source: tags/arb-6.0/GDE/MAFFT/mafft-7.055-with-extensions/core/rna.c

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

#define MEMSAVE 1

#define DEBUG 1
#define USE_PENALTY_EX  1
#define STOREWM 1



static float singleribosumscore( int n1, int n2, char **s1, char **s2, double *eff1, double *eff2, int p1, int p2 )
{
        float val;
        int i, j;
        int code1, code2;

        val = 0.0;
        for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
        {
                code1 = amino_n[(int)s1[i][p1]];
                if( code1 > 3 ) code1 = 36;
                code2 = amino_n[(int)s2[j][p2]];
                if( code2 > 3 ) code2 = 36;

//              fprintf( stderr, "'l'%c-%c: %f\n", s1[i][p1], s2[j][p2], (float)ribosumdis[code1][code2] );

                val += (float)ribosumdis[code1][code2] * eff1[i] * eff2[j];
        }
        return( val );
}
static float pairedribosumscore53( int n1, int n2, char **s1, char **s2, double *eff1, double *eff2, int p1, int p2, int c1, int c2 )
{
        float val;
        int i, j;
        int code1o, code1u, code2o, code2u, code1, code2;

        val = 0.0;
        for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
        {
                code1o = amino_n[(int)s1[i][p1]];
                code1u = amino_n[(int)s1[i][c1]];
                if( code1o > 3 ) code1 = code1o = 36;
                else if( code1u > 3 ) code1 = 36;
                else code1 = 4 + code1o * 4 + code1u;

                code2o = amino_n[(int)s2[j][p2]];
                code2u = amino_n[(int)s2[j][c2]];
                if( code2o > 3 ) code2 = code1o = 36;
                else if( code2u > 3 ) code2 = 36;
                else code2 = 4 + code2o * 4 + code2u;


//              fprintf( stderr, "%c%c-%c%c: %f\n", s1[i][p1], s1[i][c1], s2[j][p2], s2[j][c2], (float)ribosumdis[code1][code2] );

                if( code1 == 36 || code2 == 36 )
                        val += (float)n_dis[code1o][code2o] * eff1[i] * eff2[j];
                else
                        val += (float)ribosumdis[code1][code2] * eff1[i] * eff2[j];
        }
        return( val );
}

static float pairedribosumscore35( int n1, int n2, char **s1, char **s2, double *eff1, double *eff2, int p1, int p2, int c1, int c2 )
{
        float val;
        int i, j;
        int code1o, code1u, code2o, code2u, code1, code2;

        val = 0.0;
        for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
        {
                code1o = amino_n[(int)s1[i][p1]];
                code1u = amino_n[(int)s1[i][c1]];
                if( code1o > 3 ) code1 = code1o = 36;
                else if( code1u > 3 ) code1 = 36;
                else code1 = 4 + code1u * 4 + code1o;

                code2o = amino_n[(int)s2[j][p2]];
                code2u = amino_n[(int)s2[j][c2]];
                if( code2o > 3 ) code2 = code1o = 36;
                else if( code2u > 3 ) code2 = 36;
                else code2 = 4 + code2u * 4 + code2o;


//              fprintf( stderr, "%c%c-%c%c: %f\n", s1[i][p1], s1[i][c1], s2[j][p2], s2[j][c2], (float)ribosumdis[code1][code2] );

                if( code1 == 36 || code2 == 36 )
                        val += (float)n_dis[code1o][code2o] * eff1[i] * eff2[j];
                else
                        val += (float)ribosumdis[code1][code2] * eff1[i] * eff2[j];
        }
        return( val );
}


static void mccaskillextract( char **seq, char **nogap, int nseq, RNApair **pairprob, RNApair ***single, int **sgapmap, double *eff )
{
        int lgth;
        int nogaplgth;
        int i, j;
        int left, right, adpos;
        float prob;
        static TLS int *pairnum;
        RNApair *pt, *pt2;

        lgth = strlen( seq[0] );
        pairnum = calloc( lgth, sizeof( int ) );
        for( i=0; i<lgth; i++ ) pairnum[i] = 0;

        for( i=0; i<nseq; i++ )
        {
                nogaplgth = strlen( nogap[i] );
                for( j=0; j<nogaplgth; j++ ) for( pt=single[i][j]; pt->bestpos!=-1; pt++ )
                {
                        left = sgapmap[i][j];
                        right = sgapmap[i][pt->bestpos];
                        prob = pt->bestscore;


                        for( pt2=pairprob[left]; pt2->bestpos!=-1; pt2++ )
                                if( pt2->bestpos == right ) break;

