * temp; |
|---|
| 360 | } |
|---|
| 361 | bias = bias * nid2 * 0.5; |
|---|
| 362 | printf("%4.0f", bias * 100000); |
|---|
| 363 | #else |
|---|
| 364 | for (l = 0, bias = 0.0; l < Tpmradix; l++) { |
|---|
| 365 | bias += abs(freqs[i][l] - freqs[j][l]); |
|---|
| 366 | } |
|---|
| 367 | bias = bias * 0.5 / numnoinsdel; |
|---|
| 368 | printf("%4.0f", bias * 1000); |
|---|
| 369 | #endif |
|---|
| 370 | } else { |
|---|
| 371 | printf("%4.3s", Identif[i]); |
|---|
| 372 | } |
|---|
| 373 | } |
|---|
| 374 | putchar('\n'); |
|---|
| 375 | } |
|---|
| 376 | } |
|---|
| 377 | #if 0 |
|---|
| 378 | printf("\n%d\n", numspc); |
|---|
| 379 | for (i = 0; i < numspc; i++) { |
|---|
| 380 | printf("%s\n", Identif[i]); |
|---|
| 381 | for (j = 0; j < numspc; j++) { |
|---|
| 382 | for (l = 0, bias = 0.0; l < Tpmradix; l++) { |
|---|
| 383 | temp = (freqs[i][l] - freqs[j][l]); |
|---|
| 384 | bias += temp * temp; |
|---|
| 385 | } |
|---|
| 386 | bias = bias * nid2 * 0.5; |
|---|
| 387 | printf(" %7.3f", bias * 100000); |
|---|
| 388 | } |
|---|
| 389 | putchar('\n'); |
|---|
| 390 | } |
|---|
| 391 | #endif |
|---|
| 392 | } /* Align_optn */ |
|---|
| 393 | |
|---|
| 394 | free_ivector(freqall); |
|---|
| 395 | free_imatrix(freqs); |
|---|
| 396 | } /* seqfreq */ |
|---|
| 397 | |
|---|
| 398 | |
|---|
| 399 | void |
|---|
| 400 | seqtran(seqchar, numspc, numsite, insdel, numnoinsdel) |
|---|
| 401 | cmatrix seqchar; |
|---|
| 402 | int numspc, numsite; |
|---|
| 403 | ivector insdel; |
|---|
| 404 | int numnoinsdel; |
|---|
| 405 | { |
|---|
| 406 | int i, j, k, numradix, ii, jj; |
|---|
| 407 | cvector seqchi, seqchj; |
|---|
| 408 | imatrix trans; |
|---|
| 409 | ivector tranall; |
|---|
| 410 | |
|---|
| 411 | trans = new_imatrix(Tpmradix + 1, Tpmradix + 1); |
|---|
| 412 | tranall = new_ivector(Tpmradix + 1); |
|---|
| 413 | for (i = 0; i < Tpmradix + 1; i++) { |
|---|
| 414 | for (j = 0; j < Tpmradix + 1; j++) trans[i][j] = 0; |
|---|
| 415 | tranall[j] = 0; |
|---|
| 416 | } |
|---|
| 417 | for (i = 0; i < numspc - 1; i++) { |
|---|
| 418 | seqchi = seqchar[i]; |
|---|
| 419 | for (j = i + 1; j < numspc; j++) { |
|---|
| 420 | seqchj = seqchar[j]; |
|---|
| 421 | for (k = 0; k < numsite; k++) { |
|---|
| 422 | if (!insdel[k]) { |
|---|
| 423 | trans[seqchi[k]][seqchj[k]]++; |
|---|
| 424 | trans[seqchj[k]][seqchi[k]]++; |
|---|
| 425 | } |
|---|
| 426 | } |
|---|
| 427 | } |
|---|
| 428 | } |
|---|
| 429 | |
|---|
| 430 | if (Tpmradix == NUMAMI) |
|---|
| 431 | numradix = NUMAMI / 2; |
|---|
| 432 | else |
|---|
| 433 | numradix = NUMNUC; |
|---|
| 434 | |
|---|
| 435 | printf("\n%7s", " "); |
|---|
| 436 | if (Tpmradix == NUMAMI) { |
|---|
| 437 | for (j = 0; j < numradix; j++) printf("%3s%4s", Cacid1[j], Cacid3[j]); |
