msa
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@102253 bc3139a8-67e5-0310-9ffc-ced21a209358
Sonali Arora authored on 10/04/2015 00:12:33 | 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,480 @@ |
| 1 |
+/********************************************************************* |
|
| 2 |
+ * Clustal Omage - Multiple sequence alignment |
|
| 3 |
+ * |
|
| 4 |
+ * Copyright (C) 2010 University College Dublin |
|
| 5 |
+ * |
|
| 6 |
+ * Clustal-Omega is free software; you can redistribute it and/or |
|
| 7 |
+ * modify it under the terms of the GNU General Public License as |
|
| 8 |
+ * published by the Free Software Foundation; either version 2 of the |
|
| 9 |
+ * License, or (at your option) any later version. |
|
| 10 |
+ * |
|
| 11 |
+ * This file is part of Clustal-Omega. |
|
| 12 |
+ * |
|
| 13 |
+ ********************************************************************/ |
|
| 14 |
+ |
|
| 15 |
+/* |
|
| 16 |
+ * RCS $Id: main.cpp 234 2011-04-13 05:26:16Z andreas $ |
|
| 17 |
+ */ |
|
| 18 |
+ |
|
| 19 |
+/* |
|
| 20 |
+ * We are using a mix of C and C++, which means that linking has to be |
|
| 21 |
+ * done with a C++ compiler. By using this "fake" main c++ function, |
|
| 22 |
+ * automake is convinced to use a C++ compiler for linking. |
|
| 23 |
+ * |
|
| 24 |
+ */ |
|
| 25 |
+ |
|
| 26 |
+#ifdef HAVE_CONFIG_H |
|
| 27 |
+ #include "config.h" |
|
| 28 |
+#endif |
|
| 29 |
+ |
|
| 30 |
+#include <stdio.h> |
|
| 31 |
+#include <stdlib.h> |
|
| 32 |
+#include <string.h> |
|
| 33 |
+ |
|
| 34 |
+extern "C" {
|
|
| 35 |
+#include "mymain.h" |
|
| 36 |
+#include "clustal/util.h" |
|
| 37 |
+//#include "squid/squid.h" |
|
| 38 |
+} |
|
| 39 |
+ |
|
| 40 |
+ |
|
| 41 |
+/** |
|
| 42 |
+ * @brief Convert an old Clustal command line parameter in the form of |
|
| 43 |
+ * [-/]param[=value] to new parameter if possible |
|
| 44 |
+ * |
|
| 45 |
+ * @param[out] iNewArgC_p |
|
| 46 |
+ * "argc" which will be incremented for each successfully converted option |
|
| 47 |
+ * @param[out] ppcNewArgV_p |
|
| 48 |
+ * "argv" to which each successfully converted options will be added |
|
| 49 |
+ * (caller has to free) |
|
| 50 |
+ * @param[in] pcOldArg |
|
| 51 |
+ * The old parameter and value command line option |
|
| 52 |
+ * |
|
| 53 |
+ */ |
|
| 54 |
+void |
|
| 55 |
+ConvertOldCmdLineArg(int *iNewArgC_p, char ***ppcNewArgV_p, char *pcOldArg) |
|
| 56 |
+{
|
|
| 57 |
+ char *pcOldParam, *pcOldValue, *pcOldArgCopy; |
|
| 58 |
+ char zcNotImplementedMsg[] = "WARNING: Invalid old command line option"; |
|
| 59 |
+ |
|
| 60 |
+ pcOldArgCopy = CkStrdup(pcOldArg); |
|
| 61 |
+ pcOldParam = strtok(pcOldArgCopy, "="); |
|
| 62 |
+ pcOldValue = strtok(NULL, "="); |
|
| 63 |
+ |
|
| 64 |
+ |
|
| 65 |
+ /* go through all options in order of appearance in clustalw2 -help |
|
| 66 |
+ * |
|
| 67 |
+ */ |
|
| 68 |
+ |
|
| 69 |
+ /* data |
|
| 70 |
+ * |
|
| 71 |
+ */ |
|
| 72 |
