source: trunk/GDE/MAFFT/mafft-7.055-with-extensions/core/Ralignmm.c

#include "mltaln.h"
#include "dp.h"

#define MACHIGAI 0
#define OUTGAP0TRY 1
#define DEBUG 0
#define XXXXXXX    0
#define USE_PENALTY_EX  0
#define FASTMATCHCALC 1


static TLS float **impmtx = NULL;
#if 1 // tditeration to naiveRscore_imp de tsukawareru.
float imp_match_out_scR( int i1, int j1 )
{
//      fprintf( stderr, "imp+match = %f\n", impmtx[i1][j1] * fastathreshold );
//      fprintf( stderr, "val = %f\n", impmtx[i1][j1] );
        return( impmtx[i1][j1] );
}
#endif

static void imp_match_out_veadR( float *imp, int i1, int lgth2 )
{
#if FASTMATCHCALC 
        float *pt = impmtx[i1];
        while( lgth2-- )
                *imp++ += *pt++;
#else
        int j;
        float *pt = impmtx[i1];
        for( j=0; j<lgth2; j++ )
                *imp++ += pt[j];
#endif
}
static void imp_match_out_vead_tateR( float *imp, int j1, int lgth1 )
{
        int i;
        for( i=0; i<lgth1; i++ )
                *imp++ += impmtx[i][j1];
}

#if 1 // tbfast.c kara yobareru.
void imp_match_init_strictR( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom, int forscore )
{
        int i, j, k1, k2, tmpint, start1, start2, end1, end2;
        static TLS int impalloclen = 0;
        float effij;
        double effijx;
        char *pt, *pt1, *pt2;
        static TLS char *nocount1 = NULL;
        static char *nocount2 = NULL;
        LocalHom *tmpptr;

        if( impalloclen < lgth1 + 2 || impalloclen < lgth2 + 2 )
        {
                if( impmtx ) FreeFloatMtx( impmtx );
                if( nocount1 ) free( nocount1 );
                if( nocount2 ) free( nocount2 );
                impalloclen = MAX( lgth1, lgth2 ) + 2;
                impmtx = AllocateFloatMtx( impalloclen, impalloclen );
                nocount1 = AllocateCharVec( impalloclen );
                nocount2 = AllocateCharVec( impalloclen );
        }

        for( i=0; i<lgth1; i++ )
        {
                for( j=0; j<clus1; j++ )
                        if( seq1[j][i] == '-' ) break;
                if( j != clus1 ) nocount1[i] = 1; 
                else                     nocount1[i] = 0;
        }
        for( i=0; i<lgth2; i++ )
        {
                for( j=0; j<clus2; j++ )
                        if( seq2[j][i] == '-' ) break;
                if( j != clus2 ) nocount2[i] = 1;
                else                     nocount2[i] = 0;
        }

#if 0
fprintf( stderr, "nocount2 =\n" );
for( i = 0; i<impalloclen; i++ )
{
        fprintf( stderr, "nocount2[%d] = %d (%c)\n", i, nocount2[i], seq2[0][i] );
}
#endif



#if 0
        fprintf( stderr, "eff1 in _init_strict = \n" );
        for( i=0; i<clus1; i++ )
                fprintf( stderr, "eff1[] = %f\n", eff1[i] );
        for( i=0; i<clus2; i++ )
                fprintf( stderr, "eff2[] = %f\n", eff2[i] );
#endif

        for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
                impmtx[i][j] = 0.0;
        effijx =  fastathreshold;
        for( i=0; i<clus1; i++ )
        {
                for( j=0; j<clus2; j++ )
                {
                        effij = (float)( eff1[i] * eff2[j] * effijx );
                        tmpptr = localhom[i][j];
                        while( tmpptr )
                        {
//                              fprintf( stderr, "start1 = %d\n", tmpptr->start1 );
//                              fprintf( stderr, "end1   = %d\n", tmpptr->end1   );
//                              fprintf( stderr, "i = %d, seq1 = \n%s\n", i, seq1[i] );
//                              fprintf( stderr, "j = %d, seq2 = \n%s\n", j, seq2[j] );
                                pt = seq1[i];
                                tmpint = -1;
                                while( *pt != 0 )
                                {
                                        if( *pt++ != '-' ) tmpint++;
                                        if( tmpint == tmpptr->start1 ) break;
                                }
                                start1 = pt - seq1[i] - 1;
        
                                if( tmpptr->start1 == tmpptr->end1 ) end1 = start1;
                                else
                                {
#if MACHIGAI
                                        while( *pt != 0 )
                                        {
//                                              fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
                                                if( tmpint == tmpptr->end1 ) break;
                                                if( *pt++ != '-' ) tmpint++;
                                        }
                                        end1 = pt - seq1[i] - 0;
#else
                                        while( *pt != 0 )
                                        {
//                                              fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
                                                if( *pt++ != '-' ) tmpint++;
                                                if( tmpint == tmpptr->end1 ) break;
                                        }
                                        end1 = pt - seq1[i] - 1;
#endif
                                }
        
                                pt = seq2[j];
                                tmpint = -1;
                                while( *pt != 0 )
                                {
                                        if( *pt++ != '-' ) tmpint++;
                                        if( tmpint == tmpptr->start2 ) break;
                                }
                                start2 = pt - seq2[j] - 1;
                                if( tmpptr->start2 == tmpptr->end2 ) end2 = start2;
                                else
                                {
#if MACHIGAI
                                        while( *pt != 0 )
                                        {
                                                if( tmpint == tmpptr->end2 ) break;
                                                if( *pt++ != '-' ) tmpint++;
                                        }
                                        end2 = pt - seq2[j] - 0;
#else
                                        while( *pt != 0 )
                                        {
                                                if( *pt++ != '-' ) tmpint++;
                                                if( tmpint == tmpptr->end2 ) break;
                                        }
                                        end2 = pt - seq2[j] - 1;
#endif
                                }
//                              fprintf( stderr, "start1 = %d (%c), end1 = %d (%c), start2 = %d (%c), end2 = %d (%c)\n", start1, seq1[i][start1], end1, seq1[i][end1], start2, seq2[j][start2], end2, seq2[j][end2] );
//                              fprintf( stderr, "step 0\n" );
                                if( end1 - start1 != end2 - start2 )
                                {
//                                      fprintf( stderr, "CHUUI!!, start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
                                }

