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add comments of arg

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kuoi 2022-03-12 23:44:36 +00:00
parent 7031196089
commit 39036cc34e
1 changed files with 41 additions and 41 deletions
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oblong.c
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@ -194,8 +194,8 @@ void errout ( int cond , char * msg )
{ {
if ( !cond ) return ; if ( !cond ) return ;
if ( msg != NULL ) if ( msg != NULL )
fprintf ( stderr , "\n%s\n" , msg ) ; fprintf ( stderr , "\n%s\n" , msg ) ; //output to the screen, usually error
exit ( 0 ) ; exit ( 0 ) ; //exit(0)正常运行程序并退出程序；exit(1)非正常运行导致退出程序
} }
void * myalloc ( unsigned long int size ) void * myalloc ( unsigned long int size )
@ -207,85 +207,85 @@ void * myalloc ( unsigned long int size )
int stringis ( char * a , char * b ) int stringis ( char * a , char * b )
{ {
while ( * a && tolower ( * a ) == tolower ( * b ) ) { ++a ; ++ b ; } while ( * a && tolower ( * a ) == tolower ( * b ) ) { ++a ; ++ b ; } //tolower: conver letters from uppercase to lowercase
if ( * a || * b ) return 0 ; if ( * a || * b ) return 0 ; // or || ,return fake
return 1 ; return 1 ; //return true
} }
void procargs ( int nargs , char ** arg ) void procargs ( int nargs , char ** arg ) // int nargs =2 for [oblong -f] **arg = *arg [] 字符串数组
{ {
int i ; int i ;
char * cp ; char * cp ;
if ( nargs == 1 ) { if ( nargs == 1 ) { // no arguments if nargs == 1
display_help ( 0 ) ; display_help ( 0 ) ; //not show the help ouput just no argument output
exit ( 0 ) ; } exit ( 0 ) ; }
for ( i = 1 ; i < nargs ; ++ i ) { for ( i = 1 ; i < nargs ; ++ i ) {
cp = arg [ i ] ; cp = arg [ i ] ;
if ( * cp != '-' ) { if ( * cp != '-' ) { // if arguments not start with -
fprintf ( stderr , "\nWrong argument: %s\n" , arg [ i ] ) ; fprintf ( stderr , "\nWrong argument: %s\n" , arg [ i ] ) ; //show which argument is wrong
exit ( 0 ) ; } exit ( 0 ) ; }
switch ( * ++ cp ) { switch ( * ++ cp ) {
case 'a': saveall = 1 ; break ; case 'a': saveall = 1 ; break ; //save all trees
case 'b': do_branch_swapping = 0 ; break ; case 'b': do_branch_swapping = 0 ; break ; //no branch swapping
case 'e': equal_taxon_sequence = 1 ; break ; case 'e': equal_taxon_sequence = 1 ; break ;
case 'f': fasta = 1 ; break ; case 'f': fasta = 1 ; break ; //fasta format
case 'h': display_help ( 1 ) ; exit ( 0 ) ; case 'h': display_help ( 1 ) ; exit ( 0 ) ; //help
case 'i': case 'i': //use the filename -i${filename}
case '@': case '@':
if ( * cp == '@' ) multifiles = 1 ; if ( * cp == '@' ) multifiles = 1 ; //there are multi files
++ cp ; ++ cp ;
errout ( stringis ( cp , "oblong.tmp" ) , "Cannot use \"oblong.tmp\" as input file; rename it and try again" ) ; errout ( stringis ( cp , "oblong.tmp" ) , "Cannot use \"oblong.tmp\" as input file; rename it and try again" ) ;
errout ( stringis ( cp , "oblong.pts" ) , "Cannot use \"oblong.pts\" as input file; rename it and try again" ) ; errout ( stringis ( cp , "oblong.pts" ) , "Cannot use \"oblong.pts\" as input file; rename it and try again" ) ;
errout ( inp != NULL , "Can't open TWO input files" ) ; errout ( inp != NULL , "Can't open TWO input files" ) ;
