static float recalllara( char **mseq1, char **mseq2, int alloclen ) { static FILE *fp = NULL; static char *ungap1; static char *ungap2; static char *ori1; static char *ori2; int res; static char com[10000]; float value; if( fp == NULL ) { fp = fopen( "_laraout", "r" ); if( fp == NULL ) { fprintf( stderr, "Cannot open _laraout\n" ); exit( 1 ); } ungap1 = AllocateCharVec( alloclen ); ungap2 = AllocateCharVec( alloclen ); ori1 = AllocateCharVec( alloclen ); ori2 = AllocateCharVec( alloclen ); } strcpy( ori1, *mseq1 ); strcpy( ori2, *mseq2 ); fgets( com, 999, fp ); myfgets( com, 9999, fp ); strcpy( *mseq1, com ); myfgets( com, 9999, fp ); strcpy( *mseq2, com ); gappick0( ungap1, *mseq1 ); gappick0( ungap2, *mseq2 ); t2u( ungap1 ); t2u( ungap2 ); if( strcmp( ungap1, ori1 ) || strcmp( ungap2, ori2 ) ) { fprintf( stderr, "SEQUENCE CHANGED!!\n" ); fprintf( stderr, "*mseq1 = %s\n", *mseq1 ); fprintf( stderr, "ungap1 = %s\n", ungap1 ); fprintf( stderr, "ori1 = %s\n", ori1 ); fprintf( stderr, "*mseq2 = %s\n", *mseq2 ); fprintf( stderr, "ungap2 = %s\n", ungap2 ); fprintf( stderr, "ori2 = %s\n", ori2 ); exit( 1 ); } value = (float)naivepairscore11( *mseq1, *mseq2, penalty ); // fclose( fp ); // saigo dake yatta houga yoi. return( value ); }
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 ); }
int main( int argc, char **argv ) { int i, j; FILE *fp, *infp; char **seq; int *grpseq; char *tmpseq; int **pointt; static char name[M][B]; static int nlen[M]; double **mtx; double **mtx2; double score, score0; static short *table1; char b[B]; arguments( argc, argv ); if( inputfile ) { infp = fopen( inputfile, "r" ); if( !infp ) { fprintf( stderr, "Cannot open %s\n", inputfile ); exit( 1 ); } } else infp = stdin; #if 0 PreRead( stdin, &njob, &nlenmax ); #else getnumlen( infp ); #endif rewind( infp ); if( njob < 2 ) { fprintf( stderr, "At least 2 sequences should be input!\n" "Only %d sequence found.\n", njob ); exit( 1 ); } tmpseq = AllocateCharVec( nlenmax+1 ); seq = AllocateCharMtx( njob, nlenmax+1 ); grpseq = AllocateIntVec( nlenmax+1 ); pointt = AllocateIntMtx( njob, nlenmax+1 ); mtx = AllocateDoubleMtx( njob, njob ); mtx2 = AllocateDoubleMtx( njob, njob ); pamN = NOTSPECIFIED; #if 0 FRead( infp, name, nlen, seq ); #else readData( infp, name, nlen, seq ); #endif fclose( infp ); constants( njob, seq ); if( dorp == 'd' ) tsize = (int)pow( 4, 6 ); else tsize = (int)pow( 6, 6 ); maxl = 0; for( i=0; i<njob; i++ ) { gappick0( tmpseq, seq[i] ); nlen[i] = strlen( tmpseq ); if( nlen[i] < 6 ) { fprintf( stderr, "Seq %d, too short, %d characters\n", i+1, nlen[i] ); exit( 1 ); } if( nlen[i] > maxl ) maxl = nlen[i]; if( dorp == 'd' ) /* nuc */ { seq_grp_nuc( grpseq, tmpseq ); makepointtable_nuc( pointt[i], grpseq ); } else /* amino */ { seq_grp( grpseq, tmpseq ); makepointtable( pointt[i], grpseq ); } } for( i=0; i<njob; i++ ) { table1 = (short *)calloc( tsize, sizeof( short ) ); if( !table1 ) ErrorExit( "Cannot allocate table1\n" ); if( i % 10 == 0 ) { fprintf( stderr, "%4d / %4d\r", i+1, njob ); } makecompositiontable_p( table1, pointt[i] ); for( j=i; j<njob; j++ ) { score = (double)commonsextet_p( table1, pointt[j] ); mtx[i][j] = score; } free( table1 ); } for( i=0; i<njob; i++ ) { score0 = mtx[i][i]; for( j=0; j<njob; j++ ) mtx2[i][j] = ( score0 - mtx[MIN(i,j)][MAX(i,j)] ) / score0 * 3.0; } for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ ) { #if TEST double jscore; jscore = mtx[i][j] / ( MIN( strlen( seq[i] ), strlen( seq[j] ) ) - 2 ); fprintf( stdout, "jscore = %f\n", jscore ); fprintf( stdout, "mtx2[%d][%d] = %f, mtx2[%d][%d] = %f\n", i, j, mtx2[i][j], j, i, mtx2[j][i] ); #endif mtx2[i][j] = MIN( mtx2[i][j], mtx2[j][i] ); #if TEST fprintf( stdout, "sonokekka mtx2[%d][%d] %f\n", i, j, mtx2[i][j] ); #endif } if( disopt ) { for( i=0; i<njob; i++ ) { sprintf( b, "=lgth = %04d", nlen[i] ); strins( b, name[i] ); } } fp = fopen( "hat2", "w" ); if( !fp ) ErrorExit( "Cannot open hat2." ); WriteHat2( fp, njob, name, mtx2 ); fclose( fp ); fprintf( stderr, "\n" ); SHOWVERSION; exit( 0 ); }
int main( int argc, char *argv[] ) { FILE *infp; FILE *difp; int nlenmin; char **name; char **seq; char *tmpseq; char line[100]; int *nlen; int i; arguments( argc, argv ); if( inputfile ) { infp = fopen( inputfile, "r" ); if( !infp ) { fprintf( stderr, "Cannot open %s\n", inputfile ); exit( 1 ); } } else infp = stdin; if( directionfile ) { difp = fopen( directionfile, "r" ); if( !difp ) { fprintf( stderr, "Cannot open %s\n", directionfile ); exit( 1 ); } } else { fprintf( stderr, "Give directionfile!\n" ); } dorp = NOTSPECIFIED; getnumlen_casepreserve( infp, &nlenmin ); fprintf( stderr, "%d x %d - %d %c\n", njob, nlenmax, nlenmin, dorp ); seq = AllocateCharMtx( njob, nlenmax+1 ); tmpseq = AllocateCharVec( MAX( B, nlenmax )+1 ); name = AllocateCharMtx( njob, B+1 ); nlen = AllocateIntVec( njob ); readData_pointer_casepreserve( infp, name, nlen, seq ); for( i=0; i<njob; i++ ) { fgets( line, 99, difp ); if( line[0] != '_' ) { fprintf( stderr, "Format error!\n" ); exit( 1 ); } if( line[1] == 'R' ) { sreverse( tmpseq, seq[i] ); strcpy( seq[i], tmpseq ); strncpy( tmpseq, name[i]+1, B-3 ); tmpseq[B-3] = 0; strcpy( name[i]+1, "_R_" ); strcpy( name[i]+4, tmpseq ); } else if( line[1] == 'F' ) { ; } else { fprintf( stderr, "Format error!\n" ); exit( 1 ); } } for( i=0; i<njob; i++ ) { fprintf( stdout, ">%s\n", name[i]+1 ); fprintf( stdout, "%s\n", seq[i] ); } free( nlen ); FreeCharMtx( seq ); FreeCharMtx( name ); free( tmpseq ); return( 0 ); }