#if 1
                                k1 = start1; k2 = start2;
                                pt1 = seq1[i] + k1;
                                pt2 = seq2[j] + k2;
                                while( *pt1 && *pt2 )
                                {
                                        if( *pt1 != '-' && *pt2 != '-' )
                                        {
// œÅ€ß€òÆóœÅ€Ë€«€±€Ê€€€è€Š€ËÃí°Õ€·€Æ²Œ€µ€€¡£
//                                              impmtx[k1][k2] += tmpptr->wimportance * fastathreshold;
//                                              impmtx[k1][k2] += tmpptr->importance * effij;
                                                impmtx[k1][k2] += tmpptr->fimportance * effij;
//                                              fprintf( stderr, "#### impmtx[k1][k2] = %f, tmpptr->fimportance=%f, effij=%f\n", impmtx[k1][k2], tmpptr->fimportance, effij );
//                                              fprintf( stderr, "mark, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
//                                              fprintf( stderr, "%d (%c) - %d (%c)  - %f\n", k1, *pt1, k2, *pt2, tmpptr->fimportance * effij );
                                                k1++; k2++;
                                                pt1++; pt2++;
                                        }
                                        else if( *pt1 != '-' && *pt2 == '-' )
                                        {
//                                              fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
                                                k2++; pt2++;
                                        }
                                        else if( *pt1 == '-' && *pt2 != '-' )
                                        {
//                                              fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
                                                k1++; pt1++;
                                        }
                                        else if( *pt1 == '-' && *pt2 == '-' )
                                        {
//                                              fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
                                                k1++; pt1++;
                                                k2++; pt2++;
                                        }
                                        if( k1 > end1 || k2 > end2 ) break;
                                }
#else
                                while( k1 <= end1 && k2 <= end2 )
                                {
                                        fprintf( stderr, "k1,k2=%d,%d - ", k1, k2 );
                                        if( !nocount1[k1] && !nocount2[k2] )
                                        {
                                                impmtx[k1][k2] += tmpptr->wimportance * eff1[i] * eff2[j]  * fastathreshold;
                                                fprintf( stderr, "marked\n" );
                                        }
                                        else
                                                fprintf( stderr, "no count\n" );
                                        k1++; k2++;
                                }
#endif
                                tmpptr = tmpptr->next;
                        }
                }
        }
#if 0
        if( clus1 == 1 && clus2 == 6 )
        {
                fprintf( stderr, "\n" );
                fprintf( stderr, "seq1[0] =  %s\n", seq1[0] );
                fprintf( stderr, "seq2[0] =  %s\n", seq2[0] );
                fprintf( stderr, "impmtx = \n" );
                for( k2=0; k2<lgth2; k2++ )
                        fprintf( stderr, "%6.3f ", (double)k2 );
                fprintf( stderr, "\n" );
                for( k1=0; k1<lgth1; k1++ )
                {
                        fprintf( stderr, "%d ", k1 );
                        for( k2=0; k2<3; k2++ )
                                fprintf( stderr, "%2.1f ", impmtx[k1][k2] );
                        fprintf( stderr, "\n" );
                }
                exit( 1 );
        }
#endif
}
#endif


static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
{
#if FASTMATCHCALC
        int j, l;
        float scarr[26];
        float **cpmxpd = floatwork;
        int **cpmxpdn = intwork;
        float *matchpt, *cpmxpdpt, **cpmxpdptpt;
        int *cpmxpdnpt, **cpmxpdnptpt;
        if( initialize )
        {
                int count = 0;
                for( j=0; j<lgth2; j++ )
                {
                        count = 0;
                        for( l=0; l<26; l++ )
                        {
                                if( cpmx2[l][j] )
                                {
                                        cpmxpd[j][count] = cpmx2[l][j];
                                        cpmxpdn[j][count] = l;
                                        count++;
                                }
                        }
                        cpmxpdn[j][count] = -1;
                }
        }

        {
                for( l=0; l<26; l++ )
                {
                        scarr[l] = 0.0;
                        for( j=0; j<26; j++ )
                                scarr[l] += n_dis[j][l] * cpmx1[j][i1];
                }
                matchpt = match;
                cpmxpdnptpt = cpmxpdn;
                cpmxpdptpt = cpmxpd;
                while( lgth2-- )
                {
                        *matchpt = 0.0;
                        cpmxpdnpt = *cpmxpdnptpt++;
                        cpmxpdpt = *cpmxpdptpt++;
                        while( *cpmxpdnpt>-1 )
                                *matchpt += scarr[*cpmxpdnpt++] * *cpmxpdpt++;
                        matchpt++;
                } 
        }
#else
        int j, k, l;
        float scarr[26];
        float **cpmxpd = floatwork;
        int **cpmxpdn = intwork;
// simple
        if( initialize )
        {
                int count = 0;
                for( j=0; j<lgth2; j++ )
                {
                        count = 0;
                        for( l=0; l<26; l++ )
                        {
                                if( cpmx2[l][j] )
                                {
                                        cpmxpd[count][j] = cpmx2[l][j];
                                        cpmxpdn[count][j] = l;
                                        count++;
                                }
                        }
                        cpmxpdn[count][j] = -1;
                }
        }
        for( l=0; l<26; l++ )
        {
                scarr[l] = 0.0;
                for( k=0; k<26; k++ )
                        scarr[l] += n_dis[k][l] * cpmx1[k][i1];
        }
        for( j=0; j<lgth2; j++ )
        {
                match[j] = 0.0;
                for( k=0; cpmxpdn[k][j]>-1; k++ )
                        match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
        } 
#endif
}

static void Atracking_localhom( float *impwmpt, float *lasthorizontalw, float *lastverticalw, 
                                                char **seq1, char **seq2, 
                        char **mseq1, char **mseq2, 
                        float **cpmx1, float **cpmx2, 
                        int **ijp, int icyc, int jcyc )
{
        int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
        float wm;
        char *gaptable1, *gt1bk;
        char *gaptable2, *gt2bk;
        lgth1 = strlen( seq1[0] );
        lgth2 = strlen( seq2[0] );
        gt1bk = AllocateCharVec( lgth1+lgth2+1 );
        gt2bk = AllocateCharVec( lgth1+lgth2+1 );

