| /dports/biology/mafft/mafft-7.267-without-extensions/core/ |
| H A D | Lalignmm.c | 37 if( cpmx2[j][l] ) in match_ribosum()
39 cpmxpd[j][count] = cpmx2[j][l]; in match_ribosum()
115 if( cpmx2[j][l] ) in match_calc()
117 cpmxpd[j][count] = cpmx2[j][l]; in match_calc()
194 if( cpmx2[j][l] )
196 cpmxpd[j][count] = cpmx2[j][l];
2176 double **cpmx2; in Lalignmm_hmout() local
2333 FreeFloatMtx( cpmx2 ); in Lalignmm_hmout()
2378 double **cpmx2; in Lalign2m2m_hmout() local
2408 cpmx2 = AllocateFloatMtx( ll2+2, 39 ); in Lalign2m2m_hmout()
[all …]
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| H A D | MSalign11.c | 50 double **cpmx1, double **cpmx2, in Atracking() argument
319 static double **cpmx2; in MSalign11() local
356 FreeFloatMtx( cpmx2 ); in MSalign11()
385 cpmx2 = AllocateFloatMtx( nalphabets, ll2+2 ); in MSalign11()
643 Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp ); in MSalign11()
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| H A D | MSalignmm.c | 36 if( cpmx2[j][l] ) in match_calc_add()
38 cpmxpd[j][count] = cpmx2[j][l]; in match_calc_add()
115 if( cpmx2[j][l] ) in match_calc()
117 cpmxpd[j][count] = cpmx2[j][l]; 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()
1650 double **cpmx2, in freearrays() argument
1663 FreeFloatMtx( cpmx2 ); in freearrays()
1687 double **cpmx2; in MSalignmm() local
1728 cpmx2 = AllocateFloatMtx( ll2+2, nalphabets+1 ); in MSalignmm()
[all …]
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| H A D | SAalignmm.c | 23 if( cpmx2[l][j] ) in match_calc()
25 cpmxpd[count][j] = cpmx2[l][j]; in match_calc()
52 double **cpmx1, double **cpmx2, in Atracking() argument
181 static TLS double **cpmx2; in Aalign() local
217 FreeFloatMtx( cpmx2 ); in Aalign()
241 cpmx2 = AllocateFloatMtx( nalphabets, ll2+2 ); in Aalign()
280 cpmx_calc( seq2, cpmx2, eff2, strlen( seq2[0] ), jcyc ); 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 …]
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| H A D | Salignmm.c | 564 if( cpmx2[l][j] ) in match_calc_add()
566 cpmxpd[j][count] = cpmx2[l][j]; in match_calc_add()
615 if( cpmx2[l][j] ) in match_calc_add()
617 cpmxpd[count][j] = cpmx2[l][j]; in match_calc_add()
662 if( cpmx2[l][j] ) in match_calc()
664 cpmxpd[j][count] = cpmx2[l][j]; in match_calc()
713 if( cpmx2[l][j] ) in match_calc()
715 cpmxpd[count][j] = cpmx2[l][j]; in match_calc()
1051 static TLS double **cpmx2; in A__align() local
1118 FreeFloatMtx( cpmx2 ); in A__align()
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| H A D | Dalignmm.c | 455 if( cpmx2[l][j] ) in match_calc_add()
457 cpmxpd[j][count] = cpmx2[l][j]; in match_calc_add()
506 if( cpmx2[l][j] ) in match_calc_add()
508 cpmxpd[count][j] = cpmx2[l][j]; in match_calc_add()
554 if( cpmx2[l][j] ) in match_calc()
556 cpmxpd[j][count] = cpmx2[l][j]; in match_calc()
605 if( cpmx2[l][j] ) in match_calc()
607 cpmxpd[count][j] = cpmx2[l][j]; in match_calc()
2741 static TLS double **cpmx2; in D__align() local
2822 FreeFloatMtx( cpmx2 ); in D__align()
[all …]
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| H A D | Lalign11.c | 32 static void match_calc_bk( double *match, double **cpmx1, double **cpmx2, int i1, int lgth2, double…
47 if( cpmx2[l][j] )
49