//                      fprintf( stderr, "i,j=%d,%d, left=%d, right=%d, pt=%d, pt2->bestpos = %d\n", i, j, left, right, pt-single[i][j], pt2->bestpos );
                        if( pt2->bestpos == -1 )
                        {
                                pairprob[left] = (RNApair *)realloc( pairprob[left], (pairnum[left]+2) * sizeof( RNApair ) );
                                adpos = pairnum[left];
                                pairnum[left]++;
                                pairprob[left][adpos].bestscore = 0.0;
                                pairprob[left][adpos].bestpos = right;
                                pairprob[left][adpos+1].bestscore = -1.0;
                                pairprob[left][adpos+1].bestpos = -1;
                                pt2 = pairprob[left]+adpos;
                        }
                        else
                                adpos = pt2-pairprob[left];

                        pt2->bestscore += prob * eff[i];

                        if( pt2->bestpos != right )
                        {
                                fprintf( stderr, "okashii!\n" );
                                exit( 1 );
                        }
//                      fprintf( stderr, "adding %d-%d, %f\n", left, right, prob );
//                      fprintf( stderr, "pairprob[0][0].bestpos=%d\n", pairprob[0][0].bestpos );
//                      fprintf( stderr, "pairprob[0][0].bestscore=%f\n", pairprob[0][0].bestscore );
                }
        }

//      fprintf( stderr, "before taikakuka\n" );
        for( i=0; i<lgth; i++ ) for( j=0; j<pairnum[i]; j++ )
        {
                if( pairprob[i][j].bestpos > -1 )
                {
//                      pairprob[i][j].bestscore /= (float)nseq;
//                      fprintf( stderr, "pair of %d = %d (%f) %c:%c\n", i, pairprob[i][j].bestpos, pairprob[i][j].bestscore, seq[0][i], seq[0][pairprob[i][j].bestpos] );
                }
        }

#if 0
        for( i=0; i<lgth; i++ ) for( j=0; j<pairnum[i]; j++ )
        {
                right=pairprob[i][j].bestpos;
                if( right < i ) continue;
                fprintf( stderr, "no%d-%d, adding %d -> %d\n", i, j, right, i );
                pairprob[right] = (RNApair *)realloc( pairprob[right], (pairnum[right]+2) * sizeof( RNApair ) );
                pairprob[right][pairnum[right]].bestscore = pairprob[i][j].bestscore;
                pairprob[right][pairnum[right]].bestpos = i;
                pairnum[right]++;
                pairprob[right][pairnum[right]].bestscore = -1.0;
                pairprob[right][pairnum[right]].bestpos = -1;
        }
#endif

        free( pairnum );

}


void rnaalifoldcall( char **seq, int nseq, RNApair **pairprob )
{
        int lgth;
        int i;
        static TLS int *order = NULL;
        static TLS char **name = NULL;
        char gett[1000];
        FILE *fp;
        int left, right, dumm;
        float prob;
        static TLS int pid;
        static TLS char fnamein[100];
        static TLS char cmd[1000];
        static TLS int *pairnum;

        lgth = strlen( seq[0] );
        if( order == NULL )
        {
                pid = (int)getpid();
                sprintf( fnamein, "/tmp/_rnaalifoldin.%d", pid );
                order = AllocateIntVec( njob );
                name = AllocateCharMtx( njob, 10 );
                for( i=0; i<njob; i++ )
                {
                        order[i] = i;
                        sprintf( name[i], "seq%d", i );
                }
        }
        pairnum = calloc( lgth, sizeof( int ) );
        for( i=0; i<lgth; i++ ) pairnum[i] = 0;

        fp = fopen( fnamein, "w" );
        if( !fp )
        {
                fprintf( stderr, "Cannot open /tmp/_rnaalifoldin\n" );
                exit( 1 );
        }
        clustalout_pointer( fp, nseq, lgth, seq, name, NULL, NULL, order, 15 );
        fclose( fp );

        sprintf( cmd, "RNAalifold -p %s", fnamein );
        system( cmd );

        fp = fopen( "alifold.out", "r" );
        if( !fp )
        {
                fprintf( stderr, "Cannot open /tmp/_rnaalifoldin\n" );
                exit( 1 );
        }