+ if (STR_NC_EQ("INFILE", &pcOldParam[1])) {
|
|
| 73 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("-i");
|
|
| 74 |
+ if (NULL != pcOldValue) |
|
| 75 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue); |
|
| 76 |
+ |
|
| 77 |
+ } else if (STR_NC_EQ("PROFILE1", &pcOldParam[1])) {
|
|
| 78 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("--profile1");
|
|
| 79 |
+ if (NULL != pcOldValue) |
|
| 80 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue); |
|
| 81 |
+ |
|
| 82 |
+ } else if (STR_NC_EQ("PROFILE2", &pcOldParam[1])) {
|
|
| 83 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("--profile2");
|
|
| 84 |
+ if (NULL != pcOldValue) |
|
| 85 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue); |
|
| 86 |
+ |
|
| 87 |
+ /* verbs |
|
| 88 |
+ * |
|
| 89 |
+ */ |
|
| 90 |
+ |
|
| 91 |
+ /* missing: |
|
| 92 |
+ * OPTIONS |
|
| 93 |
+ */ |
|
| 94 |
+ |
|
| 95 |
+ } else if (STR_NC_EQ("HELP", &pcOldParam[1])
|
|
| 96 |
+ || STR_NC_EQ("CHECK", &pcOldParam[1])) {
|
|
| 97 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("-h");
|
|
| 98 |
+ |
|
| 99 |
+ } else if (STR_NC_EQ("FULLHELP", &pcOldParam[1])) {
|
|
| 100 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("-h");
|
|
| 101 |
+ |
|
| 102 |
+ } else if (STR_NC_EQ("ALIGN", &pcOldParam[1])) {
|
|
| 103 |
+ char msg[] = "WARNING: The ALIGN option is default in Clustal Omega"; |
|
| 104 |
+ fprintf(stderr, "%s\n", msg); |
|
| 105 |
+ |
|
| 106 |
+ /* missing: |
|
| 107 |
+ * TREE |
|
| 108 |
+ * PIM |
|
| 109 |
+ * BOOTSTRAP |
|
| 110 |
+ * CONVERT |
|
| 111 |
+ */ |
|
| 112 |
+ |
|
| 113 |
+ /* parameters |
|
| 114 |
+ * |
|
| 115 |
+ */ |
|
| 116 |
+ } else if (STR_NC_EQ("INTERACTIVE", &pcOldParam[1])) {
|
|
| 117 |
+ char msg[] = "WARNING: There is no interactive command-line menu in Clustal Omega"; |
|
| 118 |
+ fprintf(stderr, "%s\n", msg); |
|
| 119 |
+ /* trigger help */ |
|
| 120 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("-h");
|
|
| 121 |
+ |
|
| 122 |
+ } else if (STR_NC_EQ("QUICKTREE", &pcOldParam[1])) {
|
|
| 123 |
+ char msg[] = "WARNING: The QUICKTREE (i.e. k-tuple distance) option is default in Clustal Omega"; |
|
| 124 |
+ fprintf(stderr, "%s\n", msg); |
|
| 125 |
+ |
|
| 126 |
+ } else if (STR_NC_EQ("TYPE", &pcOldParam[1])) {
|
|
| 127 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("-t");
|
|
| 128 |
+ if (NULL != pcOldValue) |
|
| 129 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue); |
|
| 130 |
+ |
|
| 131 |
+ /* NEGATIVE */ |
|
| 132 |
+ |
|
| 133 |
+ } else if (STR_NC_EQ("OUTFILE", &pcOldParam[1])) {
|
|
| 134 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("-o");
|
|
| 135 |
+ if (NULL != pcOldValue) |
|
| 136 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue); |
|
| 137 |
+ |
|
| 138 |
+ |
|
| 139 |
+ } else if (STR_NC_EQ("OUTPUT", &pcOldParam[1])) {
|
|
| 140 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("--outfmt");