#if 0
        for( i=0; i<lgth1; i++ ) 
        {
                fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
        }
#endif
 
        if( outgap == 1 )
                ;
        else
        {
                wm = lastverticalw[0];
                for( i=0; i<lgth1; i++ )
                {
                        if( lastverticalw[i] >= wm )
                        {
                                wm = lastverticalw[i];
                                iin = i; jin = lgth2-1;
                                ijp[lgth1][lgth2] = +( lgth1 - i );
                        }
                }
                for( j=0; j<lgth2; j++ )
                {
                        if( lasthorizontalw[j] >= wm )
                        {
                                wm = lasthorizontalw[j];
                                iin = lgth1-1; jin = j;
                                ijp[lgth1][lgth2] = -( lgth2 - j );
                        }
                }
        }

    for( i=0; i<lgth1+1; i++ ) 
    {
        ijp[i][0] = i + 1;
    }
    for( j=0; j<lgth2+1; j++ ) 
    {
        ijp[0][j] = -( j + 1 );
    }

        gaptable1 = gt1bk + lgth1+lgth2;
        *gaptable1 = 0;
        gaptable2 = gt2bk + lgth1+lgth2;
        *gaptable2 = 0;

        iin = lgth1; jin = lgth2;
        *impwmpt = 0.0;
        for( k=0; k<=lgth1+lgth2; k++ ) 
        {
                if( ijp[iin][jin] < 0 ) 
                {
                        ifi = iin-1; jfi = jin+ijp[iin][jin];
                }
                else if( ijp[iin][jin] > 0 )
                {
                        ifi = iin-ijp[iin][jin]; jfi = jin-1;
                }
                else
                {
                        ifi = iin-1; jfi = jin-1;
                }
                l = iin - ifi;
                while( --l ) 
                {
                        *--gaptable1 = 'o';
                        *--gaptable2 = '-';
                        k++;
                }
                l= jin - jfi;
                while( --l )
                {
                        *--gaptable1 = '-';
                        *--gaptable2 = 'o';
                        k++;
                }
                if( iin == lgth1 || jin == lgth2 )
                        ;
                else
                {
                        *impwmpt += imp_match_out_scR( iin, jin );

//              fprintf( stderr, "impwm = %f (iin=%d, jin=%d) seq1=%c, seq2=%c\n", *impwmpt, iin, jin, seq1[0][iin], seq2[0][jin] );
                }
                if( iin <= 0 || jin <= 0 ) break;
                *--gaptable1 = 'o';
                *--gaptable2 = 'o';
                k++;
                iin = ifi; jin = jfi;
        }

        for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i], gaptable1 );
        for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 );

        free( gt1bk );
        free( gt2bk );
}

static float Atracking( float *lasthorizontalw, float *lastverticalw, 
                                                char **seq1, char **seq2, 
                        char **mseq1, char **mseq2, 
                        float **cpmx1, float **cpmx2, 
                        int **ijp, int icyc, int jcyc )
{
        int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
        float wm;
        char *gaptable1, *gt1bk;
        char *gaptable2, *gt2bk;
        lgth1 = strlen( seq1[0] );
        lgth2 = strlen( seq2[0] );

        gt1bk = AllocateCharVec( lgth1+lgth2+1 );
        gt2bk = AllocateCharVec( lgth1+lgth2+1 );

#if 0
        for( i=0; i<lgth1; i++ ) 
        {
                fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
        }
#endif
 
        if( outgap == 1 )
                ;
        else
        {
                wm = lastverticalw[0];
                for( i=0; i<lgth1; i++ )
                {
                        if( lastverticalw[i] >= wm )
                        {
                                wm = lastverticalw[i];
                                iin = i; jin = lgth2-1;
                                ijp[lgth1][lgth2] = +( lgth1 - i );
                        }
                }
                for( j=0; j<lgth2; j++ )
                {
                        if( lasthorizontalw[j] >= wm )
                        {
                                wm = lasthorizontalw[j];
                                iin = lgth1-1; jin = j;
                                ijp[lgth1][lgth2] = -( lgth2 - j );
                        }
                }
        }

    for( i=0; i<lgth1+1; i++ ) 
    {
        ijp[i][0] = i + 1;
    }
    for( j=0; j<lgth2+1; j++ ) 
    {
        ijp[0][j] = -( j + 1 );
    }

        gaptable1 = gt1bk + lgth1+lgth2;
        *gaptable1 = 0;
        gaptable2 = gt2bk + lgth1+lgth2;
        *gaptable2 = 0;

        iin = lgth1; jin = lgth2;
        for( k=0; k<=lgth1+lgth2; k++ ) 
        {
                if( ijp[iin][jin] < 0 ) 
                {
                        ifi = iin-1; jfi = jin+ijp[iin][jin];
                }
                else if( ijp[iin][jin] > 0 )
                {
                        ifi = iin-ijp[iin][jin]; jfi = jin-1;
                }
                else
                {
                        ifi = iin-1; jfi = jin-1;
                }
                l = iin - ifi;
                while( --l ) 
                {
                        *--gaptable1 = 'o';
                        *--gaptable2 = '-';
                        k++;
                }
                l= jin - jfi;
                while( --l )
                {
                        *--gaptable1 = '-';
                        *--gaptable2 = 'o';
                        k++;
                }
                if( iin <= 0 || jin <= 0 ) break;
                *--gaptable1 = 'o';
                *--gaptable2 = 'o';
                k++;
                iin = ifi; jin = jfi;
        }

