--- /dev/null
+#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 );
+}
+
git://source.jalview.org / jabaws.git / blobdiff