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

#include "mltaln.h"

#define DEBUG 0

char *alignmentfile;

static void fillorichar( int nseq, int *oripos, char **a, char **s )
{
        int i;
        char *pta, *pts;
        for( i=0; i<nseq; i++ )
        {
                pta = a[i];
                pts = s[oripos[i]];
                while( *pta )
                {
                        if( *pta != '-' ) *pta = *pts++;
                        if( *pta++ == 0 )
                        {
                                fprintf( stderr, "ERROR!!\n" );
                                fprintf( stderr, "alignment is inconsistent with the original sequences\n" );
                                exit( 1 );
                        }
                }
                if( *pts != 0 )
                {
                        fprintf( stderr, "ERROR!!\n" );
                        fprintf( stderr, "alignment is inconsistent with the original sequences\n" );
                        exit( 1 );
                }
        }
}

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

    while( --argc > 0 && (*++argv)[0] == '-' )
        {
        while ( (c = *++argv[0]) )
                {
            switch( c )
            {
                                case 'i':
                                        inputfile = *++argv;
                                        --argc;
                                        goto nextoption;
                                case 'a':
                                        alignmentfile = *++argv;
                                        --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 *alfp;
        char **name;
        char **aname;
        char **oname;
        char **seq;
        char **aseq;
        int *nlen;
        int *oripos;
        char *npt, *npt0, *npt2, *pt, *pt2;
        int i, o, prelen;
        int nlenmin;
        int njobs, njoba;

        arguments( argc, argv );

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

        if( alignmentfile )
        {
                alfp = fopen( alignmentfile, "r" );
                if( !alfp )
                {
                        fprintf( stderr, "Cannot open %s\n", alignmentfile );
                        exit( 1 );
                }
        }
        else
        {
                fprintf( stderr, "No alignment is given.\n" );
                exit( 1 );
        }
        
        dorp = NOTSPECIFIED;
        getnumlen_casepreserve( infp, &nlenmin );
        njobs = njob;
//      fprintf( stderr, "in infp, %d x %d - %d %c\n", njob, nlenmin, nlenmax, dorp );

        seq = AllocateCharMtx( njob, nlenmax+1 );
        name = AllocateCharMtx( njob, B+1 );
        nlen = AllocateIntVec( njob );
        oripos = AllocateIntVec( njob );
        readData_pointer_casepreserve( infp, name, nlen, seq );

        dorp = NOTSPECIFIED;
        getnumlen( alfp );
        njoba = njob;
//      fprintf( stderr, "in alfp, %d x %d %c\n", njob, nlenmax, dorp );
        aseq = AllocateCharMtx( njob, nlenmax+1 );
        aname = AllocateCharMtx( njob, B+1 );
        oname = AllocateCharMtx( njob, B+1 );
        readData_pointer( alfp, aname, nlen, aseq );

        for( i=0; i<njob; i++ ) gappick_samestring( seq[i] );

        if( njoba != njobs )
        {
                fprintf( stderr, "ERROR!!\n" );
                fprintf( stderr, "In input file,\n" );
                fprintf( stderr, "njob = %d\n", njobs );
                fprintf( stderr, "but in alignment file,\n" );
                fprintf( stderr, "njob = %d\n", njoba );
                exit( 1 );
        }

        for( i=0; i<njob; i++ )
        {
#if 0
                if( strstr( aname[i], "_seed_" ) )
                {
                        npt2 = aname[i] + 7;
                        strcpy( oname[i], "=_seed_" );
                }
                else
                {
                        npt2 = aname[i] + 1;
                        strcpy( oname[i], "=" );
                }

                fprintf( stderr, "npt2 = %s\n", npt2 );

                o = oripos[i] = atoi( npt2 );
                npt = strstr( npt2, "_oe_" );
                if( npt == NULL )
                {
                        fprintf( stderr, "Format error!\n" );
                        exit( 1 );
                }
                npt += 4;
                strcat( oname[i], npt+1 );
#endif
                npt0 = strstr( aname[i], "_os_" );
                if( npt0 == NULL )
                {
                        fprintf( stderr, "Format error!\n" );
                        exit( 1 );
                }
                npt2 = npt0 + 4;
                o = oripos[i] = atoi( npt2 );

                npt = strstr( aname[i], "_oe_" );
                if( npt == NULL )
                {
                        fprintf( stderr, "Format error!\n" );
                        exit( 1 );
                }
                npt += 4;

                pt2 = npt;
                pt = npt2 - 4;
                while( *pt ) *pt++ = *pt2++; // okashii

                prelen = npt0-aname[i];
                strncpy( oname[i], aname[i], prelen ); oname[i][prelen] = 0;
                strcat( oname[i], npt0 );

                pt = strstr( aname[i], "_numo_e" );
                if( pt ) pt += 8;
                else pt = aname[i] + 1;

//              fprintf( stderr, "aname[i] = :%s:\n", aname[i] );
//              fprintf( stderr, "pt = :%s:\n", pt );
//              fprintf( stderr, "oname[i] = :%s:\n", oname[i] );
//              fprintf( stderr, "name[o] = :%s:\n", name[o] );

                if( strncmp( pt, name[o]+1, 10 ) )
                {
                        fprintf( stderr, "ERROR!!\n" );
                        fprintf( stderr, "In input file,\n" );
                        fprintf( stderr, "name[%d] = %s\n", o, name[o] );
                        fprintf( stderr, "but in alignment file,\n" );
                        fprintf( stderr, "pt = %s\n", pt );
                        fprintf( stderr, "name[%d] = %s\n", i, aname[i] );
                        exit( 1 );
                }
#if 0
                else
                {
                        fprintf( stderr, "OK!!\n" );
                        fprintf( stderr, "In input file,\n" );
                        fprintf( stderr, "name[%d] = %s\n", o, name[o] );
                        fprintf( stderr, "and in alignment file,\n" );
                        fprintf( stderr, "name[%d] = %s\n", i, aname[i] );
                        fprintf( stderr, "\n" );
                }
#endif
        }
//      fprintf( stderr, "seq[0] = %s\n", seq[0] );
//      fprintf( stderr, "aseq[0] = %s\n", aseq[0] );

        fillorichar( njob, oripos, aseq, seq );


        writeData_pointer( stdout, njob, oname, nlen, aseq );

        FreeCharMtx( seq );
        FreeCharMtx( aseq );
        FreeCharMtx( name );
        FreeCharMtx( aname );
        FreeCharMtx( oname );
        free( nlen );
        free( oripos );

        return( 0 );
}