|
|
| 141 |
+ if (NULL != pcOldValue) |
|
| 142 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue); |
|
| 143 |
+ |
|
| 144 |
+ /* missing: |
|
| 145 |
+ * OUTORDER |
|
| 146 |
+ * CASE |
|
| 147 |
+ * SEQNOS |
|
| 148 |
+ * SEQNO_RANGE |
|
| 149 |
+ * RANGE |
|
| 150 |
+ */ |
|
| 151 |
+ |
|
| 152 |
+ } else if (STR_NC_EQ("MAXSEQLEN", &pcOldParam[1])) {
|
|
| 153 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("--maxseqlen");
|
|
| 154 |
+ if (NULL != pcOldValue) |
|
| 155 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue); |
|
| 156 |
+ |
|
| 157 |
+ } else if (STR_NC_EQ("QUIET", &pcOldParam[1])) {
|
|
| 158 |
+ char msg[] = "WARNING: The QUIET option is default in Clustal Omega"; |
|
| 159 |
+ fprintf(stderr, "%s\n", msg); |
|
| 160 |
+ |
|
| 161 |
+ /* missing: |
|
| 162 |
+ * STATS |
|
| 163 |
+ */ |
|
| 164 |
+ |
|
| 165 |
+ /* fast pariwise alignment |
|
| 166 |
+ * |
|
| 167 |
+ */ |
|
| 168 |
+ |
|
| 169 |
+ /* missing: |
|
| 170 |
+ * KTUPLE |
|
| 171 |
+ * TOPDIAGS |
|
| 172 |
+ * WINDOW |
|
| 173 |
+ * PAIRGAP |
|
| 174 |
+ * SCORE |
|
| 175 |
+ */ |
|
| 176 |
+ |
|
| 177 |
+ /* slow pairwise alignments |
|
| 178 |
+ * |
|
| 179 |
+ */ |
|
| 180 |
+ |
|
| 181 |
+ /* missing: |
|
| 182 |
+ * PWMATRIX |
|
| 183 |
+ * PWDNAMATRIX |
|
| 184 |
+ * PWGAPOPEN |
|
| 185 |
+ * PWGAPEXT |
|
| 186 |
+ */ |
|
| 187 |
+ |
|
| 188 |
+ /* multiple alignments |
|
| 189 |
+ * |
|
| 190 |
+ */ |
|
| 191 |
+ } else if (STR_NC_EQ("NEWTREE", &pcOldParam[1])) {
|
|
| 192 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("--guidetree-out");
|
|
| 193 |
+ if (NULL != pcOldValue) |
|
| 194 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue); |
|
| 195 |
+ |
|
| 196 |
+ } else if (STR_NC_EQ("USETREE", &pcOldParam[1])) {
|
|
| 197 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("--guidetree-in");
|
|
| 198 |
+ if (NULL != pcOldValue) |
|
| 199 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue); |
|
| 200 |
+ |
|
| 201 |
+ /* missing: |
|
| 202 |
+ * MATRIX |
|
| 203 |
+ * DNAMATRIX |
|
| 204 |
+ * GAPOPEN |
|
| 205 |
+ * GAPEXT |
|
| 206 |
+ * ENDGAPS |
|
| 207 |
+ * GAPDIST |
|
| 208 |
+ * NOGAP |
|
| 209 |
+ * NOHGAP |
|
| 210 |
+ * HGAPRESIDUES |
|
| 211 |
+ * MAXDIV |
|
| 212 |
+ * TYPE already handled above |
|
| 213 |
+ * TRANSWEIGHT |
|
| 214 |
+ * ITERATION |
|
| 215 |
+ * NUMITER |
|
| 216 |
+ * NOWEIGHTS |
|
| 217 |
+ */ |
|
| 218 |
+ |
|
| 219 |
+ /* profile alignments |
|
| 220 |
+ * |
|
| 221 |
+ */ |
|
| 222 |
+ |
|
| 223 |
+ /* missing: |
|
| 224 |
+ * PROFILE |
|
| 225 |
+ * NEWTREE1 |
|
| 226 |
+ * NEWTREE2 |
|
| 227 |
+ * USETREE1 |
|
| 228 |
+ * USETREE2 |
|
| 229 |
+ */ |
|
| 230 |
+ |
|
| 231 |
+ /* sequence to profile alignments |
|
| 232 |
+ * |
|
| 233 |
+ */ |
|
| 234 |
+ } else if (STR_NC_EQ("SEQUENCES", &pcOldParam[1])) {
|
|
| 235 |
+ fprintf(stderr, "WARNING: %s: %s\n", zcNotImplementedMsg, pcOldArg); |
