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|
Description: Fix_link_name_clashes
--- a/commline.c
+++ b/commline.c
@@ -35,16 +35,16 @@
/* reported to the user, arguments not preceded by a dash are assumed to */
/* be filenames. The input, output and bulk output files to be precise */
/**************************************************************************/
-int proc_comm_line( int *pargc , char ***pargv)
+int proc_comm_line( int *pargc , char ***pargv)
{
char *p;
char c;
int n;
char prog_name[64];
char root[MAX_FILENAME_LEN];
-
+
/* decide how to process argc[0] which will be the name of the programme */
-#if defined (_WINDOWS) || defined (_DOS) || defined ( WIN32 )
+#if defined (_WINDOWS) || defined (_DOS) || defined ( WIN32 )
if ( (p = strrchr(**pargv, '\\')) != NULL )
strncpy(prog_name, p+1 , 63);
else
@@ -53,26 +53,26 @@
if ( (p = strrchr(**pargv, '/')) != NULL )
strncpy(prog_name, p+1, 63);
else
- strncpy(prog_name, **pargv, 10);
+ strncpy(prog_name, **pargv, 10);
#elif defined(VMS) || defined (OPENVMS) /* maybe VMS or OPENVMS */
if ( (p = strrchr(**pargv, ']')) != NULL )
strncpy(prog_name, p+1, 63);
else
- strncpy(prog_name, **pargv, 10);
+ strncpy(prog_name, **pargv, 10);
#else
printf("UNRECOGNISED SYSTEM type won't be able to impersonate other programmes\n");
strcpy(prog_name, "codon"); /* OK I give up */
#endif
- if ( (p = strrchr(prog_name, '.')) != NULL ) /* remove file extension */
+ if ( (p = strrchr(prog_name, '.')) != NULL ) /* remove file extension */
*p = '\0'; /* tidy.exe -> tidy */
/* first call to garg initialises the function with the command line*/
/* parameters and the number of arguments, subsequent calls strip */
/* these off one by one */
-
+
/* has the user asked for help ???????????? */
- if ((p = garg(*pargc, *pargv, "-h", GARG_EXACT)) ||
+ if ((p = garg(*pargc, *pargv, "-h", GARG_EXACT)) ||
(p = garg(0, NULL, "-help", GARG_EXACT))){
printf(
"codonW [inputfile] [outputfile] [bulkoutfile] [options]\n"
@@ -80,7 +80,7 @@
" -h(elp)\tThis help message\n"
" -nomenu\tPrevent the menu interface being displayed\n"
" -nowarn\tPrevent warnings about sequences being displayed\n"
- " -silent\tOverwrite files silently\n"
+ " -silent\tOverwrite files silently\n"
" -totals\tConcatenate all genes in inputfile\n"
" -machine\tMachine readable output\n"
" -human\t\tHuman readable output\n"
@@ -100,6 +100,7 @@
"positions\n"
);
+ pause;
printf(
" -L_sym\t\tNumber of synonymous codons\n"
" -L_aa\t\tTotal number of synonymous and non-synonymous codons\n"
@@ -123,6 +124,7 @@
" -raau\t\tRelative Amino Acid Usage (RAAU)\n"
" -cu\t\tCodon Usage (CU) (default)\n"
);
+ pause;
printf(
" -cutab\t\tTabulation of codon usage\n"
" -cutot\t\tTabulation of dataset's codon usage\n"
@@ -137,37 +139,38 @@
"\nWhere {file} represents an input filename, and N an integer"
" value"
);
+ pause;
my_exit(99,""); /* after writing out help quit */
}
-
-/* These parameters are normally set in menu3 ie. the defaults menu */
+
+/* These parameters are normally set in menu3 ie. the defaults menu */
/* for a explanation of the various GARG_FLAGS see gargs */
/* -silent stops warnings about file about to be overwritten */
- if (garg(0, NULL, "-silent", GARG_THERE))
+ if (garg(0, NULL, "-silent", GARG_THERE))
pm->verbose = FALSE;
-
+
/* -total causes sequences to be concatenated and treated as one sequence */
if ( garg(0, NULL, "-total" , GARG_THERE))
- pm->totals = TRUE;
+ pm->totals = TRUE;
/* -machine or -human determines for whom the output should be formatted */