        for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i], gaptable1 );
        for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 );

        free( gt1bk );
        free( gt2bk );

        return( 0.0 );
}

float R__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2 )
/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
{
//      int k;
        register int i, j;
        int lasti, lastj;      /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
        int lgth1, lgth2;
        int resultlen;
        float wm = 0.0;   /* int ?????? */
        float g;
        float *currentw, *previousw;
//      float fpenalty = (float)penalty;
#if USE_PENALTY_EX
        float fpenalty_ex = (float)penalty_ex;
#endif
#if 1
        float *wtmp;
        int *ijppt;
        float *mjpt, *prept, *curpt;
        int *mpjpt;
#endif
        static TLS float mi, *m;
        static TLS int **ijp;
        static TLS int mpi, *mp;
        static TLS float *w1, *w2;
        static TLS float *match;
        static TLS float *initverticalw;    /* kufuu sureba iranai */
        static TLS float *lastverticalw;    /* kufuu sureba iranai */
        static TLS char **mseq1;
        static TLS char **mseq2;
        static TLS char **mseq;
        static TLS float *digf1;
        static TLS float *digf2;
        static TLS float *diaf1;
        static TLS float *diaf2;
        static TLS float *gapz1;
        static TLS float *gapz2;
        static TLS float *gapf1;
        static TLS float *gapf2;
        static TLS float *ogcp1g;
        static TLS float *ogcp2g;
        static TLS float *fgcp1g;
        static TLS float *fgcp2g;
        static TLS float *ogcp1;
        static TLS float *ogcp2;
        static TLS float *fgcp1;
        static TLS float *fgcp2;
        static TLS float **cpmx1;
        static TLS float **cpmx2;
        static TLS int **intwork;
        static TLS float **floatwork;
        static TLS int orlgth1 = 0, orlgth2 = 0;
        float fpenalty = (float)penalty;
        float tmppenal;
        float cumpenal;
        float *fgcp2pt;
        float *ogcp2pt;
        float fgcp1va;
        float ogcp1va;
        float kyokaipenal;



#if 0
        fprintf( stderr, "####  seq1[0] = %s\n", seq1[0] );
        fprintf( stderr, "####  seq2[0] = %s\n", seq2[0] );
#endif
        if( orlgth1 == 0 )
        {
                mseq1 = AllocateCharMtx( njob, 0 );
                mseq2 = AllocateCharMtx( njob, 0 );
        }


        lgth1 = strlen( seq1[0] );
        lgth2 = strlen( seq2[0] );
#if 0
        if( lgth1 == 0 || lgth2 == 0 )
        {
                fprintf( stderr, "WARNING (Aalignmm): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
        }
#endif

        if( lgth1 > orlgth1 || lgth2 > orlgth2 )
        {
                int ll1, ll2;

                if( orlgth1 > 0 && orlgth2 > 0 )
                {
                        FreeFloatVec( w1 );
                        FreeFloatVec( w2 );
                        FreeFloatVec( match );
                        FreeFloatVec( initverticalw );
                        FreeFloatVec( lastverticalw );

                        FreeFloatVec( m );
                        FreeIntVec( mp );

                        FreeCharMtx( mseq );

                        FreeFloatVec( digf1 );
                        FreeFloatVec( digf2 );
                        FreeFloatVec( diaf1 );
                        FreeFloatVec( diaf2 );
                        FreeFloatVec( gapz1 );
                        FreeFloatVec( gapz2 );
                        FreeFloatVec( gapf1 );
                        FreeFloatVec( gapf2 );
                        FreeFloatVec( ogcp1 );
                        FreeFloatVec( ogcp2 );
                        FreeFloatVec( fgcp1 );
                        FreeFloatVec( fgcp2 );
                        FreeFloatVec( ogcp1g );
                        FreeFloatVec( ogcp2g );
                        FreeFloatVec( fgcp1g );
                        FreeFloatVec( fgcp2g );


                        FreeFloatMtx( cpmx1 );
                        FreeFloatMtx( cpmx2 );

                        FreeFloatMtx( floatwork );
                        FreeIntMtx( intwork );
                }

                ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
                ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;

#if DEBUG
                fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
#endif

                w1 = AllocateFloatVec( ll2+2 );
                w2 = AllocateFloatVec( ll2+2 );
                match = AllocateFloatVec( ll2+2 );

                initverticalw = AllocateFloatVec( ll1+2 );
                lastverticalw = AllocateFloatVec( ll1+2 );

                m = AllocateFloatVec( ll2+2 );
                mp = AllocateIntVec( ll2+2 );

                mseq = AllocateCharMtx( njob, ll1+ll2 );

                digf1 = AllocateFloatVec( ll1+2 );
                digf2 = AllocateFloatVec( ll2+2 );
                diaf1 = AllocateFloatVec( ll1+2 );
                diaf2 = AllocateFloatVec( ll2+2 );
                gapz1 = AllocateFloatVec( ll1+2 );
                gapz2 = AllocateFloatVec( ll2+2 );
                gapf1 = AllocateFloatVec( ll1+2 );
                gapf2 = AllocateFloatVec( ll2+2 );
                ogcp1 = AllocateFloatVec( ll1+2 );
                ogcp2 = AllocateFloatVec( ll2+2 );
                fgcp1 = AllocateFloatVec( ll1+2 );
                fgcp2 = AllocateFloatVec( ll2+2 );
                ogcp1g = AllocateFloatVec( ll1+2 );
                ogcp2g = AllocateFloatVec( ll2+2 );
                fgcp1g = AllocateFloatVec( ll1+2 );
                fgcp2g = AllocateFloatVec( ll2+2 );

                cpmx1 = AllocateFloatMtx( 26, ll1+2 );
                cpmx2 = AllocateFloatMtx( 26, ll2+2 );

#if FASTMATCHCALC
                floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 ); 
                intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 27 ); 
#else
                floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 ); 
                intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 ); 
#endif