#if 0
        for( i=0; i<lgth; i++ ) // atode kesu
        {
                pairprob[i] = (RNApair *)realloc( pairprob[i], (2) * sizeof( RNApair ) ); // atode kesu
                pairprob[i][1].bestscore = -1.0;
                pairprob[i][1].bestpos = -1;
        }
#endif

        while( 1 )
        {
                fgets( gett, 999, fp );
                if( gett[0] == '(' ) break;
                if( gett[0] == '{' ) break;
                if( gett[0] == '.' ) break;
                if( gett[0] == ',' ) break;
                if( gett[0] != ' ' ) continue;

                sscanf( gett, "%d %d %d %f", &left, &right, &dumm, &prob );
                left--;
                right--;


#if 0
                if( prob > 50.0 && prob > pairprob[left][0].bestscore )
                {
                        pairprob[left][0].bestscore = prob;
                        pairprob[left][0].bestpos = right;
#else
                if( prob > 0.0 )
                {
                        pairprob[left] = (RNApair *)realloc( pairprob[left], (pairnum[left]+2) * sizeof( RNApair ) );
                        pairprob[left][pairnum[left]].bestscore = prob / 100.0;
                        pairprob[left][pairnum[left]].bestpos = right;
                        pairnum[left]++;
                        pairprob[left][pairnum[left]].bestscore = -1.0;
                        pairprob[left][pairnum[left]].bestpos = -1;
                        fprintf( stderr, "%d-%d, %f\n", left, right, prob );

                        pairprob[right] = (RNApair *)realloc( pairprob[right], (pairnum[right]+2) * sizeof( RNApair ) );
                        pairprob[right][pairnum[right]].bestscore = prob / 100.0;
                        pairprob[right][pairnum[right]].bestpos = left;
                        pairnum[right]++;
                        pairprob[right][pairnum[right]].bestscore = -1.0;
                        pairprob[right][pairnum[right]].bestpos = -1;
                        fprintf( stderr, "%d-%d, %f\n", left, right, prob );
#endif
                }
        }
        fclose( fp );
        sprintf( cmd, "rm -f %s", fnamein );
        system( cmd ); 

        for( i=0; i<lgth; i++ )
        {
                if( (right=pairprob[i][0].bestpos) > -1 )
                {
                        pairprob[right][0].bestpos = i;
                        pairprob[right][0].bestscore = pairprob[i][0].bestscore;
                }
        }

#if 0
        for( i=0; i<lgth; i++ ) // atode kesu
                if( pairprob[i][0].bestscore > -1 ) pairprob[i][0].bestscore = 1.0; // atode kesu
#endif

//      fprintf( stderr, "after taikakuka in rnaalifoldcall\n" );
//      for( i=0; i<lgth; i++ )
//      {
//              fprintf( stderr, "pair of %d = %d (%f) %c:%c\n", i, pairprob[i][0].bestpos, pairprob[i][0].bestscore, seq[0][i], seq[0][pairprob[i][0].bestpos] );
//      }

        free( pairnum );
}


static void utot( int n, int l, char **s )
{
        int i, j;
        for( i=0; i<l; i++ )
        {
                for( j=0; j<n; j++ )
                {
                        if     ( s[j][i] == 'a' ) s[j][i] = 'a';
                        else if( s[j][i] == 't' ) s[j][i] = 't';
                        else if( s[j][i] == 'u' ) s[j][i] = 't';
                        else if( s[j][i] == 'g' ) s[j][i] = 'g';
                        else if( s[j][i] == 'c' ) s[j][i] = 'c';
                        else if( s[j][i] == '-' ) s[j][i] = '-';
                        else                                      s[j][i] = 'n';
                }
        }
}


void foldrna( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***grouprna1, RNApair ***grouprna2, float **impmtx, int *gapmap1, int *gapmap2, RNApair *additionalpair )
{
        int i, j;
//      int ui, uj;
//      int uiup, ujup;
        int uido, ujdo;
        static TLS char **useq1, **useq2;
        static TLS char **oseq1, **oseq2, **oseq1r, **oseq2r, *odir1, *odir2;
        static TLS RNApair **pairprob1, **pairprob2;
        static TLS RNApair *pairpt1, *pairpt2;
        int lgth1 = strlen( seq1[0] );
        int lgth2 = strlen( seq2[0] );
        static TLS float **impmtx2;
        static TLS float **map;
//      double lenfac;
        float prob;
        int **sgapmap1, **sgapmap2;
//      char *nogapdum;
        float **tbppmtx;