static void pairalign( char **name, int nlen[M], char **seq, double *effarr, int alloclen ) { FILE *tmpfp; static char dumm1[B], dumm0[B]; int i, j; char *res; FILE *hat3p; static double *effarr1 = NULL; static double *effarr2 = NULL; static char **pseq; LocalHom **localhomtable, *tmpptr; float pscore = 0.0; // by D.Mathog, aguess char *aseq = NULL; // by D.Mathog char **usedseqs = NULL; // by D.Mathog char **usednames = NULL; // by D.Mathog int nused; double tsuyosa; tsuyosa = (double)nhomologs * (nhomologs-1) / njob * TSUYOSAFACTOR; fprintf( stderr, "tsuyosa = %f\n", tsuyosa ); localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) ); for( i=0; i<njob; i++) { localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) ); for( j=0; j<njob; j++) { localhomtable[i][j].start1 = -1; localhomtable[i][j].end1 = -1; localhomtable[i][j].start2 = -1; localhomtable[i][j].end2 = -1; localhomtable[i][j].opt = -1.0; localhomtable[i][j].next = NULL; } } if( effarr1 == NULL ) { effarr1 = AllocateDoubleVec( njob ); effarr2 = AllocateDoubleVec( njob ); pseq = AllocateCharMtx( 2, nlenmax*9+1 ); aseq = AllocateCharVec( nlenmax*9+1 ); usedseqs = AllocateCharMtx( njob, nlenmax*9+1 ); usednames = AllocateCharMtx( njob, B ); #if 0 #else #endif } #if 0 fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold ); #endif #if 0 for( i=0; i<njob; i++ ) fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] ); #endif // writePre( njob, name, nlen, aseq, 0 ); fprintf( stderr, "opening %s\n", pairfile ); tmpfp = fopen( pairfile, "r" ); if( !tmpfp ) { fprintf( stderr, "Cannot open %s\n", pairfile ); exit( 1 ); } searchKUorWA( tmpfp ); hat3p = fopen( "hat3", "w" ); if( !hat3p ) ErrorExit( "Cannot open hat3." ); nused = 0; while( 1 ) { res = fgets( dumm0, B-1, tmpfp ); strip( dumm0 ); if( res == NULL ) { break; } load1SeqWithoutName_new( tmpfp, pseq[0] ); gappick0( aseq, pseq[0] ); i = searchused( aseq, usedseqs, nused ); if( i == -1 ) { strcpy( usednames[nused], dumm0+1 ); strcpy( usedseqs[nused], aseq ); i = nused; nused++; } fprintf( stderr, "i = %d\n", i ); res = fgets( dumm1, B-1, tmpfp ); strip( dumm1 ); if( res == NULL ) { fprintf( stderr, "ERROR: The number of sequences in %s must be even.\n", pairfile ); exit( 1 ); } load1SeqWithoutName_new( tmpfp, pseq[1] ); gappick0( aseq, pseq[1] ); j = searchused( aseq, usedseqs, nused ); if( j == -1 ) { strcpy( usednames[nused], dumm1+1 ); strcpy( usedseqs[nused], aseq ); j = nused; nused++; } fprintf( stderr, "j = %d\n", j ); if( strlen( pseq[0] ) != strlen( pseq[1] ) ) { fprintf( stderr, "Not aligned, %s - %s\n", dumm0, dumm1 ); exit( 1 ); } fprintf( stderr, "adding %d-%d\n", i, j ); putlocalhom2( pseq[0], pseq[1], localhomtable[i]+j, 0, 0, (int)pscore, strlen( pseq[0] ) ); for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next ) { if( tmpptr->opt == -1.0 ) continue; fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt * tsuyosa, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, (void *)tmpptr->next ); } } fclose( tmpfp ); fclose( hat3p ); for( i=0; i<nused; i++ ) fprintf( stdout, ">%s\n%s\n", usednames[i], usedseqs[i] ); #if 0 fprintf( stderr, "##### writing hat3\n" ); hat3p = fopen( "hat3", "w" ); if( !hat3p ) ErrorExit( "Cannot open hat3." ); ilim = njob-1; for( i=0; i<ilim; i++ ) { for( j=i+1; j<njob; j++ ) { for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next ) { if( tmpptr->opt == -1.0 ) continue; fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt * tsuyosa, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->next ); } } } fclose( hat3p ); #endif #if DEBUG fprintf( stderr, "calling FreeLocalHomTable\n" ); #endif FreeLocalHomTable( localhomtable, njob ); #if DEBUG fprintf( stderr, "done. FreeLocalHomTable\n" ); #endif }
static void pairalign( char name[M][B], int nlen[M], char **seq, char **aseq, char **mseq1, char **mseq2, double *effarr, int alloclen ) { int i, j, ilim; int clus1, clus2; int off1, off2; float pscore = 0.0; // by D.Mathog static char *indication1, *indication2; FILE *hat2p, *hat3p; static double **distancemtx; static double *effarr1 = NULL; static double *effarr2 = NULL; char *pt; char *hat2file = "hat2"; LocalHom **localhomtable, *tmpptr; static char **pair; int intdum; double bunbo; localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) ); for( i=0; i<njob; i++) { localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) ); for( j=0; j<njob; j++) { localhomtable[i][j].start1 = -1; localhomtable[i][j].end1 = -1; localhomtable[i][j].start2 = -1; localhomtable[i][j].end2 = -1; localhomtable[i][j].opt = -1.0; localhomtable[i][j].next = NULL; localhomtable[i][j].nokori = 0; } } if( effarr1 == NULL ) { distancemtx = AllocateDoubleMtx( njob, njob ); effarr1 = AllocateDoubleVec( njob ); effarr2 = AllocateDoubleVec( njob ); indication1 = AllocateCharVec( 150 ); indication2 = AllocateCharVec( 150 ); #if 0 #else pair = AllocateCharMtx( njob, njob ); #endif } #if 0 fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold ); #endif #if 0 for( i=0; i<njob; i++ ) fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] ); #endif // writePre( njob, name, nlen, aseq, 0 ); for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) pair[i][j] = 0; for( i=0; i<njob; i++ ) pair[i][i] = 1; if( alg == 'H' ) { fprintf( stderr, "Calling FOLDALIGN with option '%s'\n", foldalignopt ); callfoldalign( njob, seq ); fprintf( stderr, "done.\n" ); } if( alg == 'B' ) { fprintf( stderr, "Calling LARA\n" ); calllara( njob, seq, "" ); fprintf( stderr, "done.\n" ); } if( alg == 'T' ) { fprintf( stderr, "Calling SLARA\n" ); calllara( njob, seq, "-s" ); fprintf( stderr, "done.\n" ); } ilim = njob - 1; for( i=0; i<ilim; i++ ) { fprintf( stderr, "% 5d / %d\r", i, njob ); for( j=i+1; j<njob; j++ ) { if( strlen( seq[i] ) == 0 || strlen( seq[j] ) == 0 ) { distancemtx[i][j] = pscore; continue; } strcpy( aseq[i], seq[i] ); strcpy( aseq[j], seq[j] ); clus1 = conjuctionfortbfast( pair, i, aseq, mseq1, effarr1, effarr, indication1 ); clus2 = conjuctionfortbfast( pair, j, aseq, mseq2, effarr2, effarr, indication2 ); // fprintf( stderr, "mseq1 = %s\n", mseq1[0] ); // fprintf( stderr, "mseq2 = %s\n", mseq2[0] ); #if 0 fprintf( stderr, "group1 = %.66s", indication1 ); fprintf( stderr, "\n" ); fprintf( stderr, "group2 = %.66s", indication2 ); fprintf( stderr, "\n" ); #endif // for( l=0; l<clus1; l++ ) fprintf( stderr, "## STEP-eff for mseq1-%d %f\n", l, effarr1[l] ); #if 1 if( use_fft ) { pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, &intdum, NULL, 0, NULL ); off1 = off2 = 0; } else #endif { switch( alg ) { case( 'a' ): pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen ); off1 = off2 = 0; break; case( 'A' ): pscore = G__align11( mseq1, mseq2, alloclen, NULL, 0, NULL ); off1 = off2 = 0; break; #if 0 case( 'V' ): pscore = VAalign11( mseq1, mseq2, alloclen, &off1, &off2, localhomtable[i]+j ); fprintf( stderr, "i,j = %d,%d, score = %f\n", i,j, pscore ); break; case( 'S' ): fprintf( stderr, "aligning %d-%d\n", i, j ); pscore = suboptalign11( mseq1, mseq2, alloclen, &off1, &off2, localhomtable[i]+j ); fprintf( stderr, "i,j = %d,%d, score = %f\n", i,j, pscore ); break; #endif case( 'N' ): pscore = genL__align11( mseq1, mseq2, alloclen, &off1, &off2 ); // fprintf( stderr, "pscore = %f\n", pscore ); break; case( 'L' ): pscore = L__align11( mseq1, mseq2, alloclen, &off1, &off2 ); // fprintf( stderr, "pscore (1) = %f\n", pscore ); // pscore = (float)naivepairscore11( *mseq1, *mseq2, penalty ); // nennnotame // fprintf( stderr, "pscore (2) = %f\n\n", pscore ); break; case( 'H' ): pscore = recallpairfoldalign( mseq1, mseq2, i, j, &off1, &off2, alloclen ); break; case( 'B' ): case( 'T' ): pscore = recalllara( mseq1, mseq2, alloclen ); off1 = off2 = 0; // fprintf( stderr, "lara, pscore = %f\n", pscore ); break; case( 's' ): pscore = callmxscarna( mseq1, mseq2, alloclen ); off1 = off2 = 0; // fprintf( stderr, "scarna, pscore = %f\n", pscore ); break; case( 'M' ): // pscore = MSalign11( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL ); pscore = MSalign11( mseq1, mseq2, alloclen ); // fprintf( stderr, "pscore = %f\n", pscore ); break; ErrorExit( "ERROR IN SOURCE FILE" ); } } distancemtx[i][j] = pscore; #if SCOREOUT fprintf( stderr, "score = %10.2f (%d,%d)\n", pscore, i, j ); #endif // fprintf( stderr, "pslocal = %d\n", pslocal ); // offset = makelocal( *mseq1, *mseq2, pslocal ); #if 0 fprintf( stderr, "off1 = %d, off2 = %d\n", off1, off2 ); fprintf( stderr, ">%d\n%s\n>%d\n%s\n>\n", i, mseq1[0], j, mseq2[0] ); #endif // putlocalhom2( mseq1[0], mseq2[0], localhomtable[i]+j, countamino( *mseq1, off1 ), countamino( *mseq2, off2 ), pscore, strlen( mseq1[0] ) ); // fprintf( stderr, "pscore = %f\n", pscore ); if( alg == 'H' ) // if( alg == 'H' || alg == 's' || alg == 'B' ) // next version putlocalhom_ext( mseq1[0], mseq2[0], localhomtable[i]+j, off1, off2, (int)pscore, strlen( mseq1[0] ) ); else if( alg != 'S' && alg != 'V' ) putlocalhom2( mseq1[0], mseq2[0], localhomtable[i]+j, off1, off2, (int)pscore, strlen( mseq1[0] ) ); } } for( i=0; i<njob; i++ ) { pscore = 0.0; for( pt=seq[i]; *pt; pt++ ) pscore += amino_dis[(int)*pt][(int)*pt]; distancemtx[i][i] = pscore; } ilim = njob-1; for( i=0; i<ilim; i++ ) { for( j=i+1; j<njob; j++ ) { bunbo = MIN( distancemtx[i][i], distancemtx[j][j] ); if( bunbo == 0.0 ) distancemtx[i][j] = 2.0; else distancemtx[i][j] = ( 1.0 - distancemtx[i][j] / bunbo ) * 2.0; } } hat2p = fopen( hat2file, "w" ); if( !hat2p ) ErrorExit( "Cannot open hat2." ); WriteHat2( hat2p, njob, name, distancemtx ); fclose( hat2p ); fprintf( stderr, "##### writing hat3\n" ); hat3p = fopen( "hat3", "w" ); if( !hat3p ) ErrorExit( "Cannot open hat3." ); ilim = njob-1; for( i=0; i<ilim; i++ ) { for( j=i+1; j<njob; j++ ) { for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next ) { if( tmpptr->opt == -1.0 ) continue; fprintf( hat3p, "%d %d %d %7.5f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, (void *)tmpptr->next ); } } } fclose( hat3p ); #if DEBUG fprintf( stderr, "calling FreeLocalHomTable\n" ); #endif FreeLocalHomTable( localhomtable, njob ); #if DEBUG fprintf( stderr, "done. FreeLocalHomTable\n" ); #endif }
void GroupAlign( int nseq1, int nseq2, char **name, int *nlen, char **seq, char **aseq, char **mseq1, char **mseq2, int ***topol, double **len, double *eff, int alloclen ) { int i; int clus1, clus2; int s1, s2; float pscore; static char **name1, **name2; double *effarr = eff; double *effarr1 = NULL; double *effarr2 = NULL; static char *indication1, *indication2; float dumfl = 0.0; int intdum; #if DEBUG double time1, time2; #endif // fprintf( stderr, "in GroupAlign fftWinSize = %d\n", fftWinSize ); // fprintf( stderr, "in GroupAlign fftThreshold = %d\n", fftThreshold ); if( effarr1 == NULL ) { name1 = AllocateCharMtx( nseq1, B ); name2 = AllocateCharMtx( nseq2, B ); indication1 = AllocateCharVec( 150 ); indication2 = AllocateCharVec( 150 ); effarr1 = AllocateDoubleVec( njob ); effarr2 = AllocateDoubleVec( njob ); #if 0 #else #endif } for( i=0; i<njob; i++ ) strcpy( aseq[i], seq[i] ); s1 = 0; s2 = nseq1; // fprintf( stdout, "nseq1 = %d\n", nseq1 ); clus1 = conjuctionforgaln( 0, nseq1, aseq, mseq1, effarr1, effarr, name, name1, indication1 ); clus2 = conjuctionforgaln( nseq1, njob, aseq, mseq2, effarr2, effarr, name, name2, indication2 ); /* fprintf( stderr, "before align all\n" ); display( aseq, njob ); fprintf( stderr, "\n" ); fprintf( stderr, "before align 1 %s \n", indication1 ); display( mseq1, clus1 ); fprintf( stderr, "\n" ); fprintf( stderr, "before align 2 %s \n", indication2 ); display( mseq2, clus2 ); fprintf( stderr, "\n" ); */ commongappick( nseq1, mseq1 ); commongappick( nseq2, mseq2 ); #if DEBUG time1 = getrusage_sec(); fprintf( stderr, "entering Falign\n" ); #endif if( use_fft ) { if( alg == 'M' ) pscore = Falign_udpari_long( NULL, NULL, n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, NULL, NULL, clus1, clus2, alloclen, &intdum ); else pscore = Falign( NULL, NULL, n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, NULL, NULL, clus1, clus2, alloclen, &intdum, NULL, 0, NULL ); } else { if( alg == 'M' ) pscore = MSalignmm( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap ); else pscore = A__align( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap ); } #if DEBUG time2 = getrusage_sec(); fprintf( stdout, "### %d - %d, %f\n", clus1, clus2, time2-time1 ); fflush( stdout ); #endif /* fprintf( stderr, "after align 1 %s \n", indication1 ); display( mseq1, clus1 ); fprintf( stderr, "\n" ); fprintf( stderr, "after align 2 %s \n", indication2 ); display( mseq2, clus2 ); fprintf( stderr, "\n" ); */ fprintf( stderr, "group-to-group %s /%s %f\n", indication1, indication2, pscore ); if( disp ) display( aseq, njob ); fprintf( stderr, "\n" ); /* trap = fopen( "pre", "r+" ); if( !trap ) ErrorExit( 1 ); WriteGapFill( trap, njob, name, nlen, aseq ); fclose( trap ); fprintf( stdout, "nseq1 = %d\n", nseq1 ); */ }
