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2119 lines
50 KiB
C
2119 lines
50 KiB
C
#include "mltaln.h"
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#include "dp.h"
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#define MACHIGAI 0
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#define OUTGAP0TRY 1
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#define DEBUG 0
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#define XXXXXXX 0
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#define USE_PENALTY_EX 0
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#define FASTMATCHCALC 1
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#if 0
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static void st_OpeningGapCount( double *ogcp, int clus, char **seq, double *eff, int len )
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{
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int i, j, gc, gb;
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double feff;
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for( i=0; i<len; i++ ) ogcp[i] = 0.0;
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for( j=0; j<clus; j++ )
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{
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feff = (double)eff[j];
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gc = 0;
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for( i=0; i<len; i++ )
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{
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gb = gc;
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gc = ( seq[j][i] == '-' );
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{
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if( !gb * gc ) ogcp[i] += feff;
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}
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}
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}
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}
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static void st_FinalGapCount( double *fgcp, int clus, char **seq, double *eff, int len )
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{
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int i, j, gc, gb;
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double feff;
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for( i=0; i<len; i++ ) fgcp[i] = 0.0;
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for( j=0; j<clus; j++ )
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{
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feff = (double)eff[j];
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gc = ( seq[j][0] == '-' );
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for( i=1; i<len+1; i++ )
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{
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gb = gc;
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gc = ( seq[j][i] == '-' );
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{
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if( gb * !gc ) fgcp[i-1] += feff;
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}
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}
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}
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}
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#endif
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static TLS int impalloclen = 0;
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static TLS double **impmtx = NULL;
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double part_imp_match_out_sc( int i1, int j1 )
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{
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// fprintf( stderr, "impalloclen = %d\n", impalloclen );
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// fprintf( stderr, "i1,j1=%d,%d -> impmtx=%f\n", i1, j1, impmtx[i1][j1] );
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return( impmtx[i1][j1] );
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#if 0
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if( i1 == l1 || j1 == l2 ) return( 0.0 );
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return( impmtx[i1+start1][j1+start2] );
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#endif
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}
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static void part_imp_match_out_vead_gapmap( double *imp, int i1, int lgth2, int start2, int *gapmap2 )
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{
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#if FASTMACHCALC
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double *pt = imp;
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int *gapmappt = gapmap2;
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while( lgth2-- )
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*pt++ += impmtx[i1][start2+*gapmappt++];
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#else
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int j;
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for( j=0; j<lgth2; j++ )
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{
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imp[j] += impmtx[i1][start2+gapmap2[j]];
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}
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#endif
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}
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static void part_imp_match_out_vead_tate_gapmap( double *imp, int j1, int lgth1, int start1, int *gapmap1 )
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{
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#if FASTMACHCALC
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double *pt = imp;
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int *gapmappt = gapmap1;
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while( lgth1-- )
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*pt++ = impmtx[start1+*gapmappt++][j1];
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#else
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int i;
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for( i=0; i<lgth1; i++ )
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{
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imp[i] += impmtx[start1+gapmap1[i]][j1];
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}
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#endif
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}
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#if 1
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void part_imp_match_init_strict( double *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, double *eff1_kozo, double *eff2_kozo, LocalHom ***localhom, char *swaplist, int forscore, int *orinum1, int *orinum2 )
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{
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// int i, j, k1, k2, tmpint, start1, start2, end1, end2;
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// double effij;
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// double effij_kozo;
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// double effijx;
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// char *pt, *pt1, *pt2;
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// static TLS char *nocount1 = NULL;
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// static TLS char *nocount2 = NULL;
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// LocalHom *tmpptr;
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if( seq1 == NULL )
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{
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if( impmtx ) FreeFloatMtx( impmtx );
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impmtx = NULL;
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// if( nocount1 ) free( nocount1 );
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// nocount1 = NULL;
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// if( nocount2 ) free( nocount2 );
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// nocount2 = NULL;
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return;
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}
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if( impalloclen < lgth1 + 2 || impalloclen < lgth2 + 2 )
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{
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if( impmtx ) FreeFloatMtx( impmtx );
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// if( nocount1 ) free( nocount1 );
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// if( nocount2 ) free( nocount2 );
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impalloclen = MAX( lgth1, lgth2 ) + 2;
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impmtx = AllocateFloatMtx( impalloclen, impalloclen );
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// nocount1 = AllocateCharVec( impalloclen );
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// nocount2 = AllocateCharVec( impalloclen );
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}
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fillimp( impmtx, imp, clus1, clus2, lgth1, lgth2, seq1, seq2, eff1, eff2, eff1_kozo, eff2_kozo, localhom, swaplist, forscore, orinum1, orinum2 );
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}
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#else
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#endif
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void part_imp_rna( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***grouprna1, RNApair ***grouprna2, int *gapmap1, int *gapmap2, RNApair *additionalpair )
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{
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foldrna( nseq1, nseq2, seq1, seq2, eff1, eff2, grouprna1, grouprna2, impmtx, gapmap1, gapmap2, additionalpair );
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}
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static void match_calc( double *match, double **cpmx1, double **cpmx2, int i1, int lgth2, double **doublework, int **intwork, int initialize )
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{
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#if FASTMATCHCALC
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int j, l;
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// double scarr[26];
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double **cpmxpd = doublework;
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int **cpmxpdn = intwork;
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double *matchpt, *cpmxpdpt, **cpmxpdptpt;
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int *cpmxpdnpt, **cpmxpdnptpt;
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double *scarr;
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scarr = calloc( nalphabets, sizeof( double ) );
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if( initialize )
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{
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int count = 0;
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for( j=0; j<lgth2; j++ )
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{
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count = 0;
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for( l=0; l<nalphabets; l++ )
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{
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if( cpmx2[l][j] )
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{
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cpmxpd[j][count] = cpmx2[l][j];
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cpmxpdn[j][count] = l;
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count++;
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}
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}
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cpmxpdn[j][count] = -1;
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}
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}
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{
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for( l=0; l<nalphabets; l++ )
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{
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scarr[l] = 0.0;
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for( j=0; j<nalphabets; j++ )
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scarr[l] += n_dis_consweight_multi[j][l] * cpmx1[j][i1];
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// scarr[l] += n_dis[j][l] * cpmx1[j][i1];
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}
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matchpt = match;
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cpmxpdnptpt = cpmxpdn;
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cpmxpdptpt = cpmxpd;
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while( lgth2-- )
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{
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*matchpt = 0.0;
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cpmxpdnpt = *cpmxpdnptpt++;
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cpmxpdpt = *cpmxpdptpt++;
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while( *cpmxpdnpt>-1 )
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*matchpt += scarr[*cpmxpdnpt++] * *cpmxpdpt++;
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matchpt++;
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}
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}
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free( scarr );
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#else
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int j, k, l;
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// double scarr[26];
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double **cpmxpd = doublework;
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int **cpmxpdn = intwork;
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double *scarr;
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scarr = calloc( nalphabets, sizeof( double ) );
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// simple
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if( initialize )
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{
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int count = 0;
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for( j=0; j<lgth2; j++ )
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{
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count = 0;
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for( l=0; l<nalphabets; l++ )
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{
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if( cpmx2[l][j] )
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{
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cpmxpd[count][j] = cpmx2[l][j];
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cpmxpdn[count][j] = l;
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count++;
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}
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}
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cpmxpdn[count][j] = -1;
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}
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}
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for( l=0; l<nalphabets; l++ )
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{
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scarr[l] = 0.0;
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for( k=0; k<nalphabets; k++ )
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scarr[l] += n_dis_consweight_multi[k][l] * cpmx1[k][i1];
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// scarr[l] += n_dis[k][l] * cpmx1[k][i1];
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}
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for( j=0; j<lgth2; j++ )
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{
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match[j] = 0.0;
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for( k=0; cpmxpdn[k][j]>-1; k++ )
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match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
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}
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#endif
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}
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static void fillzero( double *s, int l )
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{
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while( l-- ) *s++ = 0.0;
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}
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static void match_calc_del( int **which, double ***matrices, double *match, int n1, char **seq1, double *eff1, int n2, char **seq2, double *eff2, int i1, int lgth2, int mid, int nmask, int *mask1, int *mask2 )
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{
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// osoi!