#if DEBUG
                fprintf( stderr, "succeeded\n" );
#endif

                orlgth1 = ll1 - 100;
                orlgth2 = ll2 - 100;
        }


        for( i=0; i<icyc; i++ )
        {
                mseq1[i] = mseq[i];
                seq1[i][lgth1] = 0;
        }
        for( j=0; j<jcyc; j++ )
        {
                mseq2[j] = mseq[icyc+j];
                seq2[j][lgth2] = 0;
        }


        if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
        {
                int ll1, ll2;

                if( commonAlloc1 && commonAlloc2 )
                {
                        FreeIntMtx( commonIP );
                }

                ll1 = MAX( orlgth1, commonAlloc1 );
                ll2 = MAX( orlgth2, commonAlloc2 );

#if DEBUG
                fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
#endif

                commonIP = AllocateIntMtx( ll1+10, ll2+10 );

#if DEBUG
                fprintf( stderr, "succeeded\n\n" );
#endif

                commonAlloc1 = ll1;
                commonAlloc2 = ll2;
        }
        ijp = commonIP;

#if 0
        {
                float t = 0.0;
                for( i=0; i<icyc; i++ )
                        t += eff1[i];
        fprintf( stderr, "## totaleff = %f\n", t );
        }
#endif

        cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
        cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );

        if( sgap1 )
        {
                new_OpeningGapCount_zure( ogcp1g, icyc, seq1, eff1, lgth1, sgap1, egap1 );
                new_OpeningGapCount_zure( ogcp2g, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
                new_FinalGapCount_zure( fgcp1g, icyc, seq1, eff1, lgth1, sgap1, egap1 );
                new_FinalGapCount_zure( fgcp2g, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
                getdigapfreq_part( digf1, icyc, seq1, eff1, lgth1, sgap1, egap1 );
                getdigapfreq_part( digf2, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
                getdiaminofreq_part( diaf1, icyc, seq1, eff1, lgth1, sgap1, egap1 );
                getdiaminofreq_part( diaf2, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
                getgapfreq( gapf1, icyc, seq1, eff1, lgth1 );
                getgapfreq( gapf2, jcyc, seq2, eff2, lgth2 );
                getgapfreq_zure_part( gapz1, icyc, seq1, eff1, lgth1, sgap1 );
                getgapfreq_zure_part( gapz2, jcyc, seq2, eff2, lgth2, sgap1 );
        }
        else
        {
                st_OpeningGapCount( ogcp1g, icyc, seq1, eff1, lgth1 );
                st_OpeningGapCount( ogcp2g, jcyc, seq2, eff2, lgth2 );
                st_FinalGapCount_zure( fgcp1g, icyc, seq1, eff1, lgth1 );
                st_FinalGapCount_zure( fgcp2g, jcyc, seq2, eff2, lgth2 );
                getdigapfreq_st( digf1, icyc, seq1, eff1, lgth1 );
                getdigapfreq_st( digf2, jcyc, seq2, eff2, lgth2 );
                getdiaminofreq_x( diaf1, icyc, seq1, eff1, lgth1 );
                getdiaminofreq_x( diaf2, jcyc, seq2, eff2, lgth2 );
                getgapfreq( gapf1, icyc, seq1, eff1, lgth1 );
                getgapfreq( gapf2, jcyc, seq2, eff2, lgth2 );
                getgapfreq_zure( gapz1, icyc, seq1, eff1, lgth1 );
                getgapfreq_zure( gapz2, jcyc, seq2, eff2, lgth2 );
        }

#if 0
        for( i=0; i<lgth1; i++ ) 
                fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
#endif

        currentw = w1;
        previousw = w2;

        match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
        if( localhom )
                imp_match_out_vead_tateR( initverticalw, 0, lgth1 ); // 060306

        match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
        if( localhom )
                imp_match_out_veadR( currentw, 0, lgth2 ); // 060306


#if 0 // -> tbfast.c
        if( localhom )
                imp_match_calc( currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );

#endif



        kyokaipenal = 0.0;
        if( outgap == 1 )
        {
                g = 0.0;

                g += ogcp1g[0] * ( 1.0-ogcp2g[0] ) * fpenalty * 0.5;
//              if( g ) fprintf( stderr, "init-match penal1=%f, %c-%c\n", g, seq1[0][0], seq2[0][0] );

                g += ogcp2g[0] * ( 1.0-ogcp1g[0] ) * fpenalty * 0.5;
//              if( g ) fprintf( stderr, "init-match penal2=%f, %c-%c\n", g, seq1[0][0], seq2[0][0] );

                g += fgcp1g[0] * ( 1.0-fgcp2g[0] ) * fpenalty * 0.5;
//              if( g ) fprintf( stderr, "match penal1=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );

                g += fgcp2g[0] * ( 1.0-fgcp1g[0] ) * fpenalty * 0.5;
//              if( g ) fprintf( stderr, "match penal2=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );

                kyokaipenal = g;
                initverticalw[0] += g;
                currentw[0] += g;

                cumpenal = 0.0;
                for( i=1; i<lgth1+1; i++ )
                {
//                      initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;

//      Q               tmppenal = ( (1.0-gapz2[0])*(1.0-ogcp1g[0]+fgcp1g[0]-digf1[0]) ) * 0.5 * fpenalty; // mada
//                      tmppenal = ( (1.0-gapf2[j-1])*(1.0-ogcp1g[i]+fgcp1g[i]) + gapf2[j-1]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
                        tmppenal = ( (1.0-gapz2[0])*(1.0-ogcp1g[0]+0.0) + gapz2[0]*(1.0-digf1[0] - diaf1[0]) ) * 0.5 * fpenalty; // mada
//                      tmppenal = ( (1.0-0.0)*(1.0-ogcp1g[0]+0.0) + 0.0*(1.0-0.0-0.0) ) * 0.5 * fpenalty; // mada
//                      tmppenal = 0.5 * fpenalty;
//                      tmppenal -= ( (1.0-0.0) * (1.0-diaf1[0]) + 0.0 ) * 0.5 * fpenalty; // 0.
//                      tmppenal -= ( (1.0-gapf2[j-1]) * ogcp1g[i] + gapf2[j-1] ) * 0.5 * fpenalty;
//                      fprintf( stderr, "0,0<-%d,%d, tmppenal 1 = %f\n", i, 0, tmppenal );
                        initverticalw[i] += tmppenal;