- if (p = garg(0, NULL, "-human", GARG_THERE))
+ if (p = garg(0, NULL, "-human", GARG_THERE))
pm->seq_format = 'H';
if (p = garg(0, NULL, "-mach", GARG_THERE))
pm->seq_format = 'M';
-/* -code determines the genetic code */
+/* -code determines the genetic code */
if (p = garg(0, NULL, "-code", GARG_NEXT | GARG_EXACT)) {
strcpy(pm->junk, p);
n=0;
- while ( isdigit( (int) pm->junk[n]) && pm->junk[n] != '\0')
+ while ( isdigit( (int) pm->junk[n]) && pm->junk[n] != '\0')
n++;
if ( n != (int)strlen(pm->junk)
- || atoi(pm->junk) < 0 || atoi(pm->junk) > NumGeneticCodes ) {
- printf( "FATAL: The value for genetic code %s is invalid\n",
+ || atoi(pm->junk) < 0 || atoi(pm->junk) > NumGeneticCodes ) {
+ printf( "FATAL: The value for genetic code %s is invalid\n",
pm->junk);
my_exit(99,"Fatal error in genetic code value");
} else {
@@ -184,14 +187,14 @@
if (p = garg(0, NULL, "-f_type", GARG_NEXT | GARG_EXACT)) {
strcpy(pm->junk, p);
n = 0;
- while ( isdigit( (int) pm->junk[n]) && pm->junk[n] != '\0')
+ while ( isdigit( (int) pm->junk[n]) && pm->junk[n] != '\0')
n++;
- if ( n != (int)strlen(pm->junk) || atoi(pm->junk) < 0 ||
+ if ( n != (int)strlen(pm->junk) || atoi(pm->junk) < 0 ||
atoi(pm->junk) >= NumFopSpecies ) {
- printf("FATAL: The value for fop_type %s is not valid\n",
+ printf("FATAL: The value for fop_type %s is not valid\n",
pm->junk);
my_exit(99,"Fatal error in Fop value");
- } else {
+ } else {
pm->f_type = (char) atoi(p); /* define organism type for Fop */
initilize_point(pm->code, pm->f_type, pm->c_type);
}
@@ -203,11 +206,11 @@
if (p = garg(0, NULL, "-c_type", GARG_NEXT | GARG_EXACT)) {
strcpy(pm->junk,p);
n = 0;
- while ( isdigit( (int) pm->junk[n]) && pm->junk[n] != '\0')
+ while ( isdigit( (int) pm->junk[n]) && pm->junk[n] != '\0')
n++;
- if ( n != (int)strlen(pm->junk) || atoi(pm->junk) < 0 ||
+ if ( n != (int)strlen(pm->junk) || atoi(pm->junk) < 0 ||
atoi(pm->junk) >= NumCaiSpecies) {
- printf("FATAL: The value for cai_type %s is not valid\n",
+ printf("FATAL: The value for cai_type %s is not valid\n",
pm->junk);
my_exit(99,"Fatal error in CAI type value");
@@ -244,7 +247,7 @@
if (p = garg(0, NULL, "-hyd" , GARG_EXACT))
pm->hyd = TRUE;
if (p = garg(0, NULL, "-aro" , GARG_EXACT))
- pm->aro = TRUE;
+ pm->aro = TRUE;
/* Turns on all the above indices */
if (p = garg(0, NULL, "-all_indices" , GARG_EXACT)){
pm->cai = TRUE;
@@ -257,23 +260,23 @@
pm->L_sym = TRUE;
pm->L_aa = TRUE;
pm->hyd = TRUE;
- pm->aro = TRUE;
+ pm->aro = TRUE;
}
/* This section in used to input the filenames for personal choices of Fop */
/* CBI or CAI values. The name is tested to make sure the file is readable */
/* the pointer to the file is then assign to the relevant pointer in the */
/* struct Z_menu and then processed properly in codon_us.c */
-
-/* Fop */
+
+/* Fop */
if (p = garg(0, NULL, "-fop_file", GARG_NEXT | GARG_EXACT)) {
if ( (pm->fopfile = open_file( "", p, "r", FALSE)) == NULL ) {
printf("Could not open Fop file - %s\n", p);
my_exit(1,"commline open fop file");
} else
- strncpy(pm->fop_filen, pm->junk, MAX_FILENAME_LEN - 1);
+ strncpy(pm->fop_filen, pm->junk, MAX_FILENAME_LEN - 1);
/* idiot catch, if you load personal fop values you want to calculate fop */
- pm->fop=TRUE;
+ pm->fop=TRUE;
}
/* CAI */
@@ -307,15 +310,15 @@
pm->coa = 'a';
if (p = garg(0, NULL, "-coa_expert", GARG_EXACT)) /* detailed inertia */
(coa.level='e'); /* analysis */
-
-
+
+
/* These are options selectable under the advanced COA menu */