|
| 236 |
+ |
|
| 237 |
+ /* SEQUENCES and NEWTREE already handled above */ |
|
| 238 |
+ |
|
| 239 |
+ /* structure alignments |
|
| 240 |
+ * |
|
| 241 |
+ */ |
|
| 242 |
+ |
|
| 243 |
+ /* missing: |
|
| 244 |
+ * NOSECSTR1 |
|
| 245 |
+ * NOSECSTR2 |
|
| 246 |
+ * SECSTROUT |
|
| 247 |
+ * HELIXGAP |
|
| 248 |
+ * STRANDGAP |
|
| 249 |
+ * LOOPGAP |
|
| 250 |
+ * TERMINALGAP |
|
| 251 |
+ * HELIXENDIN |
|
| 252 |
+ * HELIXENDOUT |
|
| 253 |
+ * STRANDENDIN |
|
| 254 |
+ * STRANDENDOUT |
|
| 255 |
+ */ |
|
| 256 |
+ |
|
| 257 |
+ /* trees |
|
| 258 |
+ * |
|
| 259 |
+ */ |
|
| 260 |
+ |
|
| 261 |
+ /* missing: |
|
| 262 |
+ * OUTPUTTREE |
|
| 263 |
+ * SEED |
|
| 264 |
+ * KIMURA |
|
| 265 |
+ * TOSSGAPS |
|
| 266 |
+ * BOOTLABELS |
|
| 267 |
+ */ |
|
| 268 |
+#if 0 |
|
| 269 |
+ } else if (STR_NC_EQ("CLUSTERING", &pcOldParam[1])) {
|
|
| 270 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("-c");
|
|
| 271 |
+ if (NULL != pcOldValue) |
|
| 272 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue); |
|
| 273 |
+#endif |
|
| 274 |
+ |
|
| 275 |
+ } else {
|
|
| 276 |
+ fprintf(stderr, |
|
| 277 |
+ "WARNING: Unsupported old command line option '%s' will be ignored\n", |
|
| 278 |
+ pcOldArg); |
|
| 279 |
+ } |
|
| 280 |
+ |
|
| 281 |
+ /* FIXME: if not outfile was given, than the old default was to create a |
|
| 282 |
+ * filename based on the input filename but with its extension replaced by |
|
| 283 |
+ * aln. If the input already had the extension aln then the input was |
|
| 284 |
+ * overwritten. What to do here? Strictly mimic the old behaviour? |
|
| 285 |
+ */ |
|
| 286 |
+ |
|
| 287 |
+ free(pcOldArgCopy); |
|
| 288 |
+} |
|
| 289 |
+/* end ConvertOldCmdLineArg */ |
|
| 290 |
+ |
|
| 291 |
+ |
|
| 292 |
+ |
|
| 293 |
+/** |
|
| 294 |
+ * @brief Convert old command line usage to new one. Mix of old and |
|
| 295 |
+ * new style will be tolerated |
|
| 296 |
+ * |
|
| 297 |
+ * @param[out] iNewArgC_p |
|
| 298 |
+ * The updated "argc" |
|
| 299 |
+ * @param[out] ppcNewArgV_p |
|
| 300 |
+ * The updated "argv". Caller has to free. |
|
| 301 |
+ * @param[in] argc |
|
| 302 |
+ * Original "argc" |
|
| 303 |
+ * @param[in] argv |
|
| 304 |
+ * Original argv |
|
| 305 |
+ * |
|
| 306 |
+ * @note old style parameters look like this: |
|
| 307 |
+ * [/-]param[=value] |
|
| 308 |
+ * new style parameters: |
|
| 309 |
+ * -p [value] |
|
| 310 |
+ * --param [value] |
|
| 311 |
+ * |
|
| 312 |
+ */ |
|
| 313 |
+void |
|
| 314 |
+ConvertOldCmdline(int *iNewArgC_p, char ***ppcNewArgV_p, int argc, char **argv) |
|
| 315 |
+{
|
|
| 316 |
+ bool bOldCmdlineDetected = false; |
|
| 317 |
+ int i; /* aux */ |
|
| 318 |
+ |
|
| 319 |
+ /* we can have at most 2*argc converted arguments, plus the few |
|
| 320 |
+ * that we set by default (.e.g --force) |
|
| 321 |
+ */ |
|
| 322 |
+ (*ppcNewArgV_p) = (char **) CKCALLOC(argc*2+10, sizeof(char*)); |
|
| 323 |
+ |
|
| 324 |