//      Q               tmppenal = ( (1.0-gapz2[1])*(1.0-fgcp1g[i]+ogcp1g[i]-digf1[i]) ) * 0.5 * fpenalty; // mada
//                      tmppenal = ( (1.0-gapf2[j])*(1.0-fgcp1g[i]+ogcp1g[i]) + gapf2[j]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
                        tmppenal = ( (1.0-gapz2[1])*(1.0-fgcp1g[i]+ogcp1g[i]) + gapz2[1]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
//                      tmppenal = ( (1.0-gapf2[0])*(1.0-fgcp1g[i]+ogcp1g[i]) + gapf2[0]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
//                      tmppenal = 0.5 * fpenalty;
//                      tmppenal -= ( (1.0-gapf2[0]) * (1.0-diaf1[i]) + gapf2[0] ) * 0.5 * fpenalty;
//                      tmppenal -= ( (1.0-gapf2[j]) * fgcp1g[i] + gapf2[j] ) * 0.5 * fpenalty;
                        initverticalw[i] += tmppenal;
                        cumpenal += ( ogcp1g[i-0] + fgcp1g[i] ) * fpenalty * 0.5;
                        initverticalw[i] += cumpenal - fgcp1g[i] * fpenalty * 0.5; // honto ha iru
//                      fprintf( stderr, "0,0<-%d,%d, tmppenal 2 = %f, cumpenal=%f, fgcp1g[i]=%f, ogcp1g[i]=%f\n", i, 0, tmppenal, cumpenal, fgcp1g[i], ogcp1g[i] );

                }
                cumpenal = 0.0;
                for( j=1; j<lgth2+1; j++ )
                {
//                      currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;

//                      tmppenal = ( (1.0-gapz1[0])*(1.0-ogcp2g[0]+fgcp2g[0]-digf2[0]) ) * 0.5 * fpenalty; // mada
//                      tmppenal = ( (1.0-gapf1[i-1])*(1.0-ogcp2g[j]+fgcp2g[j]) + gapf1[i-1]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
                        tmppenal = ( (1.0-gapz1[0])*(1.0-ogcp2g[0]+0.0) + gapz1[0]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
//                      tmppenal = ( (1.0-0.0)*(1.0-ogcp2g[0]+0.0) + 0.0*(1.0-0.0-0.0) ) * 0.5 * fpenalty; // mada
//                      tmppenal = 0.5 * fpenalty;
//                      tmppenal -= ( (1.0-0.0) * (1.0-diaf2[0]) + 0.0 ) * 0.5 * fpenalty; // 0.
//                      tmppenal -= ( (1.0-gapf1[0]) * fgcp2g[j] + gapf1[0] ) * 0.5 * fpenalty;
//                      fprintf( stderr, "0,0<-%d,%d, tmppenal 3 = %f\n", 0, j, tmppenal );
                        currentw[j] += tmppenal;

//                      tmppenal = ( (1.0-gapz1[1])*(1.0-fgcp2g[j]+ogcp2g[j]-digf2[j]) ) * 0.5 * fpenalty; // mada
//                      tmppenal = ( (1.0-gapf1[i])*(1.0-fgcp2g[j]+ogcp2g[j]) + gapf1[i]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
                        tmppenal = ( (1.0-gapz1[1])*(1.0-fgcp2g[j]+ogcp2g[j]) + gapz1[1]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
//                      tmppenal = ( (1.0-gapf1[0])*(1.0-fgcp2g[j]+ogcp2g[j]) + gapf1[0]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
//                      tmppenal = 0.5 * fpenalty;
//                      tmppenal -= ( (1.0-gapf1[0]) * (1.0-diaf2[j]) + gapf1[0] ) * 0.5 * fpenalty;
//                      tmppenal -= ( (1.0-gapf1[0]) * ogcp2g[j] + gapf1[i-1] ) * 0.5 * fpenalty;
//                      fprintf( stderr, "0,0<-%d,%d, tmppenal 4 = %f\n", 0, j, tmppenal );
                        currentw[j] += tmppenal;
                        cumpenal += ( ogcp2g[j-0] + fgcp2g[j] ) * fpenalty * 0.5;
                        currentw[j] += cumpenal - fgcp2g[j] * fpenalty * 0.5; // honto ha iru
                }
        }
#if OUTGAP0TRY
        else
        {
                for( j=1; j<lgth2+1; j++ )
                        currentw[j] -= offset * j / 2.0;
                for( i=1; i<lgth1+1; i++ )
                        initverticalw[i] -= offset * i / 2.0;
        }
#endif

        m[0] = 0.0; // iranai
        for( j=1; j<lgth2+1; ++j ) 
        {
                mp[j] = 0;
                m[j] = currentw[j-1] + 10000 * fpenalty; //iinoka?
        }
        if( lgth2 == 0 )
                lastverticalw[0] = 0.0; // Falign kara yobaretatoki kounarukanousei ari
        else
                lastverticalw[0] = currentw[lgth2-1];

        if( outgap ) lasti = lgth1+1; else lasti = lgth1;