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int i, j, k, m;
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int c1, c2;
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// fprintf( stderr, "\nmatch_calc_dynamicmtx... %d", i1 );
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// fprintf( stderr, "\nseq1[0]=%s\n", seq1[0] );
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// fprintf( stderr, "\nseq2[0]=%s\n", seq2[0] );
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// for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
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// {
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// if( flip ) reporterr( "in match_calc_slow, which[%d][%d] = %d\n", j, i, which[j][i] );
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// else reporterr( "in match_calc_slow, which[%d][%d] = %d\n", i, j, which[i][j] );
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// }
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for( k=0; k<lgth2; k++ )
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{
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for( m=0; m<nmask; m++ )
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{
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i = mask1[m];
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j = mask2[m];
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// reporterr( "Deleting %d-%d (c=%d)\n", i, j, mid );
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// if( k==0 ) fprintf( stderr, "pairoffset[%d][%d] = %f\n", i, j, po );
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c1 = amino_n[(int)seq1[i][i1]];
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c2 = amino_n[(int)seq2[j][k]];
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// reporterr( "k=%d, c1=%d, c2=%d, seq1[i][i1]=%c, seq2[%d][%d]=%c\n", k, c1, c2, seq1[i][i1], j, k, seq2[j][k] );
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if( seq1[i][i1] == '-' || seq2[j][k] == '-' ) continue;
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if( c1 < 0 || c2 < 0 ) continue;
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// fprintf( stderr, "c1=%d, c2=%d\n", c1, c2 );
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// fprintf( stderr, "match[k] = %f -> ", match[k], mid );
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match[k] -= matrices[mid][c1][c2] * eff1[i] * eff2[j];
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// fprintf( stderr, "match[k] = %f (mid=%d)\n", match[k], mid );
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}
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}
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// fprintf( stderr, "done\n" );
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return;
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}
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static void match_calc_add( double **scoreingmtx, double *match, double **cpmx1, double **cpmx2, int i1, int lgth2, double **doublework, int **intwork, int initialize )
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{
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#if FASTMATCHCALC
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// fprintf( stderr, "\nmatch_calc... %d", i1 );
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int j, l;
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// double scarr[26];
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double **cpmxpd = doublework;
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int **cpmxpdn = intwork;
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double *matchpt, *cpmxpdpt, **cpmxpdptpt;
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int *cpmxpdnpt, **cpmxpdnptpt;
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double *scarr;
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scarr = calloc( nalphabets, sizeof( double ) );
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if( initialize )
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{
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int count = 0;
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for( j=0; j<lgth2; j++ )
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{
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count = 0;
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for( l=0; l<nalphabets; l++ )
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{
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if( cpmx2[l][j] )
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{
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cpmxpd[j][count] = cpmx2[l][j];
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cpmxpdn[j][count] = l;
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count++;
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}
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}
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cpmxpdn[j][count] = -1;
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}
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}
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{
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for( l=0; l<nalphabets; l++ )
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{
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scarr[l] = 0.0;
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for( j=0; j<nalphabets; j++ )
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// scarr[l] += n_dis[j][l] * cpmx1[j][i1];
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// scarr[l] += n_dis_consweight_multi[j][l] * cpmx1[j][i1];
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scarr[l] += scoreingmtx[j][l] * cpmx1[j][i1];
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}
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matchpt = match;
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cpmxpdnptpt = cpmxpdn;
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cpmxpdptpt = cpmxpd;
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while( lgth2-- )
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{
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// *matchpt = 0.0;
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cpmxpdnpt = *cpmxpdnptpt++;
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cpmxpdpt = *cpmxpdptpt++;
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while( *cpmxpdnpt>-1 )
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*matchpt += scarr[*cpmxpdnpt++] * *cpmxpdpt++;
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matchpt++;
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}
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}
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free( scarr );
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// fprintf( stderr, "done\n" );
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#else
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int j, k, l;
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// double scarr[26];
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double **cpmxpd = doublework;
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int **cpmxpdn = intwork;
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double *scarr;
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scarr = calloc( nalphabets, sizeof( double ) );
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// simple
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if( initialize )
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{
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int count = 0;
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for( j=0; j<lgth2; j++ )
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{
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count = 0;
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for( l=0; l<nalphabets; l++ )
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{
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if( cpmx2[l][j] )
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{
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cpmxpd[count][j] = cpmx2[l][j];
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cpmxpdn[count][j] = l;
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count++;
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}
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}
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cpmxpdn[count][j] = -1;
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}
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}
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for( l=0; l<nalphabets; l++ )
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{
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scarr[l] = 0.0;
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for( k=0; k<nalphabets; k++ )
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// scarr[l] += n_dis[k][l] * cpmx1[k][i1];
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// scarr[l] += n_dis_consweight_multi[k][l] * cpmx1[k][i1];
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scarr[l] += scoreingmtx[k][l] * cpmx1[k][i1];
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}
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for( j=0; j<lgth2; j++ )
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{
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match[j] = 0.0;
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for( k=0; cpmxpdn[k][j]>-1; k++ )
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match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
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}
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free( scarr );
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#endif
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}
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static void Atracking_localhom( double *impwmpt, double *lasthorizontalw, double *lastverticalw,
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char **seq1, char **seq2,
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char **mseq1, char **mseq2,
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int **ijp, int icyc, int jcyc,
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int start1, int end1, int start2, int end2,
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int *gapmap1, int *gapmap2,
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int *warpis, int *warpjs, int warpbase )
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{
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int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, limk;
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// char gap[] = "-";
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char *gap;
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double wm;
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gap = newgapstr;
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lgth1 = strlen( seq1[0] );
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lgth2 = strlen( seq2[0] );
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#if 0
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for( i=0; i<lgth1; i++ )
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{
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fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
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}
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#endif
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if( outgap == 1 )
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;
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else
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{
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wm = lastverticalw[0];
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for( i=0; i<lgth1; i++ )
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{
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if( lastverticalw[i] >= wm )
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{
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wm = lastverticalw[i];
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iin = i; jin = lgth2-1;
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ijp[lgth1][lgth2] = +( lgth1 - i );
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}
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}
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for( j=0; j<lgth2; j++ )
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{
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if( lasthorizontalw[j] >= wm )
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{
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wm = lasthorizontalw[j];
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iin = lgth1-1; jin = j;
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ijp[lgth1][lgth2] = -( lgth2 - j );
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}
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}
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}
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for( i=0; i<lgth1+1; i++ )
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{
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ijp[i][0] = i + 1;
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}
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for( j=0; j<lgth2+1; j++ )
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{
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ijp[0][j] = -( j + 1 );
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}
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for( i=0; i<icyc; i++ )
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{
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mseq1[i] += lgth1+lgth2;
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*mseq1[i] = 0;
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}
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for( j=0; j<jcyc; j++ )
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{
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mseq2[j] += lgth1+lgth2;
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*mseq2[j] = 0;
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}
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iin = lgth1; jin = lgth2;
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*impwmpt = 0.0;
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limk = lgth1+lgth2+1;
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for( k=0; k<limk; k++ )
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{
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if( ijp[iin][jin] >= warpbase )
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{
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ifi = warpis[ijp[iin][jin]-warpbase];
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jfi = warpjs[ijp[iin][jin]-warpbase];
|
|
}
|
|
else if( ijp[iin][jin] < 0 )
|
|
{
|
|
ifi = iin-1; jfi = jin+ijp[iin][jin];
|
|
}
|
|
else if( ijp[iin][jin] > 0 )
|
|
{
|
|
ifi = iin-ijp[iin][jin]; jfi = jin-1;
|
|
}
|
|
else
|
|
{
|
|
ifi = iin-1; jfi = jin-1;
|
|
}
|
|
if( ifi == -warpbase && jfi == -warpbase )
|
|
{
|
|
l = iin;
|
|
while( --l >= 0 )
|
|
{
|
|
for( i=0; i<icyc; i++ )
|
|
*--mseq1[i] = seq1[i][l];
|
|
for( j=0; j<jcyc; j++ )
|
|
*--mseq2[j] = *gap;
|
|
k++;
|
|
}
|
|
l= jin;
|
|
while( --l >= 0 )
|
|
{
|
|
for( i=0; i<icyc; i++ )
|
|
*--mseq1[i] = *gap;
|
|
for( j=0; j<jcyc; j++ )
|
|
*--mseq2[j] = seq2[j][l];
|
|
k++;
|
|
}
|
|
break;
|
|
}
|
|
else
|
|
{
|
|
l = iin - ifi;
|
|
while( --l )
|
|
{
|
|
for( i=0; i<icyc; i++ )
|
|
*--mseq1[i] = seq1[i][ifi+l];
|
|
for( j=0; j<jcyc; j++ )
|
|
*--mseq2[j] = *gap;
|
|
k++;
|
|
}
|
|
l= jin - jfi;
|
|
while( --l )
|
|
{
|
|
for( i=0; i<icyc; i++ )
|
|
*--mseq1[i] = *gap;
|
|
for( j=0; j<jcyc; j++ )
|
|
*--mseq2[j] = seq2[j][jfi+l];
|
|
k++;
|
|
}
|
|
}
|
|
if( iin != lgth1 && jin != lgth2 ) // ??