errout ( ( inp = fopen ( cp , "rb" ) ) == NULL , "Can't open input file" ) ; errout ( ( inp = fopen ( cp , "rb" ) ) == NULL , "Can't open input file" ) ; //input file, if the input list can't be readable in the bianry mode, on windows, binary is different
break ; break ;
case 'j': case 'j': //j${NumberofJakknife}
++ cp ; ++ cp ;
if ( isdigit ( * cp ) ) if ( isdigit ( * cp ) ) //to find if the character is the numer
jakprob = atoi ( cp ) ; jakprob = atoi ( cp ) ; //atoi: convert character to the int
dojak = changewts = 1 ; dojak = changewts = 1 ;
break ; break ;
case 'k': swapcollapse = 1 ; break ; case 'k': swapcollapse = 1 ; break ; //do TBR/SPR collapsing
case 'm': errout ( ( ( maxram = atof ( ++ cp ) ) <= 0 ) , "You must indicate RAM to use" ) ; together = 0 ; break ; case 'm': errout ( ( ( maxram = atof ( ++ cp ) ) <= 0 ) , "You must indicate RAM to use" ) ; together = 0 ; break ; //atof: transfer chracter into double
case 'N': usenexus = 1 ; break ; case 'N': usenexus = 1 ; break ; //output the nexus file
case 'o': case 'o': //-o${outfile}
++ cp ; ++ cp ;
errout ( stringis ( cp , "oblong.tmp" ) , "Cannot use \"oblong.tmp\" as output file; use a different name" ) ; errout ( stringis ( cp , "oblong.tmp" ) , "Cannot use \"oblong.tmp\" as output file; use a different name" ) ;
errout ( stringis ( cp , "oblong.pts" ) , "Cannot use \"oblong.pts\" as output file; use a different name" ) ; errout ( stringis ( cp , "oblong.pts" ) , "Cannot use \"oblong.pts\" as output file; use a different name" ) ;
errout ( outp != NULL , "Can't open TWO output files" ) ; errout ( outp != NULL , "Can't open TWO output files" ) ;
errout ( ( outp = fopen ( cp , "wb" ) ) == NULL , "Can't open output file" ) ; errout ( ( outp = fopen ( cp , "wb" ) ) == NULL , "Can't open output file" ) ;
break ; break ;
case 'p': felipe = 1 ; break ; case 'p': felipe = 1 ; break ; //file in Phylip style
case 'q': case 'q': //a quick approximmation
++ cp ; ++ cp ;
quickbremer = 1 ; quickbremer = 1 ;
if ( * cp == '0' ) bremertype = 0 ; if ( * cp == '0' ) bremertype = 0 ;
if ( * cp == '1' ) bremertype = 1 ; if ( * cp == '1' ) bremertype = 1 ;
if ( * cp == '2' ) bremertype = 2 ; if ( * cp == '2' ) bremertype = 2 ;
break ; break ;
case 'r': numreplications = atoi ( ++ cp ) ; break ; case 'r': numreplications = atoi ( ++ cp ) ; break ; //use N starting points. -r${Number}
case 'R': ranseed = atoi ( ++ cp ) ; break ; case 'R': ranseed = atoi ( ++ cp ) ; break ; //random seed
case 's': case 's': //spr use spr instead of tbr
if ( !strcmp ( cp , "spr" ) ) { use_spr = 1 ; break ; } if ( !strcmp ( cp , "spr" ) ) { use_spr = 1 ; break ; }
case 't': savejusttrees = 1 ; break ; case 't': savejusttrees = 1 ; break ; //output standrad tre format
case 'T': case 'T': //set start tree -T${treefile}
++ cp ; ++ cp ;
errout ( treeinp != NULL , "Can't open TWO tree files" ) ; errout ( treeinp != NULL , "Can't open TWO tree files" ) ;
errout ( ( treeinp = fopen ( cp , "rb" ) ) == NULL , "Can't open tree file" ) ; errout ( ( treeinp = fopen ( cp , "rb" ) ) == NULL , "Can't open tree file" ) ;
break ; break ;
case 'v': verbose = 1 ; break ; case 'v': verbose = 1 ; break ; //report rearrangements
case 'w': random_starts = 1 ; break ; case 'w': random_starts = 1 ; break ; //use random trees as start tree
