1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362
|
#define MAXARGS 100
typedef struct {
char *str;
sint *flag;
int type;
char **arg;
} cmd_line_data;
/*
command line switches
*/
sint setoptions = -1;
sint sethelp = -1;
sint setinteractive = -1;
sint setbatch = -1;
sint setgapopen = -1;
sint setgapext = -1;
sint setpwgapopen = -1;
sint setpwgapext = -1;
sint setoutorder = -1;
sint setbootlabels = -1;
sint setpwmatrix = -1;
sint setmatrix = -1;
sint setpwdnamatrix = -1;
sint setdnamatrix = -1;
sint setnegative = -1;
sint setnoweights = -1;
sint setoutput = -1;
sint setoutputtree = -1;
sint setquicktree = -1;
sint settype = -1;
sint setcase = -1;
sint setseqno = -1;
sint settransweight = -1;
sint setseed = -1;
sint setscore = -1;
sint setwindow = -1;
sint setktuple = -1;
sint setkimura = -1;
sint settopdiags = -1;
sint setpairgap = -1;
sint settossgaps = -1;
sint setnopgap = -1;
sint setnohgap = -1;
sint setnovgap = -1;
sint sethgapres = -1;
sint setvgapres = -1;
sint setuseendgaps = -1;
sint setmaxdiv = -1;
sint setgapdist = -1;
sint setdebug = -1;
sint setoutfile = -1;
sint setinfile = -1;
sint setprofile1 = -1;
sint setprofile2 = -1;
sint setalign = -1;
sint setconvert = -1;
sint setnewtree = -1;
sint setusetree = -1;
sint setnewtree1 = -1;
sint setusetree1 = -1;
sint setnewtree2 = -1;
sint setusetree2 = -1;
sint setbootstrap = -1;
sint settree = -1;
sint setprofile = -1;
sint setsequences = -1;
sint setsecstr1 = -1;
sint setsecstr2 = -1;
sint setsecstroutput = -1;
sint sethelixgap = -1;
sint setstrandgap = -1;
sint setloopgap = -1;
sint setterminalgap = -1;
sint sethelixendin = -1;
sint sethelixendout = -1;
sint setstrandendin = -1;
sint setstrandendout = -1;
/*
multiple alignment parameters
*/
float dna_gap_open = 15.0, dna_gap_extend = 6.66;
float prot_gap_open = 10.0, prot_gap_extend = 0.2;
sint profile_type = PROFILE;
sint gap_dist = 4;
sint output_order = ALIGNED;
sint divergence_cutoff = 30;
sint matnum = 3;
char mtrxname[FILENAMELEN+1] = "gonnet";
sint dnamatnum = 1;
char dnamtrxname[FILENAMELEN+1] = "iub";
char hyd_residues[] = "GPSNDQEKR";
Boolean no_weights = FALSE;
Boolean neg_matrix = FALSE;
Boolean no_hyd_penalties = FALSE;
Boolean no_var_penalties = TRUE;
Boolean no_pref_penalties = FALSE;
Boolean use_endgaps = FALSE;
Boolean endgappenalties = FALSE;
Boolean reset_alignments_new = FALSE; /* DES */
Boolean reset_alignments_all = FALSE; /* DES */
sint output_struct_penalties = 0;
sint struct_penalties1 = NONE;
sint struct_penalties2 = NONE;
Boolean use_ss1 = TRUE;
Boolean use_ss2 = TRUE;
sint helix_penalty = 4;
sint strand_penalty = 4;
sint loop_penalty = 1;
sint helix_end_minus = 3;
sint helix_end_plus = 0;
sint strand_end_minus = 1;
sint strand_end_plus = 1;
sint helix_end_penalty = 2;
sint strand_end_penalty = 2;
Boolean use_ambiguities = FALSE;
/*
pairwise alignment parameters
*/
float dna_pw_go_penalty = 15.0, dna_pw_ge_penalty = 6.66;
