| /dports/biology/mafft/mafft-7.267-without-extensions/core/ |
| H A D | SAalignmm.c | 6 static void match_calc( double *match, double **cpmx1, double **cpmx2, int i1, int lgth2, double **… in match_calc() argument
38 scarr[l] += n_dis[k][l] * cpmx1[k][i1]; in match_calc()
52 double **cpmx1, double **cpmx2, in Atracking() argument
180 static TLS double **cpmx1; in Aalign() local
216 FreeFloatMtx( cpmx1 ); in Aalign()
240 cpmx1 = AllocateFloatMtx( nalphabets, ll1+2 ); in Aalign()
279 cpmx_calc( seq1, cpmx1, eff1, strlen( seq1[0] ), icyc ); in Aalign()
282 match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, doublework, intwork, 1 ); in Aalign()
283 match_calc( currentw, cpmx1, cpmx2, 0, lgth2, doublework, intwork, 1 ); in Aalign()
312 match_calc( currentw, cpmx1, cpmx2, i, lgth2, doublework, intwork, 0 ); in Aalign()
[all …]
|
| H A D | Lalignmm.c | 53 scarr[l] += ribosumdis[k][l] * cpmx1[i1][k]; in match_ribosum()
131 scarr[l] += (n_dis[k][l]-RNAthr) * cpmx1[i1][k]; in match_calc()
210 scarr[l] += n_dis[k][l] * cpmx1[i1][k];
2175 double **cpmx1; in Lalignmm_hmout() local
2210 cpmx1 = AllocateFloatMtx( ll1+2, nalphabets+1 ); in Lalignmm_hmout()
2232 MScpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc ); in Lalignmm_hmout()
2332 FreeFloatMtx( cpmx1 ); in Lalignmm_hmout()
2377 double **cpmx1; in Lalign2m2m_hmout() local
2407 cpmx1 = AllocateFloatMtx( ll1+2, 39 ); in Lalign2m2m_hmout()
2430 MScpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc ); in Lalign2m2m_hmout()
[all …]
|
| H A D | MSalignmm.c | 53 scarr[l] += scoringmtx[k][l] * cpmx1[i1][k]; in match_calc_add()
132 scarr[l] += n_dynamicmtx[k][l] * cpmx1[i1][k]; in match_calc()
435 match_calc( n_dynamicmtx, currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, doublework, intwork, 1 ); in MSalignmm_tanni()
471 match_calc( n_dynamicmtx, currentw, cpmx1+ist, cpmx2+jst, i, lgth2, doublework, intwork, 0 ); in MSalignmm_tanni()
856 match_calc( n_dynamicmtx, currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, doublework, intwork, 1 ); in MSalignmm_rec()
926 match_calc( n_dynamicmtx, currentw, cpmx1+ist, cpmx2+jst, i, lgth2, doublework, intwork, 0 ); in MSalignmm_rec()
1649 double **cpmx1, in freearrays() argument
1662 FreeFloatMtx( cpmx1 ); in freearrays()
1686 double **cpmx1; in MSalignmm() local
1727 cpmx1 = AllocateFloatMtx( ll1+2, nalphabets+1 ); in MSalignmm()
[all …]
|
| H A D | genalign11.c | 33 double **cpmx1, double **cpmx2, in gentracking() argument
144 static TLS double **cpmx1; in genL__align11() local
185 FreeFloatMtx( cpmx1 ); in genL__align11()
229 FreeFloatMtx( cpmx1 ); in genL__align11()
258 cpmx1 = AllocateFloatMtx( nalphabets, ll1+2 ); in genL__align11()
584 …gentracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijpi, ijpj, off1pt, … in genL__align11()
|
| H A D | MSalign11.c | 50 double **cpmx1, double **cpmx2, in Atracking() argument
318 static double **cpmx1; in MSalign11() local
355 FreeFloatMtx( cpmx1 ); in MSalign11()
384 cpmx1 = AllocateFloatMtx( nalphabets, ll1+2 ); in MSalign11()
643 Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp ); in MSalign11()
|
| H A D | suboptalign11.c | 41 double **cpmx1, double **cpmx2, in gentracking() argument
160 static double **cpmx1; in suboptalign11() local
232 FreeFloatMtx( cpmx1 ); in suboptalign11()
259 cpmx1 = AllocateFloatMtx( nalphabets, ll1+2 ); in suboptalign11()
644 …resf = gentracking( used, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijpi, ijpj, off1pt, off2pt, shur… in suboptalign11()
|
| H A D | partSalignmm.c | 466 scarr[l] += n_dis_consweight_multi[j][l] * cpmx1[j][i1]; in match_calc()
513 scarr[l] += n_dis_consweight_multi[k][l] * cpmx1[k][i1]; in match_calc()
606 scarr[l] += scoreingmtx[j][l] * cpmx1[j][i1]; in match_calc_add()
655 scarr[l] += scoreingmtx[k][l] * cpmx1[k][i1]; in match_calc_add()
988 static TLS double **cpmx1; in partA__align() local
1055 FreeFloatMtx( cpmx1 ); in partA__align()
1173 FreeFloatMtx( cpmx1 ); in partA__align()
1207 cpmx1 = AllocateFloatMtx( nalphabets, ll1+2 ); in partA__align()
1261 cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc ); in partA__align()
1328 match_calc( currentw, cpmx1, cpmx2, 0, lgth2, doublework, intwork, 1 ); in partA__align()
[all …]
|
| H A D | Salignmm.c | 582 scarr[l] += scoreingmtx[j][l] * cpmx1[j][i1]; in match_calc_add()
631 scarr[l] += scoreingmtx[k][l] * cpmx1[k][i1]; in match_calc_add()
680 scarr[l] += n_dynamicmtx[j][l] * cpmx1[j][i1]; in match_calc()
729 scarr[l] += n_dynamicmtx[k][l] * cpmx1[k][i1]; in match_calc()
1050 static TLS double **cpmx1; in A__align() local
1117 FreeFloatMtx( cpmx1 ); in A__align()
1241 FreeFloatMtx( cpmx1 ); in A__align()
1275 cpmx1 = AllocateFloatMtx( nalphabets, ll1+2 ); in A__align()
1346 cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc ); in A__align()
1423 match_calc( n_dynamicmtx, currentw, cpmx1, cpmx2, 0, lgth2, doublework, intwork, 1 ); in A__align()
[all …]
|
| H A D | Dalignmm.c | 473 scarr[l] += scoreingmtx[j][l] * cpmx1[j][i1]; in match_calc_add()
522 scarr[l] += scoreingmtx[k][l] * cpmx1[k][i1]; in match_calc_add()
572 scarr[l] += n_dynamicmtx[j][l] * cpmx1[j][i1]; in match_calc()
621 scarr[l] += n_dynamicmtx[k][l] * cpmx1[k][i1]; in match_calc()
2740 static TLS double **cpmx1; in D__align() local
2821 FreeFloatMtx( cpmx1 ); in D__align()
2959 FreeFloatMtx( cpmx1 ); in D__align()
3006 cpmx1 = AllocateFloatMtx( nalphabets, ll1+2 ); in D__align()
3256 cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc ); in D__align()
3440 match_calc( n_dynamicmtx, currentw, cpmx1, cpmx2, 0, lgth2, doublework, intwork, 1 ); in D__align()
[all …]
|
| H A D | Lalign11.c | 32 static void match_calc_bk( double *match, double **cpmx1, double **cpmx2, int i1, int lgth2, double…
62 scarr[l] += n_dis[k][l] * cpmx1[k][i1];
|