|
|
{
|
|
*impwmpt += (double)part_imp_match_out_sc( gapmap1[iin]+start1, gapmap2[jin]+start2 );
|
|
// fprintf( stderr, "impwm = %f (iin=%d, jin=%d) seq1=%c, seq2=%c\n", *impwmpt, iin, jin, seq1[0][iin], seq2[0][jin] );
|
|
}
|
|
if( iin <= 0 || jin <= 0 ) break;
|
|
for( i=0; i<icyc; i++ )
|
|
*--mseq1[i] = seq1[i][ifi];
|
|
for( j=0; j<jcyc; j++ )
|
|
*--mseq2[j] = seq2[j][jfi];
|
|
k++;
|
|
iin = ifi; jin = jfi;
|
|
}
|
|
}
|
|
|
|
static double Atracking( double *lasthorizontalw, double *lastverticalw,
|
|
char **seq1, char **seq2,
|
|
char **mseq1, char **mseq2,
|
|
int **ijp, int icyc, int jcyc,
|
|
int *warpis, int *warpjs, int warpbase )
|
|
{
|
|
int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, lastk, limk;
|
|
// char gap[] = "-";
|
|
char *gap;
|
|
gap = newgapstr;
|
|
double wm = 0.0;
|
|
lgth1 = strlen( seq1[0] );
|
|
lgth2 = strlen( seq2[0] );
|
|
|
|
#if 0
|
|
for( i=0; i<lgth1; i++ )
|
|
{
|
|
fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
|
|
}
|
|
#endif
|
|
|
|
if( outgap == 1 )
|
|
;
|
|
else
|
|
{
|
|
wm = lastverticalw[0];
|
|
for( i=0; i<lgth1; i++ )
|
|
{
|
|
if( lastverticalw[i] >= wm )
|
|
{
|
|
wm = lastverticalw[i];
|
|
iin = i; jin = lgth2-1;
|
|
ijp[lgth1][lgth2] = +( lgth1 - i );
|
|
}
|
|
}
|
|
for( j=0; j<lgth2; j++ )
|
|
{
|
|
if( lasthorizontalw[j] >= wm )
|
|
{
|
|
wm = lasthorizontalw[j];
|
|
iin = lgth1-1; jin = j;
|
|
ijp[lgth1][lgth2] = -( lgth2 - j );
|
|
}
|
|
}
|
|
}
|
|
|
|
for( i=0; i<lgth1+1; i++ )
|
|
{
|
|
ijp[i][0] = i + 1;
|
|
}
|
|
for( j=0; j<lgth2+1; j++ )
|
|
{
|
|
ijp[0][j] = -( j + 1 );
|
|
}
|
|
|
|
for( i=0; i<icyc; i++ )
|
|
{
|
|
mseq1[i] += lgth1+lgth2;
|
|
*mseq1[i] = 0;
|
|
}
|
|
for( j=0; j<jcyc; j++ )
|
|
{
|
|
mseq2[j] += lgth1+lgth2;
|
|
*mseq2[j] = 0;
|
|
}
|
|
iin = lgth1; jin = lgth2;
|
|
lastk = lgth1+lgth2;
|
|
limk = lgth1+lgth2+1;
|
|
for( k=0; k<limk; k++ )
|
|
{
|
|
if( ijp[iin][jin] >= warpbase )
|
|
{
|
|
ifi = warpis[ijp[iin][jin]-warpbase];
|
|
jfi = warpjs[ijp[iin][jin]-warpbase];
|
|
}
|
|
else if( ijp[iin][jin] < 0 )
|
|
{
|
|
ifi = iin-1; jfi = jin+ijp[iin][jin];
|
|
}
|
|
else if( ijp[iin][jin] > 0 )
|
|
{
|
|
ifi = iin-ijp[iin][jin]; jfi = jin-1;
|
|
}
|
|
else
|
|
{
|
|
ifi = iin-1; jfi = jin-1;
|
|
}
|
|
if( ifi == -warpbase && jfi == -warpbase )
|
|
{
|
|
l = iin;
|
|
while( --l >= 0 )
|
|
{
|
|
for( i=0; i<icyc; i++ )
|
|
*--mseq1[i] = seq1[i][l];
|
|
for( j=0; j<jcyc; j++ )
|
|
*--mseq2[j] = *gap;
|
|
k++;
|
|
}
|
|
l= jin;
|
|
while( --l >= 0 )
|
|
{
|
|
for( i=0; i<icyc; i++ )
|
|
*--mseq1[i] = *gap;
|
|
for( j=0; j<jcyc; j++ )
|
|
*--mseq2[j] = seq2[j][l];
|
|
k++;
|
|
}
|
|
break;
|
|
}
|
|
else
|
|
{
|
|
l = iin - ifi;
|
|
while( --l )
|
|
{
|
|
for( i=0; i<icyc; i++ )
|
|
*--mseq1[i] = seq1[i][ifi+l];
|
|
for( j=0; j<jcyc; j++ )
|
|
*--mseq2[j] = *gap;
|
|
k++;
|
|
}
|
|
l= jin - jfi;
|
|
while( --l )
|
|
{
|
|
for( i=0; i<icyc; i++ )
|
|
*--mseq1[i] = *gap;
|
|
for( j=0; j<jcyc; j++ )
|
|
*--mseq2[j] = seq2[j][jfi+l];
|
|
k++;
|
|
}
|
|
}
|
|
|
|
if( iin <= 0 || jin <= 0 ) break;
|
|
for( i=0; i<icyc; i++ )
|
|
*--mseq1[i] = seq1[i][ifi];
|
|
for( j=0; j<jcyc; j++ )
|
|
*--mseq2[j] = seq2[j][jfi];
|
|
k++;
|
|
iin = ifi; jin = jfi;
|
|
}
|
|
return( 0.0 );
|
|
}
|
|
|
|
double partA__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, int constraint, double *impmatch, int start1, int end1, int start2, int end2, int *gapmap1, int *gapmap2, char *sgap1, char *sgap2, char *egap1, char *egap2, int *chudanpt, int chudanref, int *chudanres )
|
|
/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
|
|
{
|
|
// int k;
|
|
register int i, j;
|
|
int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
|
|
int lgth1, lgth2;
|
|
int resultlen;
|
|
double wm = 0.0; /* int ?????? */
|
|
double g;
|
|
double *currentw, *previousw;
|
|
#if 1
|
|
double *wtmp;
|
|
int *ijppt;
|
|
double *mjpt, *prept, *curpt;
|
|
int *mpjpt;
|
|
#endif
|
|
static TLS double mi, *m;
|
|
static TLS int **ijp;
|
|
static TLS int mpi, *mp;
|
|
static TLS double *w1, *w2;
|
|
static TLS double *match;
|
|
static TLS double *initverticalw; /* kufuu sureba iranai */
|
|
static TLS double *lastverticalw; /* kufuu sureba iranai */
|
|
static TLS char **mseq1;
|
|
static TLS char **mseq2;
|
|
static TLS char **mseq;
|
|
static TLS double *ogcp1;
|
|
static TLS double *ogcp2;
|
|
static TLS double *fgcp1;
|
|
static TLS double *fgcp2;
|
|
static TLS double **cpmx1;
|
|
static TLS double **cpmx2;
|
|
static TLS double *gapfreq1;
|
|
static TLS double *gapfreq2;
|
|
static TLS int **intwork;
|
|
static TLS double **doublework;
|
|
static TLS int orlgth1 = 0, orlgth2 = 0;
|
|
double fpenalty = (double)penalty;
|
|
double fpenalty_shift = (double)penalty_shift;
|
|
#if USE_PENALTY_EX
|
|
double fpenalty_ex = (double)penalty_ex;
|
|
#endif
|
|
double *fgcp2pt;
|
|
double *ogcp2pt;
|
|
double fgcp1va;
|
|
double ogcp1va;
|
|
double *gf2pt;
|
|
double *gf2ptpre;
|
|
double gf1va;
|
|
double gf1vapre;
|
|
double headgapfreq1;
|
|
double headgapfreq2;
|
|
|
|
int *warpis = NULL;
|
|
int *warpjs = NULL;
|
|
int *warpi = NULL;
|
|
int *warpj = NULL;
|
|
int *prevwarpi = NULL;
|
|
int *prevwarpj = NULL;
|
|
double *wmrecords = NULL;
|
|
double *prevwmrecords = NULL;
|
|
int warpn = 0;
|
|
int warpbase;
|
|
double curm = 0.0;
|
|
double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
|
|
int *warpipt, *warpjpt;
|
|
|
|
|
|
if( seq1 == NULL )
|
|
{
|
|
if( orlgth1 )
|
|
{
|
|
// fprintf( stderr, "## Freeing local arrays in A__align\n" );
|
|
orlgth1 = 0;
|
|
orlgth2 = 0;
|
|
|
|
part_imp_match_init_strict( NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL );
|
|
|
|
free( mseq1 );
|
|
free( mseq2 );
|
|
FreeFloatVec( w1 );
|
|
FreeFloatVec( w2 );
|
|
FreeFloatVec( match );
|
|
FreeFloatVec( initverticalw );
|
|
FreeFloatVec( lastverticalw );
|
|
|
|
FreeFloatVec( m );
|
|
FreeIntVec( mp );
|
|
|
|
FreeCharMtx( mseq );
|
|
|
|
FreeFloatVec( ogcp1 );
|
|
FreeFloatVec( ogcp2 );
|
|
FreeFloatVec( fgcp1 );
|
|
FreeFloatVec( fgcp2 );
|
|
|
|
|
|
FreeFloatMtx( cpmx1 );
|
|
FreeFloatMtx( cpmx2 );
|
|
|
|
FreeFloatVec( gapfreq1 );
|
|
FreeFloatVec( gapfreq2 );
|
|
|
|
FreeFloatMtx( doublework );
|
|
FreeIntMtx( intwork );
|
|
|
|
}
|
|
else
|
|
{
|
|
// fprintf( stderr, "## Not allocated\n" );
|
|
}
|
|
return( 0.0 );
|
|
}
|
|
// fprintf( stderr, "IN partA__align\n" );
|
|
|
|
|
|
lgth1 = strlen( seq1[0] );
|
|
lgth2 = strlen( seq2[0] );
|
|
#if 1
|
|
// if( lgth1 == 0 ) fprintf( stderr, "WARNING: lgth1=0 in partA__align\n" );
|
|
// if( lgth2 == 0 ) fprintf( stderr, "WARNING: lgth2=0 in partA__align\n" );
|
|
|
|
if( lgth1 == 0 && lgth2 == 0 )
|
|
return( 0.0 );
|
|
|
|
if( lgth1 == 0 )
|
|
{
|
|
for( i=0; i<icyc; i++ )
|
|
{
|
|
j = lgth2;
|
|
seq1[i][j] = 0;
|
|
while( j ) seq1[i][--j] = *newgapstr;
|
|
// fprintf( stderr, "seq1[i] = %s\n", seq1[i] );
|
|
}
|
|
return( 0.0 );
|
|
}
|
|
|
|
if( lgth2 == 0 )
|
|
{
|
|
for( i=0; i<jcyc; i++ )
|
|
{
|
|
j = lgth1;
|
|
seq2[i][j] = 0;
|
|
while( j ) seq2[i][--j] = *newgapstr;
|
|