void part_imp_match_init( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom ) { int dif, i, j, k1, k2, tmpint, start1, start2, end1, end2; static int impalloclen = 0; char *pt; static char *nocount1 = NULL; static char *nocount2 = NULL; if( impalloclen < lgth1 || impalloclen < lgth2 ) { 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 ); impalloclen -= 2; } 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 for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ ) impmtx[i][j] = 0.0; for( i=0; i<clus1; i++ ) { fprintf( stderr, "i = %d, seq1 = %s\n", i, seq1[i] ); for( j=0; j<clus2; j++ ) { fprintf( stderr, "start1 = %d\n", localhom[i][j]->start1 ); fprintf( stderr, "end1 = %d\n", localhom[i][j]->end1 ); fprintf( stderr, "j = %d, seq2 = %s\n", j, seq2[j] ); pt = seq1[i]; tmpint = -1; while( *pt != 0 ) { if( *pt++ != '-' ) tmpint++; if( tmpint == localhom[i][j]->start1 ) break; } start1 = pt - seq1[i] - 1; while( *pt != 0 ) { // fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, localhom[i][j].end1, pt-seq1[i] ); if( *pt++ != '-' ) tmpint++; if( tmpint == localhom[i][j]->end1 ) break; } end1 = pt - seq1[i] - 1; pt = seq2[j]; tmpint = -1; while( *pt != 0 ) { if( *pt++ != '-' ) tmpint++; if( tmpint == localhom[i][j]->start2 ) break; } start2 = pt - seq2[j] - 1; while( *pt != 0 ) { if( *pt++ != '-' ) tmpint++; if( tmpint == localhom[i][j]->end2 ) break; } end2 = pt - seq2[j] - 1; // fprintf( stderr, "start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 ); k1 = start1; k2 = start2; fprintf( stderr, "step 0\n" ); while( k1 <= end1 && k2 <= end2 ) { #if 0 if( !nocount1[k1] && !nocount2[k2] ) impmtx[k1][k2] += localhom[i][j].wimportance * eff1[i] * eff2[j]; k1++; k2++; #else if( !nocount1[k1] && !nocount2[k2] ) impmtx[k1][k2] += localhom[i][j]->wimportance * eff1[i] * eff2[j]; k1++; k2++; #endif } dif = ( end1 - start1 ) - ( end2 - start2 ); fprintf( stderr, "dif = %d\n", dif ); if( dif > 0 ) { do { fprintf( stderr, "dif = %d\n", dif ); k1 = start1; k2 = start2 - dif; while( k1 <= end1 && k2 <= end2 ) { if( 0 <= k2 && start2 <= k2 && !nocount1[k1] && !nocount2[k2] ) impmtx[k1][k2] = localhom[i][j]->wimportance * eff1[i] * eff2[j]; k1++; k2++; } } while( dif-- ); } else { do { k1 = start1 + dif; k2 = start2; while( k1 <= end1 ) { if( k1 >= 0 && k1 >= start1 && !nocount1[k1] && !nocount2[k2] ) impmtx[k1][k2] = localhom[i][j]->wimportance * eff1[i] * eff2[j]; k1++; k2++; } } while( dif++ ); } } } #if 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<lgth2; k2++ ) fprintf( stderr, "%6.3f ", impmtx[k1][k2] ); fprintf( stderr, "\n" ); } exit( 1 ); #endif }
static void pairalign( char name[M][B], int nlen[M], char **seq, char **aseq, char **mseq1, char **mseq2, double *equiv, double *effarr, char **strfiles, char **chainids, int alloclen ) { int i, j, ilim; int clus1, clus2; int off1, off2; float pscore = 0.0; // by D.Mathog static char *indication1, *indication2; FILE *hat2p, *hat3p; static double **distancemtx; static double *effarr1 = NULL; static double *effarr2 = NULL; char *pt; char *hat2file = "hat2"; LocalHom **localhomtable, *tmpptr; static char **pair; // int intdum; double bunbo; char **checkseq; localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) ); for( i=0; i<njob; i++) { localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) ); for( j=0; j<njob; j++) { localhomtable[i][j].start1 = -1; localhomtable[i][j].end1 = -1; localhomtable[i][j].start2 = -1; localhomtable[i][j].end2 = -1; localhomtable[i][j].opt = -1.0; localhomtable[i][j].next = NULL; localhomtable[i][j].nokori = 0; } } if( effarr1 == NULL ) { distancemtx = AllocateDoubleMtx( njob, njob ); effarr1 = AllocateDoubleVec( njob ); effarr2 = AllocateDoubleVec( njob ); indication1 = AllocateCharVec( 150 ); indication2 = AllocateCharVec( 150 ); checkseq = AllocateCharMtx( njob, alloclen ); #if 0 #else pair = AllocateCharMtx( njob, njob ); #endif } #if 0 fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold ); #endif #if 0 for( i=0; i<njob; i++ ) fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] ); #endif // writePre( njob, name, nlen, aseq, 0 ); for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) pair[i][j] = 0; for( i=0; i<njob; i++ ) pair[i][i] = 1; for( i=0; i<njob; i++ ) { strcpy( checkseq[i], seq[i] ); // fprintf( stderr, "checkseq[%d] = %s\n", i, checkseq[i] ); } ilim = njob - 1; for( i=0; i<ilim; i++ ) { fprintf( stderr, "% 5d / %d\r", i, njob ); for( j=i+1; j<njob; j++ ) { #if 0 if( strlen( seq[i] ) == 0 || strlen( seq[j] ) == 0 ) { distancemtx[i][j] = pscore; continue; } #endif strcpy( aseq[i], seq[i] ); strcpy( aseq[j], seq[j] ); clus1 = conjuctionfortbfast( pair, i, aseq, mseq1, effarr1, effarr, indication1 ); clus2 = conjuctionfortbfast( pair, j, aseq, mseq2, effarr2, effarr, indication2 ); // fprintf( stderr, "mseq1 = %s\n", mseq1[0] ); // fprintf( stderr, "mseq2 = %s\n", mseq2[0] ); #if 0 fprintf( stderr, "group1 = %.66s", indication1 ); fprintf( stderr, "\n" ); fprintf( stderr, "group2 = %.66s", indication2 ); fprintf( stderr, "\n" ); #endif // for( l=0; l<clus1; l++ ) fprintf( stderr, "## STEP-eff for mseq1-%d %f\n", l, effarr1[l] ); #if 1 { switch( alg ) { case( 'T' ): fprintf( stderr, " Calling tmalign %d-%d/%d \r", i+1, j+1, njob ); pscore = calltmalign( mseq1, mseq2, equiv, strfiles[i], chainids[i], strfiles[j], chainids[j], alloclen ); off1 = off2 = 0; break; case( 'R' ): fprintf( stderr, " Calling PDP_ASH.pl %d-%d/%d \r", i+1, j+1, njob ); pscore = callrash( i, j, mseq1, mseq2, equiv, strfiles[i], chainids[i], strfiles[j], chainids[j], alloclen ); off1 = off2 = 0; break; ErrorExit( "ERROR IN SOURCE FILE" ); } } #endif distancemtx[i][j] = pscore; #if SCOREOUT fprintf( stderr, "score = %10.2f (%d,%d)\n", pscore, i, j ); #endif putlocalhom_str( mseq1[0], mseq2[0], equiv, scale, localhomtable[i]+j, off1, off2, (int)pscore, strlen( mseq1[0] ) ); #if 1 if( alreadyoutput[i] == 0 ) { alreadyoutput[i] = 1; gappick0( seq[i], mseq1[0] ); fprintf( stdout, ">%d_%s-%s\n%s\n", i+1, strfiles[i], chainids[i], seq[i] ); strcpy( checkseq[i], seq[i] ); } else { gappick0( seq[i], mseq1[0] ); fprintf( stderr, "checking seq%d\n", i ); // fprintf( stderr, " seq=%s\n", seq[i] ); // fprintf( stderr, "checkseq=%s\n", checkseq[i] ); if( strcmp( checkseq[i], seq[i] ) ) { fprintf( stderr, "\n\nWARNING: Sequence changed!!