-/* This first option -coa_axes changes the number of axis recorded to file */
+/* This first option -coa_axes changes the number of axis recorded to file */
if (p = garg(0, NULL, "-coa_axes", GARG_NEXT | GARG_EXACT)){
- if ( isdigit( (int) *p) ){
- n = (char)atoi(p);
- /* just check that correspondence analysis has been selected */
- if ( pm->coa == 'a' && (n > 20 || n<0) || ( n<0 || n>59 )) {
+ if ( isdigit( (int) *p) ){
+ n = (char)atoi(p);
+ /* just check that correspondence analysis has been selected */
+ if ( pm->coa == 'a' && (n > 20 || n<0) || ( n<0 || n>59 )) {
fprintf(pm->my_err,"Value %d is out of range for Number COA Axis "
"adjusting to max value\n",n);
if ( pm->coa == 'a' ) pcoa->axis = 20; else pcoa->axis = 59;
@@ -324,7 +327,7 @@
}
}
}
-
+
/* Select the size of dataset to use to identify optimal codons */
if (p = garg(0, NULL, "-coa_num", GARG_NEXT|GARG_EXACT)) {
strcpy (pm->junk,p) ;
@@ -333,8 +336,8 @@
pcoa->fop_gene=atoi(pm->junk)*-1;
}else {
pcoa->fop_gene=atoi(pm->junk);
- }
- }
+ }
+ }
/* These option are mutually exclusive and are normally selected using the */
@@ -349,7 +352,7 @@
if ( p = garg(0, NULL, "-cutot", GARG_THERE)){
pm->bulk = 'C';
pm->totals =TRUE;
- }
+ }
if ( p = garg(0, NULL, "-reader", GARG_EXACT))
pm->bulk = 'R';
if ( p = garg(0, NULL, "-rscu", GARG_EXACT))
@@ -362,16 +365,16 @@
pm->bulk = 'A';
if ( p = garg(0, NULL, "-transl", GARG_THERE))
pm->bulk = 'N';
- if ( p = garg(0, NULL, "-base", GARG_THERE))
+ if ( p = garg(0, NULL, "-base", GARG_THERE))
pm->bulk = 'B';
if (p = garg(0, NULL, "-dinuc", GARG_THERE))
pm->bulk = 'D';
if (p = garg(0, NULL, "-noblk", GARG_EXACT))
pm->bulk = 'X';
-
+
/* -t is used to change the column separator used in the output files */
/* at present it must be a space, tab or comma */
-/* Must occur after -transl or it misreads transl as a seperator */
+/* Must occur after -transl or it misreads transl as a seperator */
if (p = garg(0, NULL, "-t" , GARG_NEXT | GARG_SUBSQ)) {
strcpy(pm->junk, p);
n = 0;
@@ -382,11 +385,11 @@
printf( "WARNING: The chosen separator %s is unsuitable use"
"comma, tab or space\n", pm->junk);
} else {
- pm->seperator = c;
+ pm->seperator = c;
}
}
-
-
+
+
/* These options are commandline specific, ie. they do not have an */
/* menu option */
@@ -417,67 +420,67 @@
/* programmes. In essence CodonW will impersonate other commonly used */
/* codon usage analysis programmes if called using a special name */
- if ( !strcmp(prog_name, "raau" ) )
+ if ( !strcmp(prog_name, "raau") || !strcmp(prog_name+7, "raau"))
pm->bulk = 'L';
- else if ( !strcmp(prog_name, "cu" ) )
+ else if ( !strcmp(prog_name, "cu") || !strcmp(prog_name+7, "cu"))
pm->bulk = 'C';
- else if ( !strcmp(prog_name, "cutab" ) )
+ else if ( !strcmp(prog_name, "cutab") || !strcmp(prog_name+7, "cutab"))
pm->bulk = 'O';
- else if ( !strcmp(prog_name, "reader") )
+ else if ( !strcmp(prog_name, "reader") || !strcmp(prog_name+7, "reader"))
pm->bulk = 'R';
- else if ( !strcmp(prog_name, "rscu" ) )
+ else if ( !strcmp(prog_name, "rscu") || !strcmp(prog_name+7, "rscu"))
pm->bulk = 'S';
- else if ( !strcmp(prog_name, "tidy" ) )
+ else if ( !strcmp(prog_name, "tidy") || !strcmp(prog_name+7, "tidy"))
pm->bulk = 'T';
- else if ( !strcmp(prog_name, "aau" ) )
+ else if ( !strcmp(prog_name, "aau") || !strcmp(prog_name+7, "aau"))
pm->bulk = 'A';
- else if ( !strcmp(prog_name, "dinuc" ) )
+ else if ( !strcmp(prog_name, "dinuc") || !strcmp(prog_name+7, "dinuc"))
pm->bulk = 'D';
- else if ( !strcmp(prog_name, "transl") )