+ /* copy first arg which is program name */ |
|
| 325 |
+ (*ppcNewArgV_p)[0] = CkStrdup(argv[0]); |
|
| 326 |
+ *iNewArgC_p = 1; |
|
| 327 |
+ |
|
| 328 |
+ for (i=1; i<argc; i++) {
|
|
| 329 |
+ bool bNewStyle = false; |
|
| 330 |
+ |
|
| 331 |
+ if (strlen(argv[i])<=2) {
|
|
| 332 |
+ /* e.g. -i (param) or just numbers (value) */ |
|
| 333 |
+ bNewStyle = true; |
|
| 334 |
+ |
|
| 335 |
+ } else if (strlen(argv[i])>2) {
|
|
| 336 |
+ if (argv[i][0] == '-' && argv[i][1] == '-') {
|
|
| 337 |
+ /* new style long opts */ |
|
| 338 |
+ bNewStyle = true; |
|
| 339 |
+ |
|
| 340 |
+ } else if (argv[i][0]=='/' && (NULL!=strchr(&argv[i][1], '/'))) {
|
|
| 341 |
+ /* Slash used to be a valid replacement for dash in |
|
| 342 |
+ * Clustal<=2, but could also be file in new style. If |
|
| 343 |
+ * we find at least two slashes, one at the beginning, |
|
| 344 |
+ * it should be a filename and therefore new style */ |
|
| 345 |
+ bNewStyle = true; |
|
| 346 |
+ |
|
| 347 |
+ } else if (argv[i][0] != '/' && argv[i][0] != '-') {
|
|
| 348 |
+ /* old style opts always start with slash or dash */ |
|
| 349 |
+ bNewStyle = true; |
|
| 350 |
+ |
|
| 351 |
+ } |
|
| 352 |
+ } |
|
| 353 |
+ |
|
| 354 |
+ /* copy and continue if new style arg or attempt to convert |
|
| 355 |
+ * old style arg |
|
| 356 |
+ */ |
|
| 357 |
+ if (bNewStyle) {
|
|
| 358 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(argv[i]); |
|
| 359 |
+ } else {
|
|
| 360 |
+ ConvertOldCmdLineArg(iNewArgC_p, ppcNewArgV_p, argv[i]); |
|
| 361 |
+ /*LOG_DEBUG("old command line arg: %s", argv[i]);*/
|
|
| 362 |
+ bOldCmdlineDetected = true; |
|
| 363 |
+ } |
|
| 364 |
+ } |
|
| 365 |
+ |
|
| 366 |
+ if (bOldCmdlineDetected) {
|
|
| 367 |
+ bool bOutfileOptSet = FALSE; |
|
| 368 |
+ bool bOutFormatOptSet = FALSE; |
|
| 369 |
+ |
|
| 370 |
+ |
|
| 371 |
+ /* old clustal used to write to a file called in.aln by |
|
| 372 |
+ * default. set if not |
|
| 373 |
+ * explicitely requested otherwisee |
|
| 374 |
+ */ |
|
| 375 |
+ for (i=0; i<*iNewArgC_p; i++) {
|
|
| 376 |
+ const char *pcOpt = "-o"; |
|
| 377 |
+ if (strlen(pcOpt) <= strlen((*ppcNewArgV_p)[i])) {
|
|
| 378 |
+ if (0 == strncmp((*ppcNewArgV_p)[i], pcOpt, strlen(pcOpt))) {
|
|
| 379 |
+ bOutfileOptSet = TRUE; |
|
| 380 |
+ break; |
|
| 381 |
+ } |
|
| 382 |
+ } |
|
| 383 |
+ } |
|
| 384 |
+ if (FALSE == bOutfileOptSet) {
|
|
| 385 |
+#ifdef TOO_LAZY_TO_IMPLEMENT_JUST_USING_DEFAULT_NAME_INSTEAD |
|
| 386 |
+ char *pcDotPos = NULL; |
|
| 387 |
+ char *pcInfileOpt = NULL; |
|
| 388 |
+ |
|
| 389 |
+ /* get infile arg and find last dot in it. if found replace |
|
| 390 |
+ * everything after with "aln", otherwise just add "aln" |
|
| 391 |
+ */ |
|
| 392 |
+ for (i=0; i<*iNewArgC_p; i++) {
|
|
| 393 |
+ const char *pcOpt = "-i"; |
|
| 394 |
+ if (strlen(pcOpt) <= strlen((*ppcNewArgV_p)[i])) {
|
|
| 395 |
+ if (0 == strncmp((*ppcNewArgV_p)[i], pcOpt, strlen(pcOpt))) {