\n" ); fprintf( stderr, "i=%d\n", i ); fprintf( stderr, " seq=%s\n", seq[i] ); fprintf( stderr, "checkseq=%s\n", checkseq[i] ); exit( 1 ); } } if( alreadyoutput[j] == 0 ) { alreadyoutput[j] = 1; gappick0( seq[j], mseq2[0] ); fprintf( stdout, ">%d_%s-%s\n%s\n", j+1, strfiles[j], chainids[j], seq[j] ); strcpy( checkseq[j], seq[j] ); } else { gappick0( seq[j], mseq2[0] ); fprintf( stderr, "checking seq%d\n", j ); if( strcmp( checkseq[j], seq[j] ) ) { fprintf( stderr, "\n\nWARNING: Sequence changed!!\n" ); fprintf( stderr, "j=%d\n", j ); fprintf( stderr, " seq=%s\n", seq[j] ); fprintf( stderr, "checkseq=%s\n", checkseq[j] ); exit( 1 ); } } #endif } } for( i=0; i<njob; i++ ) { pscore = 0.0; for( pt=seq[i]; *pt; pt++ ) pscore += amino_dis[(int)*pt][(int)*pt]; distancemtx[i][i] = pscore; } ilim = njob-1; for( i=0; i<ilim; i++ ) { for( j=i+1; j<njob; j++ ) { bunbo = MIN( distancemtx[i][i], distancemtx[j][j] ); if( bunbo == 0.0 ) distancemtx[i][j] = 2.0; else distancemtx[i][j] = ( 1.0 - distancemtx[i][j] / bunbo ) * 2.0; } } hat2p = fopen( hat2file, "w" ); if( !hat2p ) ErrorExit( "Cannot open hat2." ); WriteHat2( hat2p, njob, name, distancemtx ); fclose( hat2p ); fprintf( stderr, "##### writing hat3\n" ); hat3p = fopen( "hat3", "w" ); if( !hat3p ) ErrorExit( "Cannot open hat3." ); ilim = njob-1; for( i=0; i<ilim; i++ ) { for( j=i+1; j<njob; j++ ) { for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next ) { if( tmpptr->opt == -1.0 ) continue; fprintf( hat3p, "%d %d %d %7.5f %d %d %d %d k\n", i, j, tmpptr->overlapaa, tmpptr->opt, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2 ); } } } fclose( hat3p ); #if DEBUG fprintf( stderr, "calling FreeLocalHomTable\n" ); #endif FreeLocalHomTable( localhomtable, njob ); #if DEBUG fprintf( stderr, "done. FreeLocalHomTable\n" ); #endif }
static void prepareash( FILE *fp, char ***strfiles, char ***chainids, char ***seqpt, char ***mseq1pt, char ***mseq2pt, double **equivpt, int *alloclenpt ) { int i, res; char *dumseq; char line[1000]; char fname[1000]; char command[1000]; int linenum, istr, nstr; FILE *checkfp; char *sline; int use[1000]; linenum = 0; nstr = 0; while( 1 ) { fgets( line, 999, fp ); if( feof( fp ) ) break; sline = strip( line ); use[linenum] = 1; if( sline[0] == '#' || strlen( sline ) < 2 ) { use[linenum] = 0; linenum++; continue; } extractfirstword( sline ); checkfp = fopen( sline, "r" ); if( checkfp == NULL ) { fprintf( stderr, "Cannot open %s.\n", sline ); exit( 1 ); } #if 0 fgets( linec, 999, checkfp ); if( strncmp( "HEADER ", linec, 7 ) ) { fprintf( stderr, "Check the format of %s.\n", sline ); exit( 1 ); } #endif if( checkcbeta( checkfp ) ) { fprintf( stderr, "%s has no C-beta atoms.\n", sline ); exit( 1 ); } else nstr++; fclose( checkfp ); linenum++; } njob = nstr; fprintf( stderr, "nstr = %d\n", nstr ); *strfiles = AllocateCharMtx( nstr, 1000 ); *chainids = AllocateCharMtx( nstr, 2 ); rewind( fp ); istr = 0; linenum = 0; while( 1 ) { fgets( line, 999, fp ); if( feof( fp ) ) break; sline = strip( line ); if( use[linenum++] ) { (*chainids)[istr][0] = getchainid( sline ); (*chainids)[istr][1] = 0; extractfirstword( sline ); sprintf( fname, "%s", sline ); cutpath( fname ); sprintf( command, "cp %s %s.pdb", sline, fname ); system( command ); sprintf( command, "perl \"%s/clean.pl\" %s.pdb", whereispairalign, fname ); res = system( command ); if( res ) { fprintf( stderr, "error: Install clean.pl\n" ); exit( 1 ); } strcpy( (*strfiles)[istr++], fname ); } } *seqpt = AllocateCharMtx( njob, nlenmax*2+1 ); *mseq1pt = AllocateCharMtx( njob, 0 ); *mseq2pt = AllocateCharMtx( njob, 0 ); *equivpt = AllocateDoubleVec( nlenmax*2+1 ); *alloclenpt = nlenmax*2; dumseq = AllocateCharVec( nlenmax*2+1 ); alreadyoutput = AllocateIntVec( njob ); for( i=0; i<njob; i++ ) alreadyoutput[i] = 0; for( i=0; i<istr; i++ ) { fprintf( stderr, "i=%d\n", i ); (*seqpt)[i][0] = 0; (*mseq1pt)[0] = (*seqpt)[i]; (*mseq2pt)[0] = dumseq; callrash( i, i, *mseq1pt, *mseq2pt, *equivpt, (*strfiles)[i], (*chainids)[i], (*strfiles)[i], (*chainids)[i], *alloclenpt ); fprintf( stdout, ">%d_%s-%s\n%s\n", i+1, (*strfiles)[i], (*chainids)[i], (*seqpt)[i] ); alreadyoutput[i] = 1; } }
static void pairalign( char name[M][B], int nlen[M], char **seq, double *effarr, int alloclen ) { int i, j; FILE *hat3p; float pscore = 0.0; // by D.Mathog static double *effarr1 = NULL; static double *effarr2 = NULL; char *aseq; static char **pseq; LocalHom **localhomtable, *tmpptr; double tsuyosa; if( nhomologs < 1 ) nhomologs = 1; // tsuyosa=0.0 wo sakeru tsuyosa = (double)nhomologs * nhomologs * TSUYOSAFACTOR; fprintf( stderr, "tsuyosa = %f\n", tsuyosa ); localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) ); for( i=0; i<njob; i++) { localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) ); for( j=0; j<njob; j++) { localhomtable[i][j].start1 = -1; localhomtable[i][j].end1 = -1; localhomtable[i][j].start2 = -1; localhomtable[i][j].end2 = -1; localhomtable[i][j].opt = -1.0; localhomtable[i][j].next = NULL; } } if( effarr1 == NULL ) { effarr1 = AllocateDoubleVec( njob ); effarr2 = AllocateDoubleVec( njob ); pseq = AllocateCharMtx( 2, 0 ); aseq = AllocateCharVec( nlenmax*9+1 ); #if 0 #else #endif } #if 0 fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold ); #endif #if 0 for( i=0; i<njob; i++ ) fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] ); #endif // writePre( njob, name, nlen, aseq, 0 ); hat3p = fopen( "hat3", "w" ); if( !hat3p ) ErrorExit( "Cannot open hat3." ); fprintf( stderr, "\n" ); for( i=0; i<njob-1; i++ ) { for( j=i+1; j<njob; j++ ) { pseq[0] = seq[i]; pseq[1] = seq[j]; if( strlen( pseq[0] ) != strlen( pseq[1] ) ) { fprintf( stderr, "## ERROR ###\n" ); fprintf( stderr, "Not aligned, %s - %s\n", name[i], name[j] ); fprintf( stderr, "## ERROR ###\n" ); exit( 1 ); } fprintf( stderr, "adding %d-%d\r", i, j ); putlocalhom2( pseq[0], pseq[1], localhomtable[i]+j, 0, 0, (int)pscore, strlen( pseq[0] ) ); for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next ) { if( tmpptr->opt == -1.0 ) continue; if( tmpptr->start1 == -1 ) continue; fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d k\n", i+seedoffset, j+seedoffset, tmpptr->overlapaa, tmpptr->opt * tsuyosa, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2 ); } } } fprintf( stderr, "\n" ); fclose( hat3p ); #if DEBUG fprintf( stderr, "calling FreeLocalHomTable\n" ); #endif FreeLocalHomTable( localhomtable, njob ); #if DEBUG fprintf( stderr, "done. FreeLocalHomTable\n" ); #endif }