+ else if ( !strcmp(prog_name, "transl") || !strcmp(prog_name+7, "transl"))
pm->bulk = 'N';
- else if ( !strcmp(prog_name, "bases" ) )
- pm->bulk = 'B';
- else if ( !strcmp(prog_name, "base3s") ) {
+ else if ( !strcmp(prog_name, "bases") || !strcmp(prog_name+7, "bases"))
+ pm->bulk = 'B';
+ else if ( !strcmp(prog_name, "base3s") || !strcmp(prog_name+7, "base3s")) {
pm->prog = 's' ;
pm->menu = FALSE;
pm->sil_base = TRUE;
- } else if ( !strcmp(prog_name, "cai" ) ) {
+ } else if ( !strcmp(prog_name, "cai") || !strcmp(prog_name+7, "cai")) {
pm->prog = 'c';
pm->menu = FALSE;
pm->cai = TRUE;
- } else if ( !strcmp(prog_name, "fop" ) ) {
+ } else if ( !strcmp(prog_name, "fop") || !strcmp(prog_name+7, "fop")) {
pm->prog = 'f';
pm->menu = FALSE;
pm->fop = TRUE;
- } else if ( !strcmp(prog_name, "gc3s" ) ) {
+ } else if ( !strcmp(prog_name, "gc3s") || !strcmp(prog_name+7, "gc3s")) {
pm->prog = '3';
pm->menu = FALSE;
pm->gc3s = TRUE;
- } else if ( !strcmp(prog_name, "gc" ) ) {
+ } else if ( !strcmp(prog_name, "gc") || !strcmp(prog_name+7, "gc")) {
pm->prog = 'g';
pm->menu = FALSE;
pm->gc = TRUE;
- } else if ( !strcmp(prog_name, "enc" ) ) {
+ } else if ( !strcmp(prog_name, "enc") || !strcmp(prog_name+7, "enc")) {
pm->prog = 'e';
pm->menu = FALSE;
pm->enc = TRUE;
- } else if ( !strcmp(prog_name, "cbi" ) ) {
+ } else if ( !strcmp(prog_name, "cbi") || !strcmp(prog_name+7, "cbi")) {
pm->prog = 'i';
pm->menu = FALSE;
pm->cbi = TRUE;
- } else if ( !strcmp(prog_name, "cutot" ) ) {
+ } else if ( !strcmp(prog_name, "cutot") || !strcmp(prog_name+7, "cutot")) {
pm->bulk = 'C';
pm->menu = FALSE;
pm->totals =TRUE;
} else {
pm->codonW=TRUE; /* if argc[0] is not recognised assume codons*/
/* if blk output is still X then assume cu */
- if (pm->bulk=='X') pm->bulk='C';
+ if (pm->bulk=='X') pm->bulk='C';
}
if (!pm->codonW ) { /* we appear to be impersonating another prog*/
- /* now we switch to the correct greeting */
+ /* now we switch to the correct greeting */
if (pm->bulk && pm->bulk!='X'){
pm->seperator='\000'; /* stop chars being converted by tidy*/
switch (pm->bulk) {
@@ -564,7 +567,7 @@
/* so now we test for any remaining, these are unrecognised */
while (p = garg(0, NULL, "-", GARG_THERE))
- if ( pm->menu )
+ if ( pm->menu )
printf("Unrecognised argument %s\n", p);
else {
/* if we are running without a menu then abort this run */
@@ -584,24 +587,24 @@
}
/* The second should be the output filename */
if ( p = garg(0, NULL, "", GARG_THERE)) {
- if ( (pm->outputfile = open_file( "", p, "w",
+ if ( (pm->outputfile = open_file( "", p, "w",
(int) pm->verbose)) == NULL ) {
printf("Could not open output file - %s\n", p );
my_exit(1,"commline out file");
} else
strncpy(pm->curr_outfilename, pm->junk, MAX_FILENAME_LEN - 1);
- }
+ }
/* The third which only occurs if the programme is running as CodonW */
if ( pm->codonW && (p = garg(0, NULL, "", GARG_THERE)) ) {
- if ( (pm->tidyoutfile = open_file( "", p, "w",
+ if ( (pm->tidyoutfile = open_file( "", p, "w",
(int) pm->verbose)) == NULL ) {
printf("Could not open blkoutput file - %s\n", p );
my_exit(1,"commline blk outfile");
} else
strncpy(pm->curr_tidyoutname, pm->junk, MAX_FILENAME_LEN - 1);
- }
+ }
/* Now check the command line is empty ... it should be at this point */
while (p = garg(0, NULL, "", GARG_THERE))
@@ -612,25 +615,25 @@
/* we need to load an input file name */
if ( (!pm->codonW || !pm->menu) && !pm->inputfile ){
- if ( (pm->inputfile = open_file( "input filename", "input.dat",
