From 39036cc34e62dd36e92747f9e529db7cbf254246 Mon Sep 17 00:00:00 2001 From: Kuoi Date: Sat, 12 Mar 2022 23:44:36 +0000 Subject: [PATCH] add comments of arg --- oblong.c | 82 ++++++++++++++++++++++++++++---------------------------- 1 file changed, 41 insertions(+), 41 deletions(-) diff --git a/oblong.c b/oblong.c index 25bbe15..9499d0e 100644 --- a/oblong.c +++ b/oblong.c @@ -194,8 +194,8 @@ void errout ( int cond , char * msg ) { if ( !cond ) return ; if ( msg != NULL ) - fprintf ( stderr , "\n%s\n" , msg ) ; - exit ( 0 ) ; + fprintf ( stderr , "\n%s\n" , msg ) ; //output to the screen, usually error + 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 ) @@ -207,85 +207,85 @@ void * myalloc ( unsigned long int size ) int stringis ( char * a , char * b ) { - while ( * a && tolower ( * a ) == tolower ( * b ) ) { ++a ; ++ b ; } - if ( * a || * b ) return 0 ; - return 1 ; + while ( * a && tolower ( * a ) == tolower ( * b ) ) { ++a ; ++ b ; } //tolower: conver letters from uppercase to lowercase + if ( * a || * b ) return 0 ; // or || ,return fake + 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 ; char * cp ; - if ( nargs == 1 ) { - display_help ( 0 ) ; + if ( nargs == 1 ) { // no arguments if nargs == 1 + display_help ( 0 ) ; //not show the help ouput just no argument output exit ( 0 ) ; } for ( i = 1 ; i < nargs ; ++ i ) { cp = arg [ i ] ; - if ( * cp != '-' ) { - fprintf ( stderr , "\nWrong argument: %s\n" , arg [ i ] ) ; + if ( * cp != '-' ) { // if arguments not start with - + fprintf ( stderr , "\nWrong argument: %s\n" , arg [ i ] ) ; //show which argument is wrong exit ( 0 ) ; } switch ( * ++ cp ) { - case 'a': saveall = 1 ; break ; - case 'b': do_branch_swapping = 0 ; break ; + case 'a': saveall = 1 ; break ; //save all trees + case 'b': do_branch_swapping = 0 ; break ; //no branch swapping case 'e': equal_taxon_sequence = 1 ; break ; - case 'f': fasta = 1 ; break ; - case 'h': display_help ( 1 ) ; exit ( 0 ) ; - case 'i': + case 'f': fasta = 1 ; break ; //fasta format + case 'h': display_help ( 1 ) ; exit ( 0 ) ; //help + case 'i': //use the filename -i${filename} case '@': - if ( * cp == '@' ) multifiles = 1 ; + if ( * cp == '@' ) multifiles = 1 ; //there are multi files ++ cp ; errout ( stringis ( cp , "oblong.tmp" ) , "Cannot use \"oblong.tmp\" as input file; rename it and try again" ) ; errout ( stringis ( cp , "oblong.pts" ) , "Cannot use \"oblong.pts\" as input file; rename it and try again" ) ; errout ( inp != NULL , "Can't open TWO input files" ) ; - errout ( ( inp = fopen ( cp , "rb" ) ) == NULL , "Can't open input file" ) ; + errout ( ( inp = fopen ( cp , "rb" ) ) == NULL , "Can't open input file" ) ; //input file, if the input list can't be readable in the bianry mode, on windows, binary is different break ; - case 'j': + case 'j': //j${NumberofJakknife} ++ cp ; - if ( isdigit ( * cp ) ) - jakprob = atoi ( cp ) ; + if ( isdigit ( * cp ) ) //to find if the character is the numer + jakprob = atoi ( cp ) ; //atoi: convert character to the int dojak = changewts = 1 ; break ; - case 'k': swapcollapse = 1 ; break ; - case 'm': errout ( ( ( maxram = atof ( ++ cp ) ) <= 0 ) , "You must indicate RAM to use" ) ; together = 0 ; break ; - case 'N': usenexus = 1 ; break ; - case 'o': + 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 ; //atof: transfer chracter into double + case 'N': usenexus = 1 ; break ; //output the nexus file + case 'o': //-o${outfile} ++ cp ; errout ( stringis ( cp , "oblong.tmp" ) , "Cannot use \"oblong.tmp\" as output file; use a different name" ) ; errout ( stringis ( cp , "oblong.pts" ) , "Cannot use \"oblong.pts\" as output file; use a different name" ) ; errout ( outp != NULL , "Can't open TWO output files" ) ; errout ( ( outp = fopen ( cp , "wb" ) ) == NULL , "Can't open output file" ) ; break ; - case 'p': felipe = 1 ; break ; - case 'q': + case 'p': felipe = 1 ; break ; //file in Phylip style + case 'q': //a quick approximmation ++ cp ; quickbremer = 1 ; if ( * cp == '0' ) bremertype = 0 ; if ( * cp == '1' ) bremertype = 1 ; if ( * cp == '2' ) bremertype = 2 ; break ; - case 'r': numreplications = atoi ( ++ cp ) ; break ; - case 'R': ranseed = atoi ( ++ cp ) ; break ; - case 's': + case 'r': numreplications = atoi ( ++ cp ) ; break ; //use N starting points. -r${Number} + case 'R': ranseed = atoi ( ++ cp ) ; break ; //random seed + case 's': //spr use spr instead of tbr if ( !strcmp ( cp , "spr" ) ) { use_spr = 1 ; break ; } - case 't': savejusttrees = 1 ; break ; - case 'T': + case 't': savejusttrees = 1 ; break ; //output standrad tre format + case 'T': //set start tree -T${treefile} ++ cp ; errout ( treeinp != NULL , "Can't open TWO tree files" ) ; errout ( ( treeinp = fopen ( cp , "rb" ) ) == NULL , "Can't open tree file" ) ; break ; - case 'v': verbose = 1 ; break ; - case 'w': random_starts = 1 ; break ; - case 'x': + case 'v': verbose = 1 ; break ; //report rearrangements + case 'w': random_starts = 1 ; break ; //use random trees as start tree + case 'x': //-x${Numer of ratcher} ++ cp ; - if ( isdigit ( * cp ) ) ratcycles = atoi ( cp ) ; + if ( isdigit ( * cp ) ) ratcycles = atoi ( cp ) ;//if the char is number, make ratecycles= else ratcycles = 10 ; break ; 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 ( ( outp == NULL ) , "No output file specified" ) ; 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" ) ; if ( bremertype == 2 ) 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" ) ; errout ( ( !jakprob && bremertype == 2 ) , " ...but cannot use a deletion prob. P=0 to rescale!" ) ; fprintf ( stderr , "\n" ) ; } - if ( quickbremer && usenexus ) legindic [ 0 ] = 0 ; - if ( !do_branch_swapping && !ratcycles ) shownegbremers = 1 ; + if ( quickbremer && usenexus ) legindic [ 0 ] = 0 ; // *** left here temp + if ( !do_branch_swapping && !ratcycles ) shownegbremers = 1 ; // *** left here temp if ( treeinp != NULL && numreplications ) fprintf ( stderr , "\nNote: \"-T\" overrides \"-r\": number of trees in file determines starting points\n" ) ; if ( !numreplications ) numreplications = 1 ; if ( maxram > 0 ) { fprintf ( stderr , "\nUsing %.2f MBytes of RAM for matrix buffers\n" , maxram ) ; - fflush ( stderr ) ; - maxram *= 1024 * 1024 ; } + fflush ( stderr ) ; //清空缓存区 *** + maxram *= 1024 * 1024 ; } // *** reportheader = '\r' ; if ( !isatty( fileno( stderr ) ) ) { errout ( verbose , "Verbose allowed only when STDERR goes to screen" ) ;