source: branches/items/GDE/MAFFT/mafft-7.055-with-extensions/core/seq2regtable.c

#include "mltaln.h"

#define DEBUG 0

char *weboutfile = NULL;


void arguments( int argc, char *argv[] )
{
    int c;

    while( --argc > 0 && (*++argv)[0] == '-' )
        {
        while ( (c = *++argv[0]) )
                {
            switch( c )
            {
                                case 'i':
                                        inputfile = *++argv;
                                        fprintf( stderr, "inputfile = %s\n", inputfile );
                                        --argc;
                                        goto nextoption;
                                case 'w':
                                        weboutfile = *++argv;
                                        fprintf( stderr, "weboutfile = %s\n", weboutfile );
                                        --argc;
                                        goto nextoption;
                default:
                    fprintf( stderr, "illegal option %c\n", c );
                    argc = 0;
                    break;
            }
                }
                nextoption:
                        ;
        }
    if( argc != 0 ) 
    {
        fprintf( stderr, "options: Check source file !\n" );
        exit( 1 );
    }
}


int main( int argc, char *argv[] )
{
        FILE *infp;
        FILE *weboutfp;
        int nlenmin;
        int isaligned = 0;

        arguments( argc, argv );

        if( inputfile )
        {
                infp = fopen( inputfile, "r" );
                if( !infp )
                {
                        fprintf( stderr, "Cannot open %s\n", inputfile );
                        exit( 1 );
                }
        }
        else
                infp = stdin;

        if( weboutfile )
        {
                weboutfp = fopen( weboutfile, "w" );
                if( !weboutfp )
                {
                        fprintf( stderr, "Cannot open %s\n", weboutfile );
                        exit( 1 );
                }
        }

        dorp = NOTSPECIFIED;
        if( weboutfile )
        {
                getnumlen_nogap_outallreg_web( infp, weboutfp, &nlenmin, &isaligned );
                if( isaligned ) fprintf( stdout, "Aligned\n" );
                else fprintf( stdout, "Not aligned\n" );
        }
        else
                getnumlen_nogap_outallreg( infp, &nlenmin );

        return( 0 );

}