// fprintf( stderr, "seq2[i] = %s\n", seq2[i] );
|
|
}
|
|
return( 0.0 );
|
|
}
|
|
#endif
|
|
|
|
warpbase = lgth1 + lgth2;
|
|
warpis = NULL;
|
|
warpjs = NULL;
|
|
warpn = 0;
|
|
|
|
|
|
|
|
|
|
if( trywarp )
|
|
{
|
|
if( outgap == 0 )
|
|
{
|
|
fprintf( stderr, "At present, outgap must be 1.\n" );
|
|
exit( 1 );
|
|
}
|
|
wmrecords = AllocateFloatVec( lgth2+1 );
|
|
warpi = AllocateIntVec( lgth2+1 );
|
|
warpj = AllocateIntVec( lgth2+1 );
|
|
prevwmrecords = AllocateFloatVec( lgth2+1 );
|
|
prevwarpi = AllocateIntVec( lgth2+1 );
|
|
prevwarpj = AllocateIntVec( lgth2+1 );
|
|
for( i=0; i<lgth2+1; i++ ) wmrecords[i] = 0.0;
|
|
for( i=0; i<lgth2+1; i++ ) prevwmrecords[i] = 0.0;
|
|
for( i=0; i<lgth2+1; i++ ) prevwarpi[i] = -warpbase;
|
|
for( i=0; i<lgth2+1; i++ ) prevwarpj[i] = -warpbase;
|
|
for( i=0; i<lgth2+1; i++ ) warpi[i] = -warpbase;
|
|
for( i=0; i<lgth2+1; i++ ) warpj[i] = -warpbase;
|
|
}
|
|
|
|
#if 0
|
|
fprintf( stderr, "eff in SA+++align\n" );
|
|
for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
|
|
#endif
|
|
if( orlgth1 == 0 )
|
|
{
|
|
mseq1 = AllocateCharMtx( njob, 0 );
|
|
mseq2 = AllocateCharMtx( njob, 0 );
|
|
}
|
|
|
|
|
|
|
|
|
|
if( lgth1 > orlgth1 || lgth2 > orlgth2 )
|
|
{
|
|
int ll1, ll2;
|
|
|
|
if( orlgth1 > 0 && orlgth2 > 0 )
|
|
{
|
|
FreeFloatVec( w1 );
|
|
FreeFloatVec( w2 );
|
|
FreeFloatVec( match );
|
|
FreeFloatVec( initverticalw );
|
|
FreeFloatVec( lastverticalw );
|
|
|
|
FreeFloatVec( m );
|
|
FreeIntVec( mp );
|
|
|
|
FreeCharMtx( mseq );
|
|
|
|
FreeFloatVec( ogcp1 );
|
|
FreeFloatVec( ogcp2 );
|
|
FreeFloatVec( fgcp1 );
|
|
FreeFloatVec( fgcp2 );
|
|
|
|
|
|
FreeFloatMtx( cpmx1 );
|
|
FreeFloatMtx( cpmx2 );
|
|
|
|
FreeFloatVec( gapfreq1 );
|
|
FreeFloatVec( gapfreq2 );
|
|
|
|
FreeFloatMtx( doublework );
|
|
FreeIntMtx( intwork );
|
|
}
|
|
|
|
ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
|
|
ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
|
|
|
|
#if DEBUG
|
|
fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
|
|
#endif
|
|
|
|
w1 = AllocateFloatVec( ll2+2 );
|
|
w2 = AllocateFloatVec( ll2+2 );
|
|
match = AllocateFloatVec( ll2+2 );
|
|
|
|
initverticalw = AllocateFloatVec( ll1+2 );
|
|
lastverticalw = AllocateFloatVec( ll1+2 );
|
|
|
|
m = AllocateFloatVec( ll2+2 );
|
|
mp = AllocateIntVec( ll2+2 );
|
|
|
|
mseq = AllocateCharMtx( njob, ll1+ll2 );
|
|
|
|
ogcp1 = AllocateFloatVec( ll1+2 );
|
|
ogcp2 = AllocateFloatVec( ll2+2 );
|
|
fgcp1 = AllocateFloatVec( ll1+2 );
|
|
fgcp2 = AllocateFloatVec( ll2+2 );
|
|
|
|
cpmx1 = AllocateFloatMtx( nalphabets, ll1+2 );
|
|
cpmx2 = AllocateFloatMtx( nalphabets, ll2+2 );
|
|
|
|
gapfreq1 = AllocateFloatVec( ll1+2 );
|
|
gapfreq2 = AllocateFloatVec( ll2+2 );
|
|
|
|
#if FASTMATCHCALC
|
|
doublework = AllocateFloatMtx( MAX( ll1, ll2 )+2, nalphabets );
|
|
intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, nalphabets );
|
|
#else
|
|
doublework = AllocateFloatMtx( nalphabets, MAX( ll1, ll2 )+2 );
|
|
intwork = AllocateIntMtx( nalphabets, MAX( ll1, ll2 )+2 );
|
|
#endif
|
|
|
|
#if DEBUG
|
|
fprintf( stderr, "succeeded\n" );
|
|
#endif
|
|
|
|
orlgth1 = ll1 - 100;
|
|
orlgth2 = ll2 - 100;
|
|
}
|
|
|
|
|
|
for( i=0; i<icyc; i++ ) mseq1[i] = mseq[i];
|
|
for( j=0; j<jcyc; j++ ) mseq2[j] = mseq[icyc+j];
|
|
|
|
|
|
if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
|
|
{
|
|
int ll1, ll2;
|
|
|
|
if( commonAlloc1 && commonAlloc2 )
|
|
{
|
|
FreeIntMtx( commonIP );
|
|
}
|
|
|
|
ll1 = MAX( orlgth1, commonAlloc1 );
|
|
ll2 = MAX( orlgth2, commonAlloc2 );
|
|
|
|
#if DEBUG
|
|
fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
|
|
#endif
|
|
|
|
commonIP = AllocateIntMtx( ll1+10, ll2+10 );
|
|
|
|
#if DEBUG
|
|
fprintf( stderr, "succeeded\n\n" );
|
|
#endif
|
|
|
|
commonAlloc1 = ll1;
|
|
commonAlloc2 = ll2;
|
|
}
|
|
ijp = commonIP;
|
|
|
|
cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
|
|
cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
|
|
|
|
if( sgap1 )
|
|
{
|
|
new_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1, sgap1 );
|
|
new_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2, sgap2 );
|
|
new_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1, egap1 );
|
|
new_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2, egap2 );
|
|
outgapcount( &headgapfreq1, icyc, sgap1, eff1 );
|
|
outgapcount( &headgapfreq2, jcyc, sgap2, eff2 );
|
|
outgapcount( gapfreq1+lgth1, icyc, egap1, eff1 );
|
|
outgapcount( gapfreq2+lgth2, jcyc, egap2, eff2 );
|
|
}
|
|
else
|
|
{
|
|
st_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
|
|
st_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
|
|
st_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
|
|
st_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
|
|
headgapfreq1 = 0.0;
|
|
headgapfreq2 = 0.0;
|
|
gapfreq1[lgth1] = 0.0;
|
|
gapfreq2[lgth2] = 0.0;
|
|
}
|
|
|
|
if( legacygapcost == 0 )
|
|
{
|
|
gapcountf( gapfreq1, seq1, icyc, eff1, lgth1 );
|
|
gapcountf( gapfreq2, seq2, jcyc, eff2, lgth2 );
|
|
for( i=0; i<lgth1+1; i++ ) gapfreq1[i] = 1.0 - gapfreq1[i];
|
|
for( i=0; i<lgth2+1; i++ ) gapfreq2[i] = 1.0 - gapfreq2[i];
|
|
headgapfreq1 = 1.0 - headgapfreq1;
|
|
headgapfreq2 = 1.0 - headgapfreq2;
|
|
}
|
|
else
|
|
{
|
|
for( i=0; i<lgth1+1; i++ ) gapfreq1[i] = 1.0;
|
|
for( i=0; i<lgth2+1; i++ ) gapfreq2[i] = 1.0;
|
|
headgapfreq1 = 1.0;
|
|
headgapfreq2 = 1.0;
|
|
}
|
|
|
|
for( i=0; i<lgth1; i++ )
|
|
{
|
|
ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty * ( gapfreq1[i] );
|
|
fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty * ( gapfreq1[i] );
|
|
}
|
|
for( i=0; i<lgth2; i++ )
|
|
{
|
|
ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty * ( gapfreq2[i] );
|
|
fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty * ( gapfreq2[i] );
|
|
}
|
|
#if 0
|
|
for( i=0; i<lgth1; i++ )
|
|
fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
|
|
#endif
|
|
|
|
currentw = w1;
|
|
previousw = w2;
|
|
|
|
|
|
match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, doublework, intwork, 1 );
|
|
if( constraint )
|
|
part_imp_match_out_vead_tate_gapmap( initverticalw, gapmap2[0]+start2, lgth1, start1, gapmap1 );
|
|
|
|
|
|
match_calc( currentw, cpmx1, cpmx2, 0, lgth2, doublework, intwork, 1 );
|
|
if( constraint )
|
|
part_imp_match_out_vead_gapmap( currentw, gapmap1[0]+start1, lgth2, start2, gapmap2 );
|
|
#if 0 // -> tbfast.c
|
|
if( localhom )
|
|
imp_match_calc( currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
|
|
|
|
#endif
|
|
|
|
if( outgap == 1 )
|
|
{
|
|
for( i=1; i<lgth1+1; i++ )
|
|
{
|
|
// initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
|
|
initverticalw[i] += ( ogcp1[0] * headgapfreq2 + fgcp1[i-1] * gapfreq2[0] ) ;
|
|
#if USE_PENALTY_EX
|
|
tsuika hitsuyou
|
|
#endif
|
|
}
|
|
for( j=1; j<lgth2+1; j++ )
|
|
{
|
|
// currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
|
|
currentw[j] += ( ogcp2[0] * headgapfreq1 + fgcp2[j-1] * gapfreq1[0] ) ;
|
|
#if USE_PENALTY_EX
|
|
tsuika hitsuyou
|
|
#endif
|
|
}
|
|
}
|
|
#if OUTGAP0TRY
|
|
else
|
|
{
|
|
for( j=1; j<lgth2+1; j++ )