#if XXXXXXX
fprintf( stderr, "currentw = \n" );
for( i=0; i<lgth1+1; i++ )
{
        fprintf( stderr, "%5.2f ", currentw[i] );
}
fprintf( stderr, "\n" );
fprintf( stderr, "initverticalw = \n" );
for( i=0; i<lgth2+1; i++ )
{
        fprintf( stderr, "%5.2f ", initverticalw[i] );
}
fprintf( stderr, "\n" );
fprintf( stderr, "fcgp\n" );
for( i=0; i<lgth1; i++ ) 
        fprintf( stderr, "fgcp1[%d]=%f\n", i, ogcp1[i] );
for( i=0; i<lgth2; i++ ) 
        fprintf( stderr, "fgcp2[%d]=%f\n", i, ogcp2[i] );
#endif

        for( i=1; i<lasti; i++ )
        {
                wtmp = previousw; 
                previousw = currentw;
                currentw = wtmp;

                previousw[0] = initverticalw[i-1];

                match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
#if XXXXXXX
fprintf( stderr, "\n" );
fprintf( stderr, "i=%d\n", i );
fprintf( stderr, "currentw = \n" );
for( j=0; j<lgth2; j++ )
{
        fprintf( stderr, "%5.2f ", currentw[j] );
}
fprintf( stderr, "\n" );
#endif
                if( localhom )
                {
//                      fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
#if  0
                        imp_match_out_veadR( currentw, i, lgth2 );
#else
                        imp_match_out_veadR( currentw, i, lgth2 );
#endif
                }
#if XXXXXXX
fprintf( stderr, "\n" );
fprintf( stderr, "i=%d\n", i );
fprintf( stderr, "currentw = \n" );
for( j=0; j<lgth2; j++ )
{
        fprintf( stderr, "%5.2f ", currentw[j] );
}
fprintf( stderr, "\n" );
#endif
                currentw[0] = initverticalw[i];

                mpi = 0;
                mi = previousw[0] + 10000 * fpenalty;

                ijppt = ijp[i] + 1;
                mjpt = m + 1;
                prept = previousw;
                curpt = currentw + 1;
                mpjpt = mp + 1;
                fgcp2pt = fgcp2;
                ogcp2pt = ogcp2 + 1;
                fgcp1va = fgcp1[i-1];
                ogcp1va = ogcp1[i];
                lastj = lgth2+1;
                for( j=1; j<lastj; j++ )
                {
                        wm = *prept;

                        g = ogcp1g[i] * ( 1.0-ogcp2g[j] ) * fpenalty * 0.5;
//                      if( g && i==j ) fprintf( stderr, "match penal1=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
                        wm += g;

                        g = ogcp2g[j] * ( 1.0-ogcp1g[i] ) * fpenalty * 0.5;
//                      if( g && i==j ) fprintf( stderr, "match penal2=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
                        wm += g;

                        g = fgcp1g[i] * ( 1.0-fgcp2g[j] ) * fpenalty * 0.5;
//                      if( g && i==j ) fprintf( stderr, "match penal3=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
                        wm += g;

                        g = fgcp2g[j] * ( 1.0-fgcp1g[i] ) * fpenalty * 0.5;
//                      if( g && i==j ) fprintf( stderr, "match penal4=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
                        wm += g;

#if 0
                        g = fgcp2g[j] * ogcp1g[i] * fpenalty * 0.5;
                        if( g ) fprintf( stderr, "match m-penal5=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
                        wm -= g;

                        g = fgcp1g[i] * ogcp2g[j] * fpenalty * 0.5;
                        if( g ) fprintf( stderr, "match m-penal6=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
                        wm -= g;
#endif

                        *ijppt = 0;

#if 0
                        fprintf( stderr, "%5.0f->", wm );
#endif
#if 0
                        fprintf( stderr, "%5.0f?", g );
#endif
//                      tmppenal = ( (1.0-gapz1[i+1])*(1.0-fgcp2g[j]+ogcp2g[j]-digf2[j]) ) * 0.5 * fpenalty; // mada
//                      tmppenal = ( (1.0-gapf1[i])*(1.0-fgcp2g[j]) + gapf1[i]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
                        tmppenal = ( (1.0-gapz1[i+1])*(1.0-fgcp2g[j]+ogcp2g[j]) + gapz1[i+1]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
//                      tmppenal = ( (1.0-gapf1[i])*(1.0-fgcp2g[j]+ogcp2g[j]) + gapf1[i]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
//                      tmppenal = 0.5 * fpenalty;
//                      tmppenal -= ( (1.0-gapf1[i])*(1.0-diaf2[j]) + gapf1[i] ) * 0.5 * fpenalty;
//                      tmppenal -= ( (1.0-gapf1[i])*fgcp2g[j] + gapf1[i] ) * 0.5 * fpenalty;
//                      tmppenal = *fgcp2pt-fpenalty*0.5*gapf1[i];
//                      tmppenal = *fgcp2pt;
                        if( (g=mi+tmppenal) > wm )
                        {
//                              fprintf( stderr, "jump i start=%f (j=%d, fgcp2g[j]=%f, digf2[j]=%f, diaf2[j]=%f), %c-%c\n", g-mi, j, fgcp2g[j], digf2[j], diaf2[j], seq1[0][i], seq2[0][j] );
                                wm = g;
                                *ijppt = -( j - mpi );
                        }
//                      tmppenal = ( (1.0-gapz1[i])*(1.0-ogcp2g[j]+fgcp2g[j]-digf2[j]) ) * 0.5 * fpenalty; // mada
                        tmppenal = ( (1.0-gapz1[i])*(1.0-ogcp2g[j]+fgcp2g[j]) + gapz1[i]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
//                      tmppenal = ( (1.0-gapf1[i-1])*(1.0-ogcp2g[j]+fgcp2g[j]) + gapf1[i-1]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada
//                      tmppenal = *ogcp2pt-fpenalty*0.5*(gapf2[j-1]+gapf1[i-1]);
//                      tmppenal = 0.5 * fpenalty;
//                      tmppenal -= ( (1.0-gapf1[i-1])*(1.0-diaf2[j]) + gapf1[i-1] ) * 0.5 * fpenalty;
//                      tmppenal -= ( (1.0-gapf1[i-1])*ogcp2g[j] + gapf1[i-1] ) * 0.5 * fpenalty;
//                      tmppenal = *prept+*ogcp2pt;
                        if( (g=*prept+tmppenal) >= mi )
                        {
//                              fprintf( stderr, "jump i end=%f, %c-%c\n", g-*prept, seq1[0][i-1], seq2[0][j-1] );
                                mi = g;
                                mpi = j-1;
                        }
                        else if( j != 1 )
                        {
                                mi += ( ogcp2g[j-0] + fgcp2g[j] ) * fpenalty * 0.5; // CHUUI honto ha iru
//                              fprintf( stderr, "%c%c/%c%c exp, og=%f,fg=%f\n", '=', '=', seq2[0][j-1], seq2[0][j], ogcp2g[j-0] * fpenalty*0.5, fgcp2g[j] * fpenalty*0.5 );
                        }
#if USE_PENALTY_EX
                                mi += fpenalty_ex;
#endif