+ if ( (pm->inputfile = open_file( "input filename", "input.dat",
"r", FALSE)) == NULL ) {
printf("Could not open input file - %s\n", p );
my_exit(1,"commline inputfile");
- }
+ }
strncpy(pm->curr_infilename, pm->junk, MAX_FILENAME_LEN - 1);
}
-
+
/* If we have an input filename but no output then we must prompt for the */
/* output filename */
- if ( pm->inputfile && !pm->outputfile ) {
+ if ( pm->inputfile && !pm->outputfile ) {
/* If we are trying to impersonate another programme use this method*/
/* but make sure that we know what this other programme is called */
if ( !pm->codonW && strlen (prog_name) ){
strcpy(pm->curr_outfilename, prog_name);
strcat(pm->curr_outfilename, ".def");
} else {
-
+
/* Use the input filename as a root filename */
strncpy(root, pm->curr_infilename, MAX_FILENAME_LEN - 5);
for (n = (int) strlen(root); n && root[n]!='.' ; --n);
@@ -638,23 +641,23 @@
strcpy(pm->curr_outfilename, root);
strcat(pm->curr_outfilename, ".out");
- } /* matchs else */
+ } /* matchs else */
- /* now we know the suggested name for the output file lets open it */
+ /* now we know the suggested name for the output file lets open it */
if ( pm->verbose ) {
if ( (pm->outputfile = open_file( "indices output filename",
- pm->curr_outfilename, "w",(int) pm->verbose)) == NULL )
+ pm->curr_outfilename, "w",(int) pm->verbose)) == NULL )
my_exit(1,"commline");
strncpy(pm->curr_outfilename, pm->junk, MAX_FILENAME_LEN - 1);
}else{
if ( (pm->outputfile = open_file( "",
- pm->curr_outfilename, "w",(int) pm->verbose)) == NULL )
+ pm->curr_outfilename, "w",(int) pm->verbose)) == NULL )
my_exit(1,"commline");
strncpy(pm->curr_outfilename, pm->junk, MAX_FILENAME_LEN - 1);
}
} /* match if ( pm->inputfile */
-
+
/* we had a commandline inputfile name and output filename but none */
@@ -670,22 +673,22 @@
strcpy(pm->curr_tidyoutname, root);
strcat(pm->curr_tidyoutname, ".blk");
- /* now we know the suggested name for the output file lets open it */
+ /* now we know the suggested name for the output file lets open it */
if( pm->verbose) {
if ( (pm->tidyoutfile = open_file( "bulk output filename",
- pm->curr_tidyoutname, "w",(int) pm->verbose)) == NULL )
+ pm->curr_tidyoutname, "w",(int) pm->verbose)) == NULL )
my_exit(1,"commline");
strncpy(pm->curr_tidyoutname, pm->junk, MAX_FILENAME_LEN - 1);
}else{
if ( (pm->tidyoutfile = open_file( "",
- pm->curr_tidyoutname, "w",(int) pm->verbose)) == NULL )
+ pm->curr_tidyoutname, "w",(int) pm->verbose)) == NULL )
my_exit(1,"commline");
strncpy(pm->curr_tidyoutname, pm->junk, MAX_FILENAME_LEN - 1);
}
- }else{
+ }else{
/* only use one output file when impersonating other programmes */
- /* just in case we make blkout and output the same file */
- pm->tidyoutfile = pm->outputfile;
+ /* just in case we make blkout and output the same file */
+ pm->tidyoutfile = pm->outputfile;
}
}
return 1;
@@ -699,8 +702,8 @@
/* This subroutine was developed as a collaboration with Colin McFarlane */
/* GARG_EXACT The argument must match targ exactly */
/* GARG_THERE The targ may be sub-string of the argument */
-/* GARG_SUBSQ The string immediate after targ is returned */
-/* GARG_NEXT The next argument after targ is returned */
+/* GARG_SUBSQ The string immediate after targ is returned */
+/* GARG_NEXT The next argument after targ is returned */
/* else return NULL */
/***************************************************************************/
char *garg(int argc, char *argv[], const char *targ, int mode)
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