float prot_pw_go_penalty = 10.0, prot_pw_ge_penalty = 0.1;
sint pw_matnum = 3;
char pw_mtrxname[FILENAMELEN+1] = "gonnet";
sint pw_dnamatnum = 1;
char pw_dnamtrxname[FILENAMELEN+1] = "iub";
char usermtrxname[FILENAMELEN+1], pw_usermtrxname[FILENAMELEN+1];
char dnausermtrxname[FILENAMELEN+1], pw_dnausermtrxname[FILENAMELEN+1];
Boolean quick_pairalign = FALSE;
float transition_weight = 0.5;
sint new_seq;
/*
quick pairwise alignment parameters
*/
sint dna_ktup = 2; /* default parameters for DNA */
sint dna_wind_gap = 5;
sint dna_signif = 4;
sint dna_window = 4;
sint prot_ktup = 1; /* default parameters for proteins */
sint prot_wind_gap = 3;
sint prot_signif = 5;
sint prot_window = 5;
Boolean percent=TRUE;
Boolean tossgaps = FALSE;
Boolean kimura = FALSE;
sint boot_ntrials = 1000;
unsigned sint boot_ran_seed = 111;
sint debug = 0;
Boolean explicit_dnaflag = FALSE; /* Explicit setting of sequence type on comm.line*/
Boolean lowercase = TRUE; /* Flag for GDE output - set on comm. line*/
Boolean cl_seq_numbers = FALSE;
Boolean output_clustal = TRUE;
Boolean output_gcg = FALSE;
Boolean output_phylip = FALSE;
Boolean output_nbrf = FALSE;
Boolean output_gde = FALSE;
Boolean output_nexus = FALSE;
Boolean showaln = TRUE;
Boolean save_parameters = FALSE;
/* DES */
Boolean output_tree_clustal = FALSE;
Boolean output_tree_phylip = TRUE;
Boolean output_tree_distances = FALSE;
Boolean output_tree_nexus = FALSE;
sint bootstrap_format = BS_BRANCH_LABELS;
/*These are all the positively scoring groups that occur in the Gonnet Pam250
matrix. There are strong and weak groups, defined as strong score >0.5 and
weak score =<0.5. Strong matching columns to be assigned ':' and weak matches
assigned '.' in the clustal output format.
*/
char *res_cat1[] = {
"STA",
"NEQK",
"NHQK",
"NDEQ",
"QHRK",
"MILV",
"MILF",
"HY",
"FYW",
NULL };
char *res_cat2[] = {
"CSA",
"ATV",
"SAG",
"STNK",
"STPA",
"SGND",
"SNDEQK",
"NDEQHK",
"NEQHRK",
"FVLIM",
"HFY",
NULL };
static char *type_arg[] = {
"protein",
"dna",
""};
static char *bootlabels_arg[] = {
"node",
"branch",
""};
static char *outorder_arg[] = {
"input",
"aligned",
""};
static char *case_arg[] = {
"lower",
"upper",
""};
static char *seqno_arg[] = {
"off",
"on",
""};
static char *score_arg[] = {
"percent",
"absolute",
""};
static char *output_arg[] = {
"gcg",
"gde",
"pir",
"phylip",
"nexus",
""};
static char *outputtree_arg[] = {
"nj",
"phylip",
"dist",
"nexus",
""};
static char *outputsecstr_arg[] = {
"structure",
"mask",
"both",
"none",
""};
/*
command line initialisation
type = 0 no argument
type = 1 integer argument
type = 2 float argument
type = 3 string argument
type = 4 filename
type = 5 opts
*/
#define NOARG 0
#define INTARG 1
#define FLTARG 2
#define STRARG 3
#define FILARG 4
#define OPTARG 5
/* command line switches for DATA **************************/
cmd_line_data cmd_line_file[] = {