#if 0 
                        fprintf( stderr, "%5.0f?", g );
#endif
//                      tmppenal = ( (1.0-gapz2[j+1])*(1.0-fgcp1g[i]+ogcp1g[i]-digf1[i]) ) * 0.5 * fpenalty; // mada
                        tmppenal = ( (1.0-gapz2[j+1])*(1.0-fgcp1g[i]+ogcp1g[i]) + gapz2[j+1]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
//                      tmppenal = ( (1.0-gapf2[j])*(1.0-fgcp1g[i]+ogcp1g[i]) + gapf2[j]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
//                      tmppenal = ( (1.0-gapf2[j])*(1.0-fgcp1g[i]) + gapf2[j]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
//                      tmppenal = 0.5 * fpenalty;
//                      tmppenal -= ( (1.0-gapf2[j])*(1.0-diaf1[i]) + gapf2[j] ) * 0.5 * fpenalty;
//                      tmppenal -= ( (1.0-gapf2[j])*fgcp1g[i] + gapf2[j] ) * 0.5 * fpenalty;
//                      tmppenal = fgcp1va-fpenalty*0.5*gapf2[j];
//                      tmppenal = fgcp1va;
                        if( (g=*mjpt+tmppenal) > wm )
                        {
//                              if( seq1[0][i] == 'Y' && seq2[0][j] == 'B' )
//                                      fprintf( stderr, "jump j start=%f, %c-%c\n", g-*mjpt, seq1[0][i], seq2[0][j] );
                                wm = g;
                                *ijppt = +( i - *mpjpt );
                        }
//                      tmppenal = ( (1.0-gapz2[j])*(1.0-ogcp1g[i]+fgcp1g[i]-digf1[i]) ) * 0.5 * fpenalty; // mada
                        tmppenal = ( (1.0-gapz2[j])*(1.0-ogcp1g[i]+fgcp1g[i]) + gapz2[j]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
//                      tmppenal = ( (1.0-gapf2[j-1])*(1.0-ogcp1g[i]+fgcp1g[i]) + gapf2[j-1]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
//                      tmppenal = ( (1.0-gapf2[j-1])*(1.0-ogcp1g[i]) + gapf2[j-1]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada
//                      tmppenal = ogcp1va-fpenalty*0.5*(gapf1[i-1]+gapf2[j-1]);
//                      tmppenal = 0.5 * fpenalty;
//                      tmppenal -= ( (1.0-gapf2[j-1]) * (1.0-diaf1[i]) + gapf2[j-1] ) * 0.5 * fpenalty;
//                      tmppenal -= ( (1.0-gapf2[j-1]) * ogcp1g[i] + gapf2[j-1] ) * 0.5 * fpenalty;
//                      tmppenal = 0.5 * fpenalty - ( (1.0-gapf2[j-1]) * (ogcp1g[i]) + gapf2[j-1] ) * ( 0.5 * fpenalty );
//                      tmppenal = ogcp1va-fpenalty*0.5*gapf2[j-1];
//                      tmppenal = ogcp1va;
                        if( (g=*prept+tmppenal) >= *mjpt )
                        {
//                              if( seq1[0][i] == 'T' && seq2[0][j] == 'T' )
//                                      fprintf( stderr, "jump j end=%f, %c-%c\n", g-*prept, seq1[0][i-1], seq2[0][j-1] );
                                *mjpt = g;
                                *mpjpt = i-1;
                        }
                        else if( i != 1 )
                        {
                                m[j] += ( ogcp1g[i-0] + fgcp1g[i] ) * fpenalty * 0.5; // CHUUI honto ha iru
//                              fprintf( stderr, "%c%c/%c%c exp, og=%f,fg=%f\n", seq1[0][i-1], seq1[0][i], '=', '=', ogcp1g[i-0] * fpenalty*0.5, fgcp1g[i] * fpenalty*0.5 );
                        }
#if USE_PENALTY_EX
                        m[j] += fpenalty_ex;
#endif

#if 0
                        fprintf( stderr, "%5.0f ", wm );
#endif
                        *curpt++ += wm;
                        ijppt++;
                        mjpt++;
                        prept++;
                        mpjpt++;
                        fgcp2pt++;
                        ogcp2pt++;
                }
                lastverticalw[i] = currentw[lgth2-1];
        }

//      fprintf( stderr, "wm = %f\n", wm );

#if OUTGAP0TRY
        if( !outgap )
        {
                for( j=1; j<lgth2+1; j++ )
                        currentw[j] -= offset * ( lgth2 - j ) / 2.0;
                for( i=1; i<lgth1+1; i++ )
                        lastverticalw[i] -= offset * ( lgth1 - i  / 2.0);
        }
#endif
                
        /*
        fprintf( stderr, "\n" );
        for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
        fprintf( stderr, "#####\n" );
        for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
        fprintf( stderr, "====>" );
        for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
        for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
        */
        if( localhom )
        {
                Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
        }
        else
                Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );

//      fprintf( stderr, "### impmatch = %f\n", *impmatch );

        resultlen = strlen( mseq1[0] );
        if( alloclen < resultlen || resultlen > N )
        {
                fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
                ErrorExit( "LENGTH OVER!\n" );
        }


        for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
        for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
        /*
        fprintf( stderr, "\n" );
        for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
        fprintf( stderr, "#####\n" );
        for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
        */

        fprintf( stderr, "wm = %f\n", wm );


        return( wm );
}