float Falign_localhom( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int alloclen, LocalHom ***localhom, float *totalimpmatch, int *gapmap1, int *gapmap2, int *chudanpt, int chudanref, int *chudanres ) { // tditeration.c deha alloclen ha huhen nanode // prevalloclen ha iranai. int i, j, k, l, m, maxk; int nlen, nlen2, nlen4; static TLS int crossscoresize = 0; static TLS char **tmpseq1 = NULL; static TLS char **tmpseq2 = NULL; static TLS char **tmpptr1 = NULL; static TLS char **tmpptr2 = NULL; static TLS char **tmpres1 = NULL; static TLS char **tmpres2 = NULL; static TLS char **result1 = NULL; static TLS char **result2 = NULL; #if RND static TLS char **rndseq1 = NULL; static TLS char **rndseq2 = NULL; #endif static TLS Fukusosuu **seqVector1 = NULL; static TLS Fukusosuu **seqVector2 = NULL; static TLS Fukusosuu **naiseki = NULL; static TLS Fukusosuu *naisekiNoWa = NULL; static TLS double *soukan = NULL; static TLS double **crossscore = NULL; int nlentmp; static TLS int *kouho = NULL; static TLS Segment *segment = NULL; static TLS Segment *segment1 = NULL; static TLS Segment *segment2 = NULL; static TLS Segment **sortedseg1 = NULL; static TLS Segment **sortedseg2 = NULL; static TLS int *cut1 = NULL; static TLS int *cut2 = NULL; static TLS char *sgap1, *egap1, *sgap2, *egap2; static TLS int localalloclen = 0; int lag; int tmpint; int count, count0; int len1, len2; int totallen; float totalscore; float impmatch; extern Fukusosuu *AllocateFukusosuuVec(); extern Fukusosuu **AllocateFukusosuuMtx(); if( seq1 == NULL ) { if( result1 ) { // fprintf( stderr, "Freeing localarrays in Falign\n" ); localalloclen = 0; mymergesort( 0, 0, NULL ); alignableReagion( 0, 0, NULL, NULL, NULL, NULL, NULL ); fft( 0, NULL, 1 ); A__align( NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 ); G__align11( NULL, NULL, 0, 0, 0 ); partA__align( NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL ); blockAlign2( NULL, NULL, NULL, NULL, NULL, NULL ); if( crossscore ) FreeDoubleMtx( crossscore ); FreeCharMtx( result1 ); FreeCharMtx( result2 ); FreeCharMtx( tmpres1 ); FreeCharMtx( tmpres2 ); FreeCharMtx( tmpseq1 ); FreeCharMtx( tmpseq2 ); free( sgap1 ); free( egap1 ); free( sgap2 ); free( egap2 ); free( kouho ); free( cut1 ); free( cut2 ); free( tmpptr1 ); free( tmpptr2 ); free( segment ); free( segment1 ); free( segment2 ); free( sortedseg1 ); free( sortedseg2 ); if( !kobetsubunkatsu ) { FreeFukusosuuMtx ( seqVector1 ); FreeFukusosuuMtx ( seqVector2 ); FreeFukusosuuVec( naisekiNoWa ); FreeFukusosuuMtx( naiseki ); FreeDoubleVec( soukan ); } } else { // fprintf( stderr, "Did not allocate localarrays in Falign\n" ); } return( 0.0 ); } len1 = strlen( seq1[0] ); len2 = strlen( seq2[0] ); nlentmp = MAX( len1, len2 ); nlen = 1; while( nlentmp >= nlen ) nlen <<= 1; #if 0 fprintf( stderr, "### nlen = %d\n", nlen ); #endif nlen2 = nlen/2; nlen4 = nlen2 / 2; #if DEBUG fprintf( stderr, "len1 = %d, len2 = %d\n", len1, len2 ); fprintf( stderr, "nlentmp = %d, nlen = %d\n", nlentmp, nlen ); #endif if( !localalloclen ) { sgap1 = AllocateCharVec( njob ); egap1 = AllocateCharVec( njob ); sgap2 = AllocateCharVec( njob ); egap2 = AllocateCharVec( njob ); kouho = AllocateIntVec( NKOUHO ); cut1 = AllocateIntVec( MAXSEG ); cut2 = AllocateIntVec( MAXSEG ); tmpptr1 = AllocateCharMtx( njob, 0 ); tmpptr2 = AllocateCharMtx( njob, 0 ); result1 = AllocateCharMtx( njob, alloclen ); result2 = AllocateCharMtx( njob, alloclen ); tmpres1 = AllocateCharMtx( njob, alloclen ); tmpres2 = AllocateCharMtx( njob, alloclen ); // crossscore = AllocateDoubleMtx( MAXSEG, MAXSEG ); segment = (Segment *)calloc( MAXSEG, sizeof( Segment ) ); segment1 = (Segment *)calloc( MAXSEG, sizeof( Segment ) ); segment2 = (Segment *)calloc( MAXSEG, sizeof( Segment ) ); sortedseg1 = (Segment **)calloc( MAXSEG, sizeof( Segment * ) ); sortedseg2 = (Segment **)calloc( MAXSEG, sizeof( Segment * ) ); if( !( segment && segment1 && segment2 && sortedseg1 && sortedseg2 ) ) ErrorExit( "Allocation error\n" ); if ( scoremtx == -1 ) n20or4or2 = 4; else if( fftscore == 1 ) n20or4or2 = 2; else n20or4or2 = 20; } if( localalloclen < nlen ) { if( localalloclen ) { #if 1 if( !kobetsubunkatsu ) { FreeFukusosuuMtx ( seqVector1 ); FreeFukusosuuMtx ( seqVector2 ); FreeFukusosuuVec( naisekiNoWa ); FreeFukusosuuMtx( naiseki ); FreeDoubleVec( soukan ); } FreeCharMtx( tmpseq1 ); FreeCharMtx( tmpseq2 ); #endif #if RND FreeCharMtx( rndseq1 ); FreeCharMtx( rndseq2 ); #endif } tmpseq1 = AllocateCharMtx( njob, nlen ); tmpseq2 = AllocateCharMtx( njob, nlen ); if( !kobetsubunkatsu ) { naisekiNoWa = AllocateFukusosuuVec( nlen ); naiseki = AllocateFukusosuuMtx( n20or4or2, nlen ); seqVector1 = AllocateFukusosuuMtx( n20or4or2+1, nlen+1 ); seqVector2 = AllocateFukusosuuMtx( n20or4or2+1, nlen+1 ); soukan = AllocateDoubleVec( nlen+1 ); } #if RND rndseq1 = AllocateCharMtx( njob, nlen ); rndseq2 = AllocateCharMtx( njob, nlen ); for( i=0; i<njob; i++ ) { generateRndSeq( rndseq1[i], nlen ); generateRndSeq( rndseq2[i], nlen ); } #endif localalloclen = nlen; } for( j=0; j<clus1; j++ ) strcpy( tmpseq1[j], seq1[j] ); for( j=0; j<clus2; j++ ) strcpy( tmpseq2[j], seq2[j] ); #if 0 fftfp = fopen( "input_of_Falign", "w" ); fprintf( fftfp, "nlen = %d\n", nlen ); fprintf( fftfp, "seq1: ( %d sequences ) \n", clus1 ); for( i=0; i<clus1; i++ ) fprintf( fftfp, "%s\n", seq1[i] ); fprintf( fftfp, "seq2: ( %d sequences ) \n", clus2 ); for( i=0; i<clus2; i++ ) fprintf( fftfp, "%s\n", seq2[i] ); fclose( fftfp ); system( "less input_of_Falign < /dev/tty > /dev/tty" ); #endif if( !kobetsubunkatsu ) { fprintf( stderr, "FFT ... " ); for( j=0; j<n20or4or2; j++ ) vec_init( seqVector1[j], nlen ); if( fftscore && scoremtx != -1 ) { for( i=0; i<clus1; i++ ) { seq_vec_2( seqVector1[0], polarity, eff1[i], tmpseq1[i] ); seq_vec_2( seqVector1[1], volume, eff1[i], tmpseq1[i] ); } } else { #if 0 for( i=0; i<clus1; i++ ) for( j=0; j<n20or4or2; j++ ) seq_vec( seqVector1[j], amino[j], eff1[i], tmpseq1[i] ); #else for( i=0; i<clus1; i++ ) seq_vec_3( seqVector1, eff1[i], tmpseq1[i] ); #endif } #if RND for( i=0; i<clus1; i++ ) { vec_init2( seqVector1, rndseq1[i], eff1[i], len1, nlen ); } #endif #if 0 fftfp = fopen( "seqVec", "w" ); fprintf( fftfp, "before transform\n" ); for( k=0; k<n20or4or2; k++ ) { fprintf( fftfp, "nlen=%d\n", nlen ); fprintf( fftfp, "%c\n", amino[k] ); for( l=0; l<nlen; l++ ) fprintf( fftfp, "%f %f\n", seqVector1[k][l].R, seqVector1[k][l].I ); } fclose( fftfp ); system( "less seqVec < /dev/tty > /dev/tty" ); #endif for( j=0; j<n20or4or2; j++ ) vec_init( seqVector2[j], nlen ); if( fftscore && scoremtx != -1 ) { for( i=0; i<clus2; i++ ) { seq_vec_2( seqVector2[0], polarity, eff2[i], tmpseq2[i] ); seq_vec_2( seqVector2[1], volume, eff2[i], tmpseq2[i] ); } } else { #if 0 for( i=0; i<clus2; i++ ) for( j=0; j<n20or4or2; j++ ) seq_vec( seqVector2[j], amino[j], eff2[i], tmpseq2[i] ); #else for( i=0; i<clus2; i++ ) seq_vec_3( seqVector2, eff2[i], tmpseq2[i] ); #endif } #if RND for( i=0; i<clus2; i++ ) { vec_init2( seqVector2, rndseq2[i], eff2[i], len2, nlen ); } #endif #if 0 fftfp = fopen( "seqVec2", "w" ); fprintf( fftfp, "before fft\n" ); for( k=0; k<n20or4or2; k++ ) { fprintf( fftfp, "%c\n", amino[k] ); for( l=0; l<nlen; l++ ) fprintf( fftfp, "%f %f\n", seqVector2[k][l].R, seqVector2[k][l].I ); } fclose( fftfp ); system( "less seqVec2 < /dev/tty > /dev/tty" ); #endif for( j=0; j<n20or4or2; j++ ) { fft( nlen, seqVector2[j], (j==0) ); fft( nlen, seqVector1[j], 0 ); } #if 0 fftfp = fopen( "seqVec2", "w" ); fprintf( fftfp, "#after fft\n" ); for( k=0; k<n20or4or2; k++ ) { fprintf( fftfp, "#%c\n", amino[k] ); for( l=0; l<nlen; l++ ) fprintf( fftfp, "%f %f\n", seqVector2[k][l].R, seqVector2[k][l].I ); } fclose( fftfp ); system( "less seqVec2 < /dev/tty > /dev/tty" ); #endif for( k=0; k<n20or4or2; k++ ) { for( l=0; l<nlen; l++ ) calcNaiseki( naiseki[k]+l, seqVector1[k]+l, seqVector2[k]+l ); } for( l=0; l<nlen; l++ ) { naisekiNoWa[l].R = 0.0; naisekiNoWa[l].I = 0.0; for( k=0; k<n20or4or2; k++ ) { naisekiNoWa[l].R += naiseki[k][l].R; naisekiNoWa[l].I += naiseki[k][l].I; } } #if 0 fftfp = fopen( "naisekiNoWa", "w" ); fprintf( fftfp, "#Before fft\n" ); for( l=0; l<nlen; l++ ) fprintf( fftfp, "%d %f %f\n", l, naisekiNoWa[l].R, naisekiNoWa[l].I ); fclose( fftfp ); system( "less naisekiNoWa < /dev/tty > /dev/tty " ); #endif fft( -nlen, naisekiNoWa, 0 ); for( m=0; m<=nlen2; m++ ) soukan[m] = naisekiNoWa[nlen2-m].R; for( m=nlen2+1; m<nlen; m++ ) soukan[m] = naisekiNoWa[nlen+nlen2-m].R; #if 0 fftfp = fopen( "naisekiNoWa", "w" ); fprintf( fftfp, "#After fft\n" ); for( l=0; l<nlen; l++ ) fprintf( fftfp, "%d %f\n", l, naisekiNoWa[l].R ); fclose( fftfp ); fftfp = fopen( "list.plot", "w" ); fprintf( fftfp, "plot 'naisekiNoWa'\npause -1" ); fclose( fftfp ); system( "/usr/bin/gnuplot list.plot &" ); #endif #if 0 fprintf( stderr, "frt write start\n" ); fftfp = fopen( "frt", "w" ); for( l=0; l<nlen; l++ ) fprintf( fftfp, "%d %f\n", l-nlen2, soukan[l] ); fclose( fftfp ); system( "less frt < /dev/tty > /dev/tty" ); #if 0 fftfp = fopen( "list.plot", "w" ); fprintf( fftfp, "plot 'frt'\n pause +1" ); fclose( fftfp ); system( "/usr/bin/gnuplot list.plot" ); #endif #endif getKouho( kouho, NKOUHO, soukan, nlen ); #if 0 for( i=0; i<NKOUHO; i++ ) { fprintf( stderr, "kouho[%d] = %d\n", i, kouho[i] ); } #endif } #if KEIKA fprintf( stderr, "Searching anchors ... " ); #endif count = 0; #define CAND 0 #if CAND fftfp = fopen( "cand", "w" ); fclose( fftfp ); #endif if( kobetsubunkatsu ) { maxk = 1; kouho[0] = 0; } else { maxk = NKOUHO; } for( k=0; k<maxk; k++ ) { lag = kouho[k]; zurasu2( lag, clus1, clus2, seq1, seq2, tmpptr1, tmpptr2 ); #if CAND fftfp = fopen( "cand", "a" ); fprintf( fftfp, "Candidate No.%d lag = %d\n", k+1, lag ); fprintf( fftfp, "%s\n", tmpptr1[0] ); fprintf( fftfp, "%s\n", tmpptr2[0] ); fclose( fftfp ); #endif tmpint = alignableReagion( clus1, clus2, tmpptr1, tmpptr2, eff1, eff2, segment+count ); if( count+tmpint > MAXSEG -3 ) ErrorExit( "TOO MANY SEGMENTS.\n" ); while( tmpint-- > 0 ) { if( lag > 0 ) { segment1[count].start = segment[count].start ; segment1[count].end = segment[count].end ; segment1[count].center = segment[count].center; segment1[count].score = segment[count].score; segment2[count].start = segment[count].start + lag; segment2[count].end = segment[count].end + lag; segment2[count].center = segment[count].center + lag; segment2[count].score = segment[count].score ; } else { segment1[count].start = segment[count].start - lag; segment1[count].end = segment[count].end - lag; segment1[count].center = segment[count].center - lag; segment1[count].score = segment[count].score ; segment2[count].start = segment[count].start ; segment2[count].end = segment[count].end ; segment2[count].center = segment[count].center; segment2[count].score = segment[count].score ; } #if 0 fftfp = fopen( "cand", "a" ); fprintf( fftfp, "Goukaku=%dko\n", tmpint ); fprintf( fftfp, "in 1 %d\n", segment1[count].center ); fprintf( fftfp, "in 2 %d\n", segment2[count].center ); fclose( fftfp ); #endif segment1[count].pair = &segment2[count]; segment2[count].pair = &segment1[count]; count++; #if 0 fprintf( stderr, "count=%d\n", count ); #endif } } #if 1 if( !kobetsubunkatsu ) fprintf( stderr, "%d segments found\n", count ); #endif if( !count && fftNoAnchStop ) ErrorExit( "Cannot detect anchor!" ); #if 0 fftfp = fopen( "fft", "a" ); fprintf( fftfp, "RESULT before sort:\n" ); for( l=0; l<count; l++ ) { fprintf( fftfp, "cut[%d]=%d, ", l, segment1[l].center ); fprintf( fftfp, "%d score = %f\n", segment2[l].center, segment1[l].score ); } fclose( fftfp ); #endif #if KEIKA fprintf( stderr, "Aligning anchors ... " ); #endif for( i=0; i<count; i++ ) { sortedseg1[i] = &segment1[i]; sortedseg2[i] = &segment2[i]; } #if 0 tmpsort( count, sortedseg1 ); tmpsort( count, sortedseg2 ); qsort( sortedseg1, count, sizeof( Segment * ), segcmp ); qsort( sortedseg2, count, sizeof( Segment * ), segcmp ); #else mymergesort( 0, count-1, sortedseg1 ); mymergesort( 0, count-1, sortedseg2 ); #endif for( i=0; i<count; i++ ) sortedseg1[i]->number = i; for( i=0; i<count; i++ ) sortedseg2[i]->number = i; if( kobetsubunkatsu ) { for( i=0; i<count; i++ ) { cut1[i+1] = sortedseg1[i]->center; cut2[i+1] = sortedseg2[i]->center; } cut1[0] = 0; cut2[0] = 0; cut1[count+1] = len1; cut2[count+1] = len2; count += 2; } else { if( crossscoresize < count+2 ) { crossscoresize = count+2; #if 1 fprintf( stderr, "######allocating crossscore, size = %d\n", crossscoresize ); #endif if( crossscore ) FreeDoubleMtx( crossscore ); crossscore = AllocateDoubleMtx( crossscoresize, crossscoresize ); } for( i=0; i<count+2; i++ ) for( j=0; j<count+2; j++ ) crossscore[i][j] = 0.0; for( i=0; i<count; i++ ) { crossscore[segment1[i].number+1][segment1[i].pair->number+1] = segment1[i].score; cut1[i+1] = sortedseg1[i]->center; cut2[i+1] = sortedseg2[i]->center; } #if DEBUG fprintf( stderr, "AFTER SORT\n" ); for( i=0; i<count; i++ ) fprintf( stderr, "%d, %d\n", segment1[i].start, segment2[i].start ); #endif crossscore[0][0] = 10000000.0; cut1[0] = 0; cut2[0] = 0; crossscore[count+1][count+1] = 10000000.0; cut1[count+1] = len1; cut2[count+1] = len2; count += 2; count0 = count; blockAlign2( cut1, cut2, sortedseg1, sortedseg2, crossscore, &count ); if( count0 > count ) { #if 0 fprintf( stderr, "\7 REPEAT!? \n" ); #else fprintf( stderr, "REPEAT!? \n" ); #endif if( fftRepeatStop ) exit( 1 ); } #if KEIKA else fprintf( stderr, "done\n" ); #endif } #if 0 fftfp = fopen( "fft", "a" ); fprintf( fftfp, "RESULT after sort:\n" ); for( l=0; l<count; l++ ) { fprintf( fftfp, "cut[%d]=%d, ", l, segment1[l].center ); fprintf( fftfp, "%d\n", segment2[l].center ); } fclose( fftfp ); #endif #if 0 fftfp = fopen( "fft", "a" ); fprintf( fftfp, "RESULT after sort:\n" ); for( l=0; l<count; l++ ) { fprintf( fftfp, "cut : %d %d\n", cut1[l], cut2[l] ); } fclose( fftfp ); #endif #if KEIKA fprintf( trap_g, "Devided to %d segments\n", count-1 ); fprintf( trap_g, "%d %d forg\n", MIN( clus1, clus2 ), count-1 ); #endif totallen = 0; for( j=0; j<clus1; j++ ) result1[j][0] = 0; for( j=0; j<clus2; j++ ) result2[j][0] = 0; totalscore = 0.0; *totalimpmatch = 0.0; for( i=0; i<count-1; i++ ) { #if DEBUG fprintf( stderr, "DP %03d / %03d %4d to ", i+1, count-1, totallen ); #else #if KEIKA fprintf( stderr, "DP %03d / %03d\r", i+1, count-1 ); #endif #endif if( cut1[i] ) { getkyokaigap( sgap1, seq1, cut1[i]-1, clus1 ); getkyokaigap( sgap2, seq2, cut2[i]-1, clus2 ); } else { for( j=0; j<clus1; j++ ) sgap1[j] = 'o'; for( j=0; j<clus2; j++ ) sgap2[j] = 'o'; } if( cut1[i+1] != len1 ) { getkyokaigap( egap1, seq1, cut1[i+1], clus1 ); getkyokaigap( egap2, seq2, cut2[i+1], clus2 ); } else { for( j=0; j<clus1; j++ ) egap1[j] = 'o'; for( j=0; j<clus2; j++ ) egap2[j] = 'o'; } for( j=0; j<clus1; j++ ) { strncpy( tmpres1[j], seq1[j]+cut1[i], cut1[i+1]-cut1[i] ); tmpres1[j][cut1[i+1]-cut1[i]] = 0; } if( kobetsubunkatsu ) commongappick_record( clus1, tmpres1, gapmap1 ); for( j=0; j<clus2; j++ ) { strncpy( tmpres2[j], seq2[j]+cut2[i], cut2[i+1]-cut2[i] ); tmpres2[j][cut2[i+1]-cut2[i]] = 0; } if( kobetsubunkatsu ) commongappick_record( clus2, tmpres2, gapmap2 ); #if 0 fprintf( stderr, "count = %d\n", count ); fprintf( stderr, "### reg1 = %d-%d\n", cut1[i], cut1[i+1]-1 ); fprintf( stderr, "### reg2 = %d-%d\n", cut2[i], cut2[i+1]-1 ); #endif switch( alg ) { case( 'a' ): totalscore += Aalign( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen ); break; case( 'Q' ): totalscore += partQ__align( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, localhom, &impmatch, cut1[i], cut1[i+1]-1, cut2[i], cut2[i+1]-1, gapmap1, gapmap2, sgap1, sgap2, egap1, egap2 ); *totalimpmatch += impmatch; // fprintf( stderr, "*totalimpmatch in Falign_localhom = %f\n", *totalimpmatch ); break; case( 'A' ): totalscore += partA__align( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, localhom, &impmatch, cut1[i], cut1[i+1]-1, cut2[i], cut2[i+1]-1, gapmap1, gapmap2, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres ); *totalimpmatch += impmatch; // fprintf( stderr, "*totalimpmatch in Falign_localhom = %f\n", *totalimpmatch ); break; default: fprintf( stderr, "alg = %c\n", alg ); ErrorExit( "ERROR IN SOURCE FILE Falign.c" ); break; } #ifdef enablemultithread if( chudanres && *chudanres ) { // fprintf( stderr, "\n\n## CHUUDAN!!! at Falign_localhom\n" ); return( -1.0 ); } #endif nlen = strlen( tmpres1[0] ); if( totallen + nlen > alloclen ) { fprintf( stderr, "totallen=%d + nlen=%d > alloclen = %d\n", totallen, nlen, alloclen ); ErrorExit( "LENGTH OVER in Falign\n " ); } for( j=0; j<clus1; j++ ) strcat( result1[j], tmpres1[j] ); for( j=0; j<clus2; j++ ) strcat( result2[j], tmpres2[j] ); totallen += nlen; #if 0 fprintf( stderr, "%4d\r", totallen ); fprintf( stderr, "\n\n" ); for( j=0; j<clus1; j++ ) { fprintf( stderr, "%s\n", tmpres1[j] ); } fprintf( stderr, "-------\n" ); for( j=0; j<clus2; j++ ) { fprintf( stderr, "%s\n", tmpres2[j] ); } #endif } #if KEIKA fprintf( stderr, "DP ... done \n" ); #endif for( j=0; j<clus1; j++ ) strcpy( seq1[j], result1[j] ); for( j=0; j<clus2; j++ ) strcpy( seq2[j], result2[j] ); #if 0 for( j=0; j<clus1; j++ ) { fprintf( stderr, "%s\n", result1[j] ); } fprintf( stderr, "- - - - - - - - - - -\n" ); for( j=0; j<clus2; j++ ) { fprintf( stderr, "%s\n", result2[j] ); } #endif return( totalscore ); }