//      fprintf( stderr, "nseq1=%d, lgth1=%d\n", nseq1, lgth1 );
        useq1 = AllocateCharMtx( nseq1, lgth1+10 );
        useq2 = AllocateCharMtx( nseq2, lgth2+10 );
        oseq1 = AllocateCharMtx( nseq1, lgth1+10 );
        oseq2 = AllocateCharMtx( nseq2, lgth2+10 );
        oseq1r = AllocateCharMtx( nseq1, lgth1+10 );
        oseq2r = AllocateCharMtx( nseq2, lgth2+10 );
        odir1 = AllocateCharVec( lgth1+10 );
        odir2 = AllocateCharVec( lgth2+10 );
        sgapmap1 = AllocateIntMtx( nseq1, lgth1+1 );
        sgapmap2 = AllocateIntMtx( nseq2, lgth2+1 );
//      nogapdum = AllocateCharVec( MAX( lgth1, lgth2 ) );
        pairprob1 = (RNApair **)calloc( lgth1, sizeof( RNApair *) );
        pairprob2 = (RNApair **)calloc( lgth2, sizeof( RNApair *) );
        map = AllocateFloatMtx( lgth1, lgth2 );
        impmtx2 = AllocateFloatMtx( lgth1, lgth2 );
        tbppmtx = AllocateFloatMtx( lgth1, lgth2 );

        for( i=0; i<nseq1; i++ ) strcpy( useq1[i], seq1[i] );
        for( i=0; i<nseq2; i++ ) strcpy( useq2[i], seq2[i] );
        for( i=0; i<nseq1; i++ ) strcpy( oseq1[i], seq1[i] );
        for( i=0; i<nseq2; i++ ) strcpy( oseq2[i], seq2[i] );

        for( i=0; i<nseq1; i++ ) commongappick_record( 1, useq1+i, sgapmap1[i] );
        for( i=0; i<nseq2; i++ ) commongappick_record( 1, useq2+i, sgapmap2[i] );

        for( i=0; i<lgth1; i++ )
        {
                pairprob1[i] = (RNApair *)calloc( 1, sizeof( RNApair ) );
                pairprob1[i][0].bestpos = -1;
                pairprob1[i][0].bestscore = -1;
        }
        for( i=0; i<lgth2; i++ )
        {
                pairprob2[i] = (RNApair *)calloc( 1, sizeof( RNApair ) );
                pairprob2[i][0].bestpos = -1;
                pairprob2[i][0].bestscore = -1;
        }

        utot( nseq1, lgth1, oseq1 );
        utot( nseq2, lgth2, oseq2 );

//      fprintf( stderr, "folding group1\n" );
//      rnalocal( oseq1, useq1, eff1, eff1, nseq1, nseq1, lgth1+10, pair1 );

/* base-pairing probability of group 1 */
        if( rnaprediction == 'r' )
                rnaalifoldcall( oseq1, nseq1, pairprob1 );
        else
                mccaskillextract( oseq1, useq1, nseq1, pairprob1, grouprna1, sgapmap1, eff1 );


//      fprintf( stderr, "folding group2\n" );
//      rnalocal( oseq2, useq2, eff2, eff2, nseq2, nseq2, lgth2+10, pair2 );

/* base-pairing probability of group 2 */
        if( rnaprediction == 'r' )
                rnaalifoldcall( oseq2, nseq2, pairprob2 );
        else
                mccaskillextract( oseq2, useq2, nseq2, pairprob2, grouprna2, sgapmap2, eff2 );



#if 0
        makerseq( oseq1, oseq1r, odir1, pairprob1, nseq1, lgth1 );
        makerseq( oseq2, oseq2r, odir2, pairprob2, nseq2, lgth2 );

        fprintf( stderr, "%s\n", odir2 );

        for( i=0; i<nseq1; i++ )
        {
                fprintf( stdout, ">ori\n%s\n", oseq1[0] );
                fprintf( stdout, ">rev\n%s\n", oseq1r[0] );
        }
#endif

/* similarity score */
        Lalignmm_hmout( oseq1, oseq2, eff1, eff2, nseq1, nseq2, 10000, NULL, NULL, NULL, NULL, map );