|
|
currentw[j] -= offset * j / 2.0;
|
|
for( i=1; i<lgth1+1; i++ )
|
|
initverticalw[i] -= offset * i / 2.0;
|
|
}
|
|
#endif
|
|
|
|
for( j=1; j<lgth2+1; ++j )
|
|
{
|
|
// m[j] = currentw[j-1] + ogcp1[1]; mp[j] = 0;
|
|
m[j] = currentw[j-1] + ogcp1[1] * gapfreq2[j-1]; mp[j] = 0;;
|
|
}
|
|
|
|
lastverticalw[0] = currentw[lgth2-1];
|
|
|
|
if( outgap ) lasti = lgth1+1; else lasti = lgth1;
|
|
lastj = lgth2+1;
|
|
|
|
#if XXXXXXX
|
|
fprintf( stderr, "currentw = \n" );
|
|
for( i=0; i<lgth1+1; i++ )
|
|
{
|
|
fprintf( stderr, "%5.2f ", currentw[i] );
|
|
}
|
|
fprintf( stderr, "\n" );
|
|
fprintf( stderr, "initverticalw = \n" );
|
|
for( i=0; i<lgth2+1; i++ )
|
|
{
|
|
fprintf( stderr, "%5.2f ", initverticalw[i] );
|
|
}
|
|
fprintf( stderr, "\n" );
|
|
fprintf( stderr, "fcgp\n" );
|
|
for( i=0; i<lgth1; i++ )
|
|
fprintf( stderr, "fgcp1[%d]=%f\n", i, ogcp1[i] );
|
|
for( i=0; i<lgth2; i++ )
|
|
fprintf( stderr, "fgcp2[%d]=%f\n", i, ogcp2[i] );
|
|
#endif
|
|
|
|
for( i=1; i<lasti; i++ )
|
|
{
|
|
|
|
#ifdef enablemultithread
|
|
// fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
|
|
if( chudanpt && *chudanpt != chudanref )
|
|
{
|
|
// fprintf( stderr, "\n\n## CHUUDAN!!! i\n" );
|
|
*chudanres = 1;
|
|
return( -1.0 );
|
|
}
|
|
#endif
|
|
|
|
wtmp = previousw;
|
|
previousw = currentw;
|
|
currentw = wtmp;
|
|
|
|
previousw[0] = initverticalw[i-1];
|
|
|
|
match_calc( currentw, cpmx1, cpmx2, i, lgth2, doublework, intwork, 0 );
|
|
#if 0
|
|
fprintf( stderr, "\n" );
|
|
fprintf( stderr, "i=%d\n", i );
|
|
fprintf( stderr, "currentw before imp = \n" );
|
|
for( j=0; j<lgth2; j++ )
|
|
{
|
|
fprintf( stderr, "%5.2f ", currentw[j] );
|
|
}
|
|
fprintf( stderr, "\n" );
|
|
#endif
|
|
if( constraint )
|
|
{
|
|
// fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
|
|
// imp_match_out_vead( currentw, i, lgth2 );
|
|
part_imp_match_out_vead_gapmap( currentw, gapmap1[i]+start1, lgth2, start2, gapmap2 );
|
|
}
|
|
#if 0
|
|
fprintf( stderr, "specificity = 0\n" );
|
|
fprintf( stderr, "i=%d\n", i );
|
|
fprintf( stderr, "currentw = \n" );
|
|
for( j=0; j<lgth2; j++ )
|
|
{
|
|
fprintf( stderr, "%5.2f ", currentw[j] );
|
|
}
|
|
fprintf( stderr, "\n" );
|
|
#endif
|
|
currentw[0] = initverticalw[i];
|
|
|
|
|
|
// mi = previousw[0] + ogcp2[1]; mpi = 0;
|
|
mi = previousw[0] + ogcp2[1] * gapfreq1[i-1]; mpi=0;
|
|
|
|
ijppt = ijp[i] + 1;
|
|
mjpt = m + 1;
|
|
prept = previousw;
|
|
curpt = currentw + 1;
|
|
mpjpt = mp + 1;
|
|
fgcp2pt = fgcp2;
|
|
ogcp2pt = ogcp2+1;
|
|
fgcp1va = fgcp1[i-1];
|
|
ogcp1va = ogcp1[i];
|
|
gf1va = gapfreq1[i];
|
|
gf1vapre = gapfreq1[i-1];
|
|
gf2pt = gapfreq2+1;
|
|
gf2ptpre = gapfreq2;
|
|
|
|
if( trywarp )
|
|
{
|
|
prevwmrecordspt = prevwmrecords;
|
|
wmrecordspt = wmrecords+1;
|
|
wmrecords1pt = wmrecords;
|
|
warpipt = warpi + 1;
|
|
warpjpt = warpj + 1;
|
|
}
|
|
|
|
for( j=1; j<lastj; j++ )
|
|
{
|
|
#ifdef xxxenablemultithread
|
|
// fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
|
|
if( chudanpt && *chudanpt != chudanref )
|
|
{
|
|
// fprintf( stderr, "\n\n## CHUUDAN!!! j\n" );
|
|
*chudanres = 1;
|
|
return( -1.0 );
|
|
}
|
|
#endif
|
|
wm = *prept;
|
|
*ijppt = 0;
|
|
|
|
#if 0
|
|
fprintf( stderr, "%5.0f->", wm );
|
|
#endif
|
|
// g = mi + *fgcp2pt * gapfreq1[i];
|
|
if( (g = mi + *fgcp2pt * gf1va) > wm )
|
|
{
|
|
wm = g;
|
|
*ijppt = -( j - mpi );
|
|
}
|
|
// g = *prept + *ogcp2pt * gapfreq1[i-1];
|
|
// if( (g = *prept + *ogcp2pt * gf1vapre) >= mi )
|
|
if( (g = *prept + *ogcp2pt * gf1vapre) > mi ) // 2018/Apr
|
|
{
|
|
mi = g;
|
|
mpi = j-1;
|
|
}
|
|
#if USE_PENALTY_EX
|
|
mi += fpenalty_ex;
|
|
#endif
|
|
|
|
// g = *mjpt + fgcp1va * gapfreq2[j];
|
|
if( (g = *mjpt + fgcp1va * *gf2pt) > wm )
|
|
{
|
|
wm = g;
|
|
*ijppt = +( i - *mpjpt );
|
|
}
|
|
// g = *prept + ogcp1va * gapfreq2[j-1];
|
|
// if( (g = *prept + ogcp1va * *gf2ptpre) >= *mjpt )
|
|
if( (g = *prept + ogcp1va * *gf2ptpre) > *mjpt ) // 2018/Apr
|
|
{
|
|
*mjpt = g;
|
|
*mpjpt = i-1;
|
|
}
|
|
#if USE_PENALTY_EX
|
|
m[j] += fpenalty_ex;
|
|
#endif
|
|
if( trywarp )
|
|
{
|
|
#if USE_PENALTY_EX
|
|
if( ( g=*prevwmrecordspt++ + fpenalty_shift + fpenalty_ex * ( i - prevwarpi[j-1] + j - prevwarpj[j-1] ) ) > wm ) // naka ha osokute kamawanai
|
|
#else
|
|
if( ( g=*prevwmrecordspt++ + fpenalty_shift ) > wm ) // naka ha osokute kamawanai
|
|
#endif
|
|
{
|
|
// fprintf( stderr, "WARP in partA__align\n" );
|
|
if( warpn && prevwarpi[j-1] == warpis[warpn-1] && prevwarpj[j-1] == warpjs[warpn-1] )
|
|
{
|
|
*ijppt = warpbase + warpn - 1;
|
|
}
|
|
else
|
|
{
|
|
*ijppt = warpbase + warpn;
|
|
warpis = realloc( warpis, sizeof(int) * ( warpn+1 ) );
|
|
warpjs = realloc( warpjs, sizeof(int) * ( warpn+1 ) );
|
|
warpis[warpn] = prevwarpi[j-1];
|
|
warpjs[warpn] = prevwarpj[j-1];
|
|
warpn++;
|
|
}
|
|
wm = g;
|
|
}
|
|
curm = *curpt + wm;
|
|
if( *wmrecords1pt > *wmrecordspt )
|
|
{
|
|
*wmrecordspt = *wmrecords1pt;
|
|
*warpipt = *(warpipt-1);
|
|
*warpjpt = *(warpjpt-1);
|
|
}
|
|
if( curm > *wmrecordspt )
|
|
{
|
|
*wmrecordspt = curm;
|
|
*warpipt = i;
|
|
*warpjpt = j;
|
|
}
|
|
wmrecordspt++;
|
|
wmrecords1pt++;
|
|
warpipt++;
|
|
warpjpt++;
|
|
}
|
|
|
|
#if 0
|
|
fprintf( stderr, "%5.0f ", wm );
|
|
#endif
|
|
*curpt += wm;
|
|
ijppt++;
|
|
mjpt++;
|
|
prept++;
|
|
mpjpt++;
|
|
curpt++;
|
|
fgcp2pt++;
|
|
ogcp2pt++;
|
|
gf2ptpre++;
|
|
gf2pt++;
|
|
|
|
}
|
|
lastverticalw[i] = currentw[lgth2-1];
|
|
|
|
if( trywarp )
|
|
{
|
|
fltncpy( prevwmrecords, wmrecords, lastj );
|
|
intncpy( prevwarpi, warpi, lastj );
|
|
intncpy( prevwarpj, warpj, lastj );
|
|
}
|
|
}
|
|
if( trywarp )
|
|
{
|
|
// fprintf( stderr, "wm = %f\n", wm );
|
|
// fprintf( stderr, "warpn = %d\n", warpn );
|
|
free( wmrecords );
|
|
free( prevwmrecords );
|
|
free( warpi );
|
|
free( warpj );
|
|
free( prevwarpi );
|
|
free( prevwarpj );
|
|
}
|
|
|
|
#if OUTGAP0TRY
|
|
if( !outgap )
|
|
{
|
|
for( j=1; j<lgth2+1; j++ )
|
|
currentw[j] -= offset * ( lgth2 - j ) / 2.0;
|
|
for( i=1; i<lgth1+1; i++ )
|
|
lastverticalw[i] -= offset * ( lgth1 - i / 2.0);
|
|
}
|
|
#endif
|
|
|
|
/*
|
|
fprintf( stderr, "\n" );
|
|
for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
|
|
fprintf( stderr, "#####\n" );
|
|
for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
|
|
fprintf( stderr, "====>" );
|
|
for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
|
|
for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
|
|
*/
|
|
if( constraint )
|
|
{
|
|
Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, start1, end1, start2, end2, gapmap1, gapmap2, warpis, warpjs, warpbase );
|
|
}
|
|
else
|
|
Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, warpis, warpjs, warpbase );
|
|
|
|
if( warpis ) free( warpis );
|
|
if( warpjs ) free( warpjs );
|
|
|
|
// fprintf( stderr, "### impmatch = %f\n", *impmatch );
|
|
|
|
resultlen = strlen( mseq1[0] );
|
|
if( alloclen < resultlen || resultlen > N )
|
|
{
|
|
fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
|
|
ErrorExit( "LENGTH OVER!\n" );
|
|
}
|
|
|
|
|
|