"infile", &setinfile, FILARG, NULL,
"profile1", &setprofile1, FILARG, NULL,
"profile2", &setprofile2, FILARG, NULL,
"", NULL, -1};
/* command line switches for VERBS **************************/
cmd_line_data cmd_line_verb[] = {
"help", &sethelp, NOARG, NULL,
"check", &sethelp, NOARG, NULL,
"options", &setoptions, NOARG, NULL,
"align", &setalign, NOARG, NULL,
"newtree", &setnewtree, FILARG, NULL,
"usetree", &setusetree, FILARG, NULL,
"newtree1", &setnewtree1, FILARG, NULL,
"usetree1", &setusetree1, FILARG, NULL,
"newtree2", &setnewtree2, FILARG, NULL,
"usetree2", &setusetree2, FILARG, NULL,
"bootstrap", &setbootstrap, NOARG, NULL,
"tree", &settree, NOARG, NULL,
"quicktree", &setquicktree, NOARG, NULL,
"convert", &setconvert, NOARG, NULL,
"interactive", &setinteractive, NOARG, NULL,
"batch", &setbatch, NOARG, NULL,
"", NULL, -1};
/* command line switches for PARAMETERS **************************/
cmd_line_data cmd_line_para[] = {
"type", &settype, OPTARG, type_arg,
"profile", &setprofile, NOARG, NULL,
"sequences", &setsequences, NOARG, NULL,
"matrix", &setmatrix, FILARG, NULL,
"dnamatrix", &setdnamatrix, FILARG, NULL,
"negative", &setnegative, NOARG, NULL,
"noweights", &setnoweights, NOARG, NULL,
"gapopen", &setgapopen, FLTARG, NULL,
"gapext", &setgapext, FLTARG, NULL,
"endgaps", &setuseendgaps, NOARG, NULL,
"nopgap", &setnopgap, NOARG, NULL,
"nohgap", &setnohgap, NOARG, NULL,
"novgap", &setnovgap, NOARG, NULL,
"hgapresidues", &sethgapres, STRARG, NULL,
"maxdiv", &setmaxdiv, INTARG, NULL,
"gapdist", &setgapdist, INTARG, NULL,
"pwmatrix", &setpwmatrix, FILARG, NULL,
"pwdnamatrix", &setpwdnamatrix, FILARG, NULL,
"pwgapopen", &setpwgapopen, FLTARG, NULL,
"pwgapext", &setpwgapext, FLTARG, NULL,
"ktuple", &setktuple, INTARG, NULL,
"window", &setwindow, INTARG, NULL,
"pairgap", &setpairgap, INTARG, NULL,
"topdiags", &settopdiags, INTARG, NULL,
"score", &setscore, OPTARG, score_arg,
"transweight", &settransweight, FLTARG, NULL,
"seed", &setseed, INTARG, NULL,
"kimura", &setkimura, NOARG, NULL,
"tossgaps", &settossgaps, NOARG, NULL,
"bootlabels", &setbootlabels, OPTARG, bootlabels_arg,
"debug", &setdebug, INTARG, NULL,
"output", &setoutput, OPTARG, output_arg,
"outputtree", &setoutputtree, OPTARG, outputtree_arg,
"outfile", &setoutfile, FILARG, NULL,
"outorder", &setoutorder, OPTARG, outorder_arg,
"case", &setcase, OPTARG, case_arg,
"seqnos", &setseqno, OPTARG, seqno_arg,
"nosecstr1", &setsecstr1, NOARG, NULL,
"nosecstr2", &setsecstr2, NOARG, NULL,
"secstrout", &setsecstroutput, OPTARG, outputsecstr_arg,
"helixgap", &sethelixgap, INTARG, NULL,
"strandgap", &setstrandgap, INTARG, NULL,
"loopgap", &setloopgap, INTARG, NULL,
"terminalgap", &setterminalgap, INTARG, NULL,
"helixendin", &sethelixendin, INTARG, NULL,
"helixendout", &sethelixendout, INTARG, NULL,
"strandendin", &setstrandendin, INTARG, NULL,
"strandendout",&setstrandendout, INTARG, NULL,
"", NULL, -1};
|