case 'x': case 'x': //-x${Numer of ratcher}
++ cp ; ++ cp ;
if ( isdigit ( * cp ) ) ratcycles = atoi ( cp ) ; if ( isdigit ( * cp ) ) ratcycles = atoi ( cp ) ;//if the char is number, make ratecycles=
else ratcycles = 10 ; else ratcycles = 10 ;
break ; break ;
default: fprintf ( stderr , "\nUnrecognized option: %s\n" , arg [ i ] ) ; exit ( 0 ) ; }} default: fprintf ( stderr , "\nUnrecognized option: %s\n" , arg [ i ] ) ; exit ( 0 ) ; }}
errout ( ( fasta && felipe ) , "Cannot use both Phylip and Fasta formats" ) ; errout ( ( fasta && felipe ) , "Cannot use both Phylip and Fasta formats" ) ; //fasta = 1 and felipe = 1, it can't be identified as different type
errout ( ( inp == NULL ) , "No data set specified" ) ; errout ( ( inp == NULL ) , "No data set specified" ) ;
errout ( ( outp == NULL ) , "No output file specified" ) ; errout ( ( outp == NULL ) , "No output file specified" ) ;
if ( quickbremer && dojak ) { if ( quickbremer && dojak ) {
dojak = changewts = 0 ; dojak = changewts = 0 ; //if quick approximmation and jack both are set, the jack won't be done
fprintf ( stderr , "\nNOTE: Cannot do both jackknifing and bremer at the same time!\n" ) ; fprintf ( stderr , "\nNOTE: Cannot do both jackknifing and bremer at the same time!\n" ) ;
if ( bremertype == 2 ) if ( bremertype == 2 )
fprintf ( stderr , " deletion prob P=%.2f will be used to rescale supports (1-P)\n" , ( double ) jakprob / 100 ) ; fprintf ( stderr , " deletion prob P=%.2f will be used to rescale supports (1-P)\n" , ( double ) jakprob / 100 ) ;
@ -294,15 +294,15 @@ void procargs ( int nargs , char ** arg )
else fprintf ( stderr , " will do relative bremer supports instead\n" ) ; else fprintf ( stderr , " will do relative bremer supports instead\n" ) ;
errout ( ( !jakprob && bremertype == 2 ) , " ...but cannot use a deletion prob. P=0 to rescale!" ) ; errout ( ( !jakprob && bremertype == 2 ) , " ...but cannot use a deletion prob. P=0 to rescale!" ) ;
fprintf ( stderr , "\n" ) ; } fprintf ( stderr , "\n" ) ; }
if ( quickbremer && usenexus ) legindic [ 0 ] = 0 ; if ( quickbremer && usenexus ) legindic [ 0 ] = 0 ; // *** left here temp
if ( !do_branch_swapping && !ratcycles ) shownegbremers = 1 ; if ( !do_branch_swapping && !ratcycles ) shownegbremers = 1 ; // *** left here temp
if ( treeinp != NULL && numreplications ) if ( treeinp != NULL && numreplications )
fprintf ( stderr , "\nNote: \"-T\" overrides \"-r\": number of trees in file determines starting points\n" ) ; fprintf ( stderr , "\nNote: \"-T\" overrides \"-r\": number of trees in file determines starting points\n" ) ;
if ( !numreplications ) numreplications = 1 ; if ( !numreplications ) numreplications = 1 ;
if ( maxram > 0 ) { if ( maxram > 0 ) {
fprintf ( stderr , "\nUsing %.2f MBytes of RAM for matrix buffers\n" , maxram ) ; fprintf ( stderr , "\nUsing %.2f MBytes of RAM for matrix buffers\n" , maxram ) ;
fflush ( stderr ) ; fflush ( stderr ) ; //清空缓存区 ***
maxram *= 1024 * 1024 ; } maxram *= 1024 * 1024 ; } // ***
reportheader = '\r' ; reportheader = '\r' ;
if ( !isatty( fileno( stderr ) ) ) { if ( !isatty( fileno( stderr ) ) ) {
errout ( verbose , "Verbose allowed only when STDERR goes to screen" ) ; errout ( verbose , "Verbose allowed only when STDERR goes to screen" ) ;