|---|
| 438 | } else { |
|---|
| 439 | for (j = 0; j < numradix; j++) printf("%5s%2s", Cacid1[j], " "); |
|---|
| 440 | } |
|---|
| 441 | putchar('\n'); |
|---|
| 442 | for (i = 0; i < Tpmradix; i++) { |
|---|
| 443 | if (Tpmradix == NUMAMI) { |
|---|
| 444 | printf("%3s%4s", Cacid1[i], Cacid3[i]); |
|---|
| 445 | } else { |
|---|
| 446 | printf("%5s%2s", Cacid1[i], " "); |
|---|
| 447 | } |
|---|
| 448 | for (j = 0; j < numradix ; j++) { |
|---|
| 449 | printf("%7d", trans[i][j]); |
|---|
| 450 | } |
|---|
| 451 | putchar('\n'); |
|---|
| 452 | } |
|---|
| 453 | |
|---|
| 454 | if (Tpmradix == NUMAMI) { |
|---|
| 455 | printf("\n%7s", " "); |
|---|
| 456 | if (Tpmradix == NUMAMI) { |
|---|
| 457 | for (j = numradix; j < Tpmradix; j++) |
|---|
| 458 | printf("%3s%4s", Cacid1[j], Cacid3[j]); |
|---|
| 459 | } else { |
|---|
| 460 | for (j = numradix; j < Tpmradix; j++) |
|---|
| 461 | printf("%5s%2s", Cacid1[j], " "); |
|---|
| 462 | } |
|---|
| 463 | putchar('\n'); |
|---|
| 464 | for (i = 0; i < Tpmradix; i++) { |
|---|
| 465 | if (Tpmradix == NUMAMI) { |
|---|
| 466 | printf("%3s%4s", Cacid1[i], Cacid3[i]); |
|---|
| 467 | } else { |
|---|
| 468 | printf("%5s%2s", Cacid1[i], " "); |
|---|
| 469 | } |
|---|
| 470 | for (j = numradix; j < Tpmradix ; j++) { |
|---|
| 471 | printf("%7d", trans[i][j]); |
|---|
| 472 | } |
|---|
| 473 | putchar('\n'); |
|---|
| 474 | } |
|---|
| 475 | } |
|---|
| 476 | |
|---|
| 477 | #if 0 |
|---|
| 478 | for (i = 0; i < numspc - 1; i++) { |
|---|
| 479 | seqchi = seqchar[i]; |
|---|
| 480 | for (j = i + 1; j < numspc; j++) { |
|---|
| 481 | seqchj = seqchar[j]; |
|---|
| 482 | for (ii = 0; ii < Tpmradix + 1; ii++) { |
|---|
| 483 | for (jj = 0; jj < Tpmradix + 1; jj++) trans[ii][jj] = 0; |
|---|
| 484 | } |
|---|
| 485 | for (k = 0; k < numsite; k++) { |
|---|
| 486 | if (!insdel[k]) { |
|---|
| 487 | trans[seqchi[k]][seqchj[k]]++; |
|---|
| 488 | trans[seqchj[k]][seqchi[k]]++; |
|---|
| 489 | } |
|---|
| 490 | } |
|---|
| 491 | |
|---|
| 492 | printf("\n%-3d %-3d %s %s\n", i+1, j+1, Identif[i], Identif[j]); |
|---|
| 493 | for (jj = 0; jj < Tpmradix; jj++) printf("%4s", Cacid1[jj]); |
|---|
| 494 | putchar('\n'); |
|---|
| 495 | for (ii = 0; ii < Tpmradix; ii++) { |
|---|
| 496 | printf("%1s", Cacid1[ii]); |
|---|
| 497 | printf("%3d", trans[ii][0]); |
|---|
| 498 | for (jj = 1; jj < Tpmradix ; jj++) { |
|---|
| 499 | printf("%4d", trans[ii][jj]); |
|---|
| 500 | } |
|---|
| 501 | putchar('\n'); |
|---|
| 502 | } |
|---|
| 503 | |
|---|
| 504 | } |
|---|
| 505 | } |
|---|
| 506 | #endif |
|---|
| 507 | |
|---|
| 508 | free_ivector(tranall); |
|---|
| 509 | free_imatrix(trans); |
|---|
| 510 | } /* seqtran */ |
|---|