for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
|
|
for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
|
|
/*
|
|
fprintf( stderr, "\n" );
|
|
for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
|
|
fprintf( stderr, "#####\n" );
|
|
for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
|
|
*/
|
|
|
|
|
|
return( wm );
|
|
}
|
|
|
|
double partA__align_variousdist( int **which, double ***matrices, double **n_dynamicmtx, char **seq1, char **seq2, double *eff1, double *eff2, double **eff1s, double **eff2s, int icyc, int jcyc, int alloclen, int constraint, double *impmatch, int start1, int end1, int start2, int end2, int *gapmap1, int *gapmap2, char *sgap1, char *sgap2, char *egap1, char *egap2, int *chudanpt, int chudanref, int *chudanres )
|
|
/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
|
|
{
|
|
// int k;
|
|
register int i, j, c;
|
|
int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
|
|
int lgth1, lgth2;
|
|
int resultlen;
|
|
double wm = 0.0; /* int ?????? */
|
|
double g;
|
|
double *currentw, *previousw;
|
|
#if 1
|
|
double *wtmp;
|
|
int *ijppt;
|
|
double *mjpt, *prept, *curpt;
|
|
int *mpjpt;
|
|
#endif
|
|
static TLS double mi, *m;
|
|
static TLS int **ijp;
|
|
static TLS int mpi, *mp;
|
|
static TLS double *w1, *w2;
|
|
static TLS double *match;
|
|
static TLS double *initverticalw; /* kufuu sureba iranai */
|
|
static TLS double *lastverticalw; /* kufuu sureba iranai */
|
|
static TLS char **mseq1;
|
|
static TLS char **mseq2;
|
|
static TLS char **mseq;
|
|
static TLS double *ogcp1;
|
|
static TLS double *ogcp2;
|
|
static TLS double *fgcp1;
|
|
static TLS double *fgcp2;
|
|
static TLS double ***cpmx1s;
|
|
static TLS double ***cpmx2s;
|
|
static TLS double *gapfreq1;
|
|
static TLS double *gapfreq2;
|
|
static TLS int ***intwork;
|
|
static TLS double ***doublework;
|
|
static TLS int orlgth1 = 0, orlgth2 = 0;
|
|
double fpenalty = (double)penalty;
|
|
double fpenalty_shift = (double)penalty_shift;
|
|
#if USE_PENALTY_EX
|
|
double fpenalty_ex = (double)penalty_ex;
|
|
#endif
|
|
double *fgcp2pt;
|
|
double *ogcp2pt;
|
|
double fgcp1va;
|
|
double ogcp1va;
|
|
double *gf2pt;
|
|
double *gf2ptpre;
|
|
double gf1va;
|
|
double gf1vapre;
|
|
double headgapfreq1;
|
|
double headgapfreq2;
|
|
|
|
int *warpis = NULL;
|
|
int *warpjs = NULL;
|
|
int *warpi = NULL;
|
|
int *warpj = NULL;
|
|
int *prevwarpi = NULL;
|
|
int *prevwarpj = NULL;
|
|
double *wmrecords = NULL;
|
|
double *prevwmrecords = NULL;
|
|
int warpn = 0;
|
|
int warpbase;
|
|
double curm = 0.0;
|
|
double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
|
|
int *warpipt, *warpjpt;
|
|
int *nmask, **masklist1, **masklist2;
|
|
|
|
|
|
if( seq1 == NULL )
|
|
{
|
|
if( orlgth1 )
|
|
{
|
|
// fprintf( stderr, "## Freeing local arrays in A__align\n" );
|
|
orlgth1 = 0;
|
|
orlgth2 = 0;
|
|
|
|
part_imp_match_init_strict( NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL );
|
|
|
|
free( mseq1 );
|
|
free( mseq2 );
|
|
FreeFloatVec( w1 );
|
|
FreeFloatVec( w2 );
|
|
FreeFloatVec( match );
|
|
FreeFloatVec( initverticalw );
|
|
FreeFloatVec( lastverticalw );
|
|
|
|
FreeFloatVec( m );
|
|
FreeIntVec( mp );
|
|
|
|
FreeCharMtx( mseq );
|
|
|
|
FreeFloatVec( ogcp1 );
|
|
FreeFloatVec( ogcp2 );
|
|
FreeFloatVec( fgcp1 );
|
|
FreeFloatVec( fgcp2 );
|
|
|
|
|
|
FreeFloatCub( cpmx1s );
|
|
FreeFloatCub( cpmx2s );
|
|
|
|
FreeFloatVec( gapfreq1 );
|
|
FreeFloatVec( gapfreq2 );
|
|
|
|
FreeFloatCub( doublework );
|
|
FreeIntCub( intwork );
|
|
|
|
}
|
|
else
|
|
{
|
|
// fprintf( stderr, "## Not allocated\n" );
|
|
}
|
|
return( 0.0 );
|
|
}
|
|
|
|
masklist1 = AllocateIntMtx( maxdistclass, 0 );
|
|
masklist2 = AllocateIntMtx( maxdistclass, 0 );
|
|
nmask = calloc( maxdistclass, sizeof( int ) );
|
|
|
|
for( c=0; c<maxdistclass; c++ )
|
|
{
|
|
for( i=0; i<icyc; i++ ) for( j=0; j<jcyc; j++ )
|
|
{
|
|
if( eff1s[c][i] * eff2s[c][j] != 0.0 )
|
|
{
|
|
|
|
if( c != which[i][j] )
|
|
{
|
|
masklist1[c] = realloc( masklist1[c], sizeof( int ) * (nmask[c]+1) );
|
|
masklist2[c] = realloc( masklist2[c], sizeof( int ) * (nmask[c]+1) );
|
|
masklist1[c][nmask[c]] = i;
|
|
masklist2[c][nmask[c]] = j;
|
|
nmask[c]++;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
for( c=0; c<maxdistclass; c++ ) if( nmask[c] ) break;
|
|
if( c<maxdistclass ) reporterr( "Found a complex grouping. This step may be a bit slow.\n" );
|
|
|
|
lgth1 = strlen( seq1[0] );
|
|
lgth2 = strlen( seq2[0] );
|
|
#if 1
|
|
// if( lgth1 == 0 ) fprintf( stderr, "WARNING: lgth1=0 in partA__align\n" );
|
|
// if( lgth2 == 0 ) fprintf( stderr, "WARNING: lgth2=0 in partA__align\n" );
|
|
|
|
if( lgth1 == 0 && lgth2 == 0 )
|
|
return( 0.0 );
|
|
|
|
if( lgth1 == 0 )
|
|
{
|
|
for( i=0; i<icyc; i++ )
|
|
{
|
|
j = lgth2;
|
|
seq1[i][j] = 0;
|
|
while( j ) seq1[i][--j] = *newgapstr;
|
|
// fprintf( stderr, "seq1[i] = %s\n", seq1[i] );
|
|
}
|
|
return( 0.0 );
|
|
}
|
|
|
|
if( lgth2 == 0 )
|
|
{
|
|
for( i=0; i<jcyc; i++ )
|
|
{
|
|
j = lgth1;
|
|
seq2[i][j] = 0;
|
|
while( j ) seq2[i][--j] = *newgapstr;
|
|
// fprintf( stderr, "seq2[i] = %s\n", seq2[i] );
|
|
}
|
|
return( 0.0 );
|
|
}
|
|
#endif
|
|
|
|
warpbase = lgth1 + lgth2;
|
|
warpis = NULL;
|
|
warpjs = NULL;
|
|
warpn = 0;
|
|
|
|
|
|
if( trywarp )
|
|
{
|
|
// fprintf( stderr, "IN partA__align_variousdist\n" );
|
|
if( outgap == 0 )
|
|
{
|
|
fprintf( stderr, "At present, outgap must be 1 to allow shift.\n" );
|
|
exit( 1 );
|
|
}
|
|
wmrecords = AllocateFloatVec( lgth2+1 );
|
|
warpi = AllocateIntVec( lgth2+1 );
|
|
warpj = AllocateIntVec( lgth2+1 );
|
|
prevwmrecords = AllocateFloatVec( lgth2+1 );
|
|
prevwarpi = AllocateIntVec( lgth2+1 );
|
|
prevwarpj = AllocateIntVec( lgth2+1 );
|
|
for( i=0; i<lgth2+1; i++ ) wmrecords[i] = 0.0;
|
|
for( i=0; i<lgth2+1; i++ ) prevwmrecords[i] = 0.0;
|
|
for( i=0; i<lgth2+1; i++ ) prevwarpi[i] = -warpbase;
|
|
for( i=0; i<lgth2+1; i++ ) prevwarpj[i] = -warpbase;
|
|
for( i=0; i<lgth2+1; i++ ) warpi[i] = -warpbase;
|
|
for( i=0; i<lgth2+1; i++ ) warpj[i] = -warpbase;
|
|
}
|
|
|
|
#if 0
|
|
fprintf( stderr, "eff in SA+++align\n" );
|
|
for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
|
|
#endif
|
|
if( orlgth1 == 0 )
|
|
{
|
|
mseq1 = AllocateCharMtx( njob, 0 );
|
|
mseq2 = AllocateCharMtx( njob, 0 );
|
|
}
|
|
|
|
|
|
|
|
|
|
if( lgth1 > orlgth1 || lgth2 > orlgth2 )
|
|
{
|
|
int ll1, ll2;
|
|
|
|
if( orlgth1 > 0 && orlgth2 > 0 )
|
|
{
|
|
FreeFloatVec( w1 );
|
|
FreeFloatVec( w2 );
|
|
FreeFloatVec( match );
|
|
FreeFloatVec( initverticalw );
|
|
FreeFloatVec( lastverticalw );
|
|
|
|
FreeFloatVec( m );
|
|
FreeIntVec( mp );
|
|
|
|
FreeCharMtx( mseq );
|
|
|
|
FreeFloatVec( ogcp1 );
|
|
FreeFloatVec( ogcp2 );
|
|
FreeFloatVec( fgcp1 );
|
|
FreeFloatVec( fgcp2 );
|
|
|
|
|
|
FreeFloatCub( cpmx1s );
|
|
FreeFloatCub( cpmx2s );
|
|
|
|
FreeFloatVec( gapfreq1 );
|
|
FreeFloatVec( gapfreq2 );
|
|
|
|
FreeFloatCub( doublework );
|
|
FreeIntCub( intwork );
|
|
}
|
|
|
|
ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
|
|
ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