|
|
| 396 |
+ if (*iNewArgC_p<= i+1) {
|
|
| 397 |
+ fprintf(stderr, |
|
| 398 |
+ "Oups...error while trying to convert old commandline (%s).\n", |
|
| 399 |
+ "No more arguments left after -i"); |
|
| 400 |
+ throw 1; |
|
| 401 |
+ } |
|
| 402 |
+ pcInfileOpt = (*ppcNewArgV_p)[i+1]; |
|
| 403 |
+ break; |
|
| 404 |
+ } |
|
| 405 |
+ } |
|
| 406 |
+ } |
|
| 407 |
+ if (NULL == pcInfileOpt) {
|
|
| 408 |
+ fprintf(stderr, |
|
| 409 |
+ "Oups...error while trying to convert old commandline (%s)\n", |
|
| 410 |
+ "No infile opt found"); |
|
| 411 |
+ throw 1; |
|
| 412 |
+ } |
|
| 413 |
+ |
|
| 414 |
+ fprintf(stderr, "FIXME: unfinished\n"); |
|
| 415 |
+ throw 1; |
|
| 416 |
+#endif |
|
| 417 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("-o");
|
|
| 418 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("clustal.aln");
|
|
| 419 |
+ } |
|
| 420 |
+ |
|
| 421 |
+ |
|
| 422 |
+ /* old clustal used the clustal format by default. set if not |
|
| 423 |
+ * explicitely requested otherwisee |
|
| 424 |
+ */ |
|
| 425 |
+ for (i=0; i<*iNewArgC_p; i++) {
|
|
| 426 |
+ const char *pcOpt = "--outfmt"; |
|
| 427 |
+ if (strlen(pcOpt) <= strlen((*ppcNewArgV_p)[i])) {
|
|
| 428 |
+ if (0 == strncmp((*ppcNewArgV_p)[i], pcOpt, strlen(pcOpt))) {
|
|
| 429 |
+ bOutFormatOptSet = TRUE; |
|
| 430 |
+ break; |
|
| 431 |
+ } |
|
| 432 |
+ } |
|
| 433 |
+ } |
|
| 434 |
+ if (FALSE == bOutFormatOptSet) {
|
|
| 435 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("--outfmt=clustal");
|
|
| 436 |
+ } |
|
| 437 |
+ |
|
| 438 |
+ |
|
| 439 |
+ /* old clustal was verbose by default |
|
| 440 |
+ */ |
|
| 441 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("-v");
|
|
| 442 |
+ |
|
| 443 |
+ /* old clustal used to overwrite files by default |
|
| 444 |
+ */ |
|
| 445 |
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("--force");
|
|
| 446 |
+ |
|
| 447 |
+ fprintf(stderr, |
|
| 448 |
+ "WARNING: Your old-style command-line options were converted to: "); |
|
| 449 |
+ for (i=0; i<*iNewArgC_p; i++) {
|
|
| 450 |
+ fprintf(stderr, " %s", (*ppcNewArgV_p)[i]); |
|
| 451 |
+ } |
|
| 452 |
+ fprintf(stderr, "\n"); |
|
| 453 |
+ } |
|
| 454 |
+ |
|
| 455 |
+} |
|
| 456 |
+/* end ConvertOldCmdline */ |
|
| 457 |
+ |
|
| 458 |
+ |
|
| 459 |
+ |
|
| 460 |
+int |
|
| 461 |
+main(int argc, char **argv) |
|
| 462 |
+{
|
|
| 463 |
+ ClustalOmegaInput msaInput; |
|
| 464 |
+ ClustalOmegaOutput msaOutput; |
|
| 465 |
+ |
|
| 466 |
+ int i; /* aux */ |
|
| 467 |
+ int new_argc = 0; |
|
| 468 |
+ char **new_argv = NULL; |
|
| 469 |
+ |
|
| 470 |
+ ConvertOldCmdline(&new_argc, &new_argv, argc, argv); |
|
| 471 |
+ |
|
| 472 |
+ executeClustalOmega(new_argc, new_argv, &msaInput, &msaOutput); |
|
| 473 |
+ |
|
| 474 |
+ for (i=0; i<new_argc; i++) {
|
|
| 475 |
+ free(new_argv[i]); |
|
| 476 |
+ } |
|
| 477 |
+ free(new_argv); |
|
| 478 |
+ |
|
| 479 |
+ return 0; |
|
| 480 |
+} |