        if( 1 )
        {
                if( RNAscoremtx == 'n' )
                {
                        for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
                        {
//                              impmtx2[i][j] = osoiaveragescore( nseq1, nseq2, oseq1, oseq2, eff1, eff2, i, j ) * consweight_multi;
                                impmtx2[i][j] = 0.0;
                        }
                }
                else if( RNAscoremtx == 'r' )
                {
                        for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ ) 
                        {
                                tbppmtx[i][j] = 1.0;
                                impmtx2[i][j] = 0.0;
                        }
                        for( i=0; i<lgth1; i++ ) for( pairpt1=pairprob1[i]; pairpt1->bestpos!=-1; pairpt1++ )
                        {
                                for( j=0; j<lgth2; j++ ) for( pairpt2=pairprob2[j]; pairpt2->bestpos!=-1; pairpt2++ )
                                {
                                        uido = pairpt1->bestpos;
                                        ujdo = pairpt2->bestpos;
                                        prob = pairpt1->bestscore * pairpt2->bestscore;
                                        if( uido > -1  && ujdo > -1 )
                                        {
                                                if( uido > i && j > ujdo )
                                                {
                                                        impmtx2[i][j] += prob * pairedribosumscore53( nseq1, nseq2, oseq1, oseq2, eff1, eff2, i, j, uido, ujdo ) * consweight_multi;
                                                        tbppmtx[i][j] -= prob;
                                                }
                                                else if( i < uido && j < ujdo )
                                                {
                                                        impmtx2[i][j] += prob * pairedribosumscore35( nseq1, nseq2, oseq1, oseq2, eff1, eff2, i, j, uido, ujdo ) * consweight_multi;
                                                        tbppmtx[i][j] -= prob;
                                                }
                                        }
                                }
                        }
        
        
                        for( i=0; i<lgth1; i++ )
                        {
                                for( j=0; j<lgth2; j++ )
                                {
                                        impmtx2[i][j] += tbppmtx[i][j] * singleribosumscore( nseq1, nseq2, oseq1, oseq2, eff1, eff2, i, j ) * consweight_multi;
                                }
                        }
                }


/* four-way consistency */

                for( i=0; i<lgth1; i++ ) for( pairpt1=pairprob1[i]; pairpt1->bestpos!=-1; pairpt1++ )
                {

//                      if( pairprob1[i] == NULL ) continue;

                        for( j=0; j<lgth2; j++ ) for( pairpt2=pairprob2[j]; pairpt2->bestpos!=-1; pairpt2++ )
                        {
//                              fprintf( stderr, "i=%d, j=%d, pn1=%d, pn2=%d\n", i, j, pairpt1-pairprob1[i], pairpt2-pairprob2[j] ); 
//                              if( pairprob2[j] == NULL ) continue;

                                uido = pairpt1->bestpos;
                                ujdo = pairpt2->bestpos;
                                prob = pairpt1->bestscore * pairpt2->bestscore;
//                              prob = 1.0;
//                              fprintf( stderr, "i=%d->uido=%d, j=%d->ujdo=%d\n", i, uido, j, ujdo );

//                              fprintf( stderr, "impmtx2[%d][%d] = %f\n", i, j, impmtx2[i][j] );

//                              if( i < uido && j > ujdo ) continue;
//                              if( i > uido && j < ujdo ) continue;


//                              posdistj = abs( ujdo-j );

//                              if( uido > -1 && ujdo > -1 )  
                                if( uido > -1 && ujdo > -1 && ( ( i > uido && j > ujdo ) || ( i < uido && j < ujdo ) ) )
                                {
                                        {
                                                impmtx2[i][j] += MAX( 0, map[uido][ujdo] ) * consweight_rna * 600 * prob; // osoi
                                        }
                                }

                        }
                }
                for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
                {
                        impmtx[i][j] += impmtx2[i][j];
//                      fprintf( stderr, "fastathreshold=%f, consweight_multi=%f, consweight_rna=%f\n", fastathreshold, consweight_multi, consweight_rna );
//                      impmtx[i][j] *= 0.5;
                }

//              impmtx[0][0] += 10000.0;
//              impmtx[lgth1-1][lgth2-1] += 10000.0;



#if 0
                fprintf( stdout, "#impmtx2 = \n" );
                for( i=0; i<lgth1; i++ )
                {
                        for( j=0; j<lgth2; j++ )
                        {
                                fprintf( stdout, "%d %d %f\n", i, j, impmtx2[i][j] );
                        }
                        fprintf( stdout, "\n" );
                }
                exit( 1 );
#endif
        }

        FreeCharMtx( useq1 );
        FreeCharMtx( useq2 );
        FreeCharMtx( oseq1 );
        FreeCharMtx( oseq2 );
        FreeCharMtx( oseq1r );
        FreeCharMtx( oseq2r );
        free( odir1 );
        free( odir2 );
        FreeFloatMtx( impmtx2 );
        FreeFloatMtx( map );
        FreeIntMtx( sgapmap1 );
        FreeIntMtx( sgapmap2 );
        FreeFloatMtx( tbppmtx );

        for( i=0; i<lgth1; i++ ) free( pairprob1[i] );
        for( i=0; i<lgth2; i++ ) free( pairprob2[i] );
        free( pairprob1 );
        free( pairprob2 );
}