|
|
|
|
#if DEBUG
|
|
fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
|
|
#endif
|
|
|
|
w1 = AllocateFloatVec( ll2+2 );
|
|
w2 = AllocateFloatVec( ll2+2 );
|
|
match = AllocateFloatVec( ll2+2 );
|
|
|
|
initverticalw = AllocateFloatVec( ll1+2 );
|
|
lastverticalw = AllocateFloatVec( ll1+2 );
|
|
|
|
m = AllocateFloatVec( ll2+2 );
|
|
mp = AllocateIntVec( ll2+2 );
|
|
|
|
mseq = AllocateCharMtx( njob, ll1+ll2 );
|
|
|
|
ogcp1 = AllocateFloatVec( ll1+2 );
|
|
ogcp2 = AllocateFloatVec( ll2+2 );
|
|
fgcp1 = AllocateFloatVec( ll1+2 );
|
|
fgcp2 = AllocateFloatVec( ll2+2 );
|
|
|
|
cpmx1s = AllocateFloatCub( maxdistclass, nalphabets, ll1+2 );
|
|
cpmx2s = AllocateFloatCub( maxdistclass, nalphabets, ll2+2 );
|
|
|
|
gapfreq1 = AllocateFloatVec( ll1+2 );
|
|
gapfreq2 = AllocateFloatVec( ll2+2 );
|
|
|
|
doublework = AllocateFloatCub( maxdistclass, MAX( ll1, ll2 )+2, nalphabets );
|
|
intwork = AllocateIntCub( maxdistclass, MAX( ll1, ll2 )+2, nalphabets );
|
|
|
|
#if DEBUG
|
|
fprintf( stderr, "succeeded\n" );
|
|
#endif
|
|
|
|
orlgth1 = ll1 - 100;
|
|
orlgth2 = ll2 - 100;
|
|
}
|
|
|
|
|
|
for( i=0; i<icyc; i++ ) mseq1[i] = mseq[i];
|
|
for( j=0; j<jcyc; j++ ) mseq2[j] = mseq[icyc+j];
|
|
|
|
|
|
if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
|
|
{
|
|
int ll1, ll2;
|
|
|
|
if( commonAlloc1 && commonAlloc2 )
|
|
{
|
|
FreeIntMtx( commonIP );
|
|
}
|
|
|
|
ll1 = MAX( orlgth1, commonAlloc1 );
|
|
ll2 = MAX( orlgth2, commonAlloc2 );
|
|
|
|
#if DEBUG
|
|
fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
|
|
#endif
|
|
|
|
commonIP = AllocateIntMtx( ll1+10, ll2+10 );
|
|
|
|
#if DEBUG
|
|
fprintf( stderr, "succeeded\n\n" );
|
|
#endif
|
|
|
|
commonAlloc1 = ll1;
|
|
commonAlloc2 = ll2;
|
|
}
|
|
ijp = commonIP;
|
|
|
|
// cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
|
|
// cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
|
|
for( c=0; c<maxdistclass; c++ )
|
|
{
|
|
cpmx_calc_new( seq1, cpmx1s[c], eff1s[c], lgth1, icyc );
|
|
cpmx_calc_new( seq2, cpmx2s[c], eff2s[c], lgth2, jcyc );
|
|
}
|
|
|
|
if( sgap1 )
|
|
{
|
|
new_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1, sgap1 );
|
|
new_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2, sgap2 );
|
|
new_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1, egap1 );
|
|
new_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2, egap2 );
|
|
outgapcount( &headgapfreq1, icyc, sgap1, eff1 );
|
|
outgapcount( &headgapfreq2, jcyc, sgap2, eff2 );
|
|
outgapcount( gapfreq1+lgth1, icyc, egap1, eff1 );
|
|
outgapcount( gapfreq2+lgth2, jcyc, egap2, eff2 );
|
|
}
|
|
else
|
|
{
|
|
st_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
|
|
st_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
|
|
st_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
|
|
st_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
|
|
headgapfreq1 = 0.0;
|
|
headgapfreq2 = 0.0;
|
|
gapfreq1[lgth1] = 0.0;
|
|
gapfreq2[lgth2] = 0.0;
|
|
}
|
|
|
|
if( legacygapcost == 0 )
|
|
{
|
|
gapcountf( gapfreq1, seq1, icyc, eff1, lgth1 );
|
|
gapcountf( gapfreq2, seq2, jcyc, eff2, lgth2 );
|
|
for( i=0; i<lgth1+1; i++ ) gapfreq1[i] = 1.0 - gapfreq1[i];
|
|
for( i=0; i<lgth2+1; i++ ) gapfreq2[i] = 1.0 - gapfreq2[i];
|
|
headgapfreq1 = 1.0 - headgapfreq1;
|
|
headgapfreq2 = 1.0 - headgapfreq2;
|
|
}
|
|
else
|
|
{
|
|
for( i=0; i<lgth1+1; i++ ) gapfreq1[i] = 1.0;
|
|
for( i=0; i<lgth2+1; i++ ) gapfreq2[i] = 1.0;
|
|
headgapfreq1 = 1.0;
|
|
headgapfreq2 = 1.0;
|
|
}
|
|
|
|
for( i=0; i<lgth1; i++ )
|
|
{
|
|
ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty * ( gapfreq1[i] );
|
|
fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty * ( gapfreq1[i] );
|
|
}
|
|
for( i=0; i<lgth2; i++ )
|
|
{
|
|
ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty * ( gapfreq2[i] );
|
|
fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty * ( gapfreq2[i] );
|
|
}
|
|
#if 0
|
|
for( i=0; i<lgth1; i++ )
|
|
fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
|
|
#endif
|
|
|
|
currentw = w1;
|
|
previousw = w2;
|
|
|
|
|
|
// match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, doublework, intwork, 1 );
|
|
fillzero( initverticalw, lgth1 );
|
|
for( c=0; c<maxdistclass; c++ )
|
|
{
|
|
match_calc_add( matrices[c], initverticalw, cpmx2s[c], cpmx1s[c], 0, lgth1, doublework[c], intwork[c], 1 );
|
|
if( nmask[c] ) match_calc_del( which, matrices, initverticalw, jcyc, seq2, eff2, icyc, seq1, eff1, 0, lgth1, c, nmask[c], masklist2[c], masklist1[c] );
|
|
}
|
|
|
|
if( constraint )
|
|
part_imp_match_out_vead_tate_gapmap( initverticalw, gapmap2[0]+start2, lgth1, start1, gapmap1 );
|
|
|
|
|
|
// match_calc( currentw, cpmx1, cpmx2, 0, lgth2, doublework, intwork, 1 );
|
|
fillzero( currentw, lgth2 );
|
|
for( c=0; c<maxdistclass; c++ )
|
|
{
|
|
match_calc_add( matrices[c], currentw, cpmx1s[c], cpmx2s[c], 0, lgth2, doublework[c], intwork[c], 1 );
|
|
if( nmask[c] ) match_calc_del( which, matrices, currentw, icyc, seq1, eff1, jcyc, seq2, eff2, 0, lgth2, c, nmask[c], masklist1[c], masklist2[c] );
|
|
}
|
|
if( constraint )
|
|
part_imp_match_out_vead_gapmap( currentw, gapmap1[0]+start1, lgth2, start2, gapmap2 );
|
|
#if 0 // -> tbfast.c, localhom ga hitsuyou
|
|
if( localhom )
|
|
imp_match_calc( currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
|
|
|
|
#endif
|
|
|
|
if( outgap == 1 )
|
|
{
|
|
for( i=1; i<lgth1+1; i++ )
|
|
{
|
|
// initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
|
|
initverticalw[i] += ( ogcp1[0] * headgapfreq2 + fgcp1[i-1] * gapfreq2[0] ) ;
|
|
#if USE_PENALTY_EX
|
|
tsuika hitsuyou
|
|
#endif
|
|
}
|
|
for( j=1; j<lgth2+1; j++ )
|
|
{
|
|
// currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
|
|
currentw[j] += ( ogcp2[0] * headgapfreq1 + fgcp2[j-1] * gapfreq1[0] ) ;
|
|
#if USE_PENALTY_EX
|
|
tsuika hitsuyou
|
|
#endif
|
|
}
|
|
}
|
|
#if OUTGAP0TRY
|
|
else
|
|
{
|
|
for( j=1; j<lgth2+1; j++ )
|
|
currentw[j] -= offset * j / 2.0;
|
|
for( i=1; i<lgth1+1; i++ )
|
|
initverticalw[i] -= offset * i / 2.0;
|
|
}
|
|
#endif
|
|
|
|
for( j=1; j<lgth2+1; ++j )
|
|
{
|
|
// m[j] = currentw[j-1] + ogcp1[1]; mp[j] = 0;
|
|
m[j] = currentw[j-1] + ogcp1[1] * gapfreq2[j-1]; mp[j] = 0;;
|
|
}
|
|
|
|
lastverticalw[0] = currentw[lgth2-1];
|
|
|
|
if( outgap ) lasti = lgth1+1; else lasti = lgth1;
|
|
lastj = lgth2+1;
|
|
|
|
#if XXXXXXX
|
|
fprintf( stderr, "currentw = \n" );
|
|
for( i=0; i<lgth1+1; i++ )
|
|
{
|
|
fprintf( stderr, "%5.2f ", currentw[i] );
|
|
}
|
|
fprintf( stderr, "\n" );
|
|
fprintf( stderr, "initverticalw = \n" );
|
|
for( i=0; i<lgth2+1; i++ )
|
|
{
|
|
fprintf( stderr, "%5.2f ", initverticalw[i] );
|
|
}
|
|
fprintf( stderr, "\n" );
|
|
fprintf( stderr, "fcgp\n" );
|
|
for( i=0; i<lgth1; i++ )
|
|
fprintf( stderr, "fgcp1[%d]=%f\n", i, ogcp1[i] );
|
|
for( i=0; i<lgth2; i++ )
|
|
fprintf( stderr, "fgcp2[%d]=%f\n", i, ogcp2[i] );
|
|
#endif
|
|
|
|
for( i=1; i<lasti; i++ )
|
|
{
|
|
|
|
#ifdef enablemultithread
|
|
// fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
|
|
if( chudanpt && *chudanpt != chudanref )
|
|
{
|
|
// fprintf( stderr, "\n\n## CHUUDAN!!! i\n" );
|
|
*chudanres = 1;
|
|
if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL;
|
|
if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL;
|
|
if( nmask ) free( nmask ); nmask = NULL;
|
|
return( -1.0 );
|
|
}
|
|
#endif
|
|
|
|
wtmp = previousw;
|
|
previousw = currentw;
|
|
currentw = wtmp;
|
|
|
|
previousw[0] = initverticalw[i-1];
|
|
|
|
// match_calc( currentw, cpmx1, cpmx2, i, lgth2, doublework, intwork, 0 );
|
|
fillzero( currentw, lgth2 );
|
|
for( c=0; c<maxdistclass; c++ )
|
|
{
|
|
match_calc_add( matrices[c], currentw, cpmx1s[c], cpmx2s[c], i, lgth2, doublework[c], intwork[c], 0 );
|
|
if( nmask[c] ) match_calc_del( which, matrices, currentw, icyc, seq1, eff1, jcyc, seq2, eff2, i, lgth2, c, nmask[c], masklist1[c], masklist2[c] );
|
|
}
|
|
#if 0
|
|
fprintf( stderr, "\n" );
|
|
fprintf( stderr, "i=%d\n", i );
|
|
fprintf( stderr, "currentw before imp = \n" );
|
|
for( j=0; j<lgth2; j++ )
|
|
{
|
|
fprintf( stderr, "%5.2f ", currentw[j] );
|
|
}
|
|
fprintf( stderr, "\n" );
|
|
#endif
|
|
if( constraint )
|
|
{
|
|
// fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
|
|
// imp_match_out_vead( currentw, i, lgth2 );
|
|
part_imp_match_out_vead_gapmap( currentw, gapmap1[i]+start1, lgth2, start2, gapmap2 );
|
|
}
|
|
#if 0
|
|
fprintf( stderr, "specificity = %f\n", specificityconsideration );
|
|
fprintf( stderr, "i=%d\n", i );
|
|
fprintf( stderr, "currentw = \n" );
|
|
for( j=0; j<lgth2; j++ )
|
|
{
|
|
fprintf( stderr, "%5.2f ", currentw[j] );
|
|
}
|
|
fprintf( stderr, "\n" );
|
|
#endif
|
|
currentw[0] = initverticalw[i];
|
|
|
|
|
|
// mi = previousw[0] + ogcp2[1]; mpi = 0;
|
|
mi = previousw[0] + ogcp2[1] * gapfreq1[i-1]; mpi=0;
|
|
|
|
ijppt = ijp[i] + 1;
|
|
mjpt = m + 1;
|
|
prept = previousw;
|
|
curpt = currentw + 1;
|
|
mpjpt = mp + 1;
|
|
fgcp2pt = fgcp2;
|
|
ogcp2pt = ogcp2+1;
|
|
fgcp1va = fgcp1[i-1];
|
|
ogcp1va = ogcp1[i];
|
|
gf1va = gapfreq1[i];
|
|
gf1vapre = gapfreq1[i-1];
|
|
gf2pt = gapfreq2+1;
|
|
gf2ptpre = gapfreq2;
|
|
|
|
if( trywarp )
|
|
{
|
|
prevwmrecordspt = prevwmrecords;
|
|
wmrecordspt = wmrecords+1;
|
|
wmrecords1pt = wmrecords;
|
|
warpipt = warpi + 1;
|
|
warpjpt = warpj + 1;
|
|
}
|
|
|
|
for( j=1; j<lastj; j++ )
|
|
{
|
|
#ifdef xxxenablemultithread
|
|
// fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
|
|
if( chudanpt && *chudanpt != chudanref )
|
|
{
|
|
// fprintf( stderr, "\n\n## CHUUDAN!!! j\n" );
|
|
*chudanres = 1;
|
|
if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL;
|
|
if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL;
|
|
if( nmask ) free( nmask ); nmask = NULL;
|
|
return( -1.0 );
|
|
}
|
|
#endif
|
|
wm = *prept;
|
|
*ijppt = 0;
|
|
|
|
#if 0
|
|
fprintf( stderr, "%5.0f->", wm );
|
|
#endif
|
|
// g = mi + *fgcp2pt * gapfreq1[i];
|
|
if( (g = mi + *fgcp2pt * gf1va) > wm )
|
|
{
|
|
wm = g;
|
|
*ijppt = -( j - mpi );
|
|
}
|
|
// g = *prept + *ogcp2pt * gapfreq1[i-1];
|
|
// if( (g = *prept + *ogcp2pt * gf1vapre) >= mi )
|
|
if( (g = *prept + *ogcp2pt * gf1vapre) > mi ) // 2018/Apr
|
|
{
|
|
mi = g;
|
|
mpi = j-1;
|
|
}
|
|
#if USE_PENALTY_EX
|
|
mi += fpenalty_ex;
|
|
#endif
|
|
|
|
// g = *mjpt + fgcp1va * gapfreq2[j];
|
|
if( (g = *mjpt + fgcp1va * *gf2pt) > wm )
|
|
{
|
|
wm = g;
|
|
*ijppt = +( i - *mpjpt );
|
|
}
|
|
// g = *prept + ogcp1va * gapfreq2[j-1];
|
|
// if( (g = *prept + ogcp1va * *gf2ptpre) >= *mjpt )
|
|
if( (g = *prept + ogcp1va * *gf2ptpre) > *mjpt ) // 2018/Apr
|
|
{
|
|
*mjpt = g;
|
|
*mpjpt = i-1;
|
|
}
|
|
#if USE_PENALTY_EX
|
|
m[j] += fpenalty_ex;
|
|
#endif
|
|
if( trywarp )
|
|
{
|
|
#if USE_PENALTY_EX
|
|
if( ( g=*prevwmrecordspt++ + fpenalty_shift + fpenalty_ex * ( i - prevwarpi[j-1] + j - prevwarpj[j-1] ) ) > wm ) // naka ha osokute kamawanai
|
|
#else
|
|
if( ( g=*prevwmrecordspt++ + fpenalty_shift ) > wm ) // naka ha osokute kamawanai
|
|
#endif
|
|
{
|
|
if( warpn && prevwarpi[j-1] == warpis[warpn-1] && prevwarpj[j-1] == warpjs[warpn-1] )
|
|
{
|
|
*ijppt = warpbase + warpn - 1;
|
|
}
|
|
else
|
|
{
|
|
*ijppt = warpbase + warpn;
|
|
warpis = realloc( warpis, sizeof(int) * ( warpn+1 ) );
|
|
warpjs = realloc( warpjs, sizeof(int) * ( warpn+1 ) );
|
|
warpis[warpn] = prevwarpi[j-1];
|
|
warpjs[warpn] = prevwarpj[j-1];
|
|
warpn++;
|
|
}
|
|
wm = g;
|
|
}
|
|
|
|
curm = *curpt + wm;
|
|
if( *wmrecords1pt > *wmrecordspt )
|
|
{
|
|
*wmrecordspt = *wmrecords1pt;
|
|
*warpipt = *(warpipt-1);
|
|
*warpjpt = *(warpjpt-1);
|
|
}
|
|
if( curm > *wmrecordspt )
|
|
{
|
|
*wmrecordspt = curm;
|
|
*warpipt = i;
|
|
*warpjpt = j;
|
|
}
|
|
wmrecordspt++;
|
|
wmrecords1pt++;
|
|
warpipt++;
|
|
warpjpt++;
|
|
}
|
|
|
|
#if 0
|
|
fprintf( stderr, "%5.0f ", wm );
|
|
#endif
|
|
*curpt += wm;
|
|
ijppt++;
|
|
mjpt++;
|
|
prept++;
|
|
mpjpt++;
|
|
curpt++;
|
|
fgcp2pt++;
|
|
ogcp2pt++;
|
|
gf2ptpre++;
|
|
gf2pt++;
|
|
|
|
}
|
|
lastverticalw[i] = currentw[lgth2-1];
|
|
|
|
if( trywarp )
|
|
{
|
|
fltncpy( prevwmrecords, wmrecords, lastj );
|
|
intncpy( prevwarpi, warpi, lastj );
|
|
intncpy( prevwarpj, warpj, lastj );
|
|
}
|
|
}
|
|
if( trywarp )
|
|
{
|
|
// fprintf( stderr, "wm = %f\n", wm );
|
|
// fprintf( stderr, "warpn = %d\n", warpn );
|
|
free( wmrecords );
|
|
free( prevwmrecords );
|
|
free( warpi );
|
|
free( warpj );
|
|
free( prevwarpi );
|
|
free( prevwarpj );
|
|
}
|
|
|
|
#if OUTGAP0TRY
|
|
if( !outgap )
|
|
{
|
|
for( j=1; j<lgth2+1; j++ )
|
|
currentw[j] -= offset * ( lgth2 - j ) / 2.0;
|
|
for( i=1; i<lgth1+1; i++ )
|
|
lastverticalw[i] -= offset * ( lgth1 - i / 2.0);
|
|
}
|
|
#endif
|
|
|
|
/*
|
|
fprintf( stderr, "\n" );
|
|
for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
|
|
fprintf( stderr, "#####\n" );
|
|
for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
|
|
fprintf( stderr, "====>" );
|
|
for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
|
|
for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
|
|
*/
|
|
if( constraint )
|
|
{
|
|
Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, start1, end1, start2, end2, gapmap1, gapmap2, warpis, warpjs, warpbase );
|
|
}
|
|
else
|
|
Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, warpis, warpjs, warpbase );
|
|
|
|
if( warpis ) free( warpis );
|
|
if( warpjs ) free( warpjs );
|
|
|
|
// fprintf( stderr, "### impmatch = %f\n", *impmatch );
|
|
|
|
resultlen = strlen( mseq1[0] );
|
|
if( alloclen < resultlen || resultlen > N )
|
|
{
|
|
fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
|
|
ErrorExit( "LENGTH OVER!\n" );
|
|
}
|
|
|
|
|
|
for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
|
|
for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
|
|
/*
|
|
fprintf( stderr, "\n" );
|
|
for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
|
|
fprintf( stderr, "#####\n" );
|
|
for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
|
|
*/
|
|
|
|
if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL;
|
|
if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL;
|
|
if( nmask ) free( nmask ); nmask = NULL;
|
|
|
|
return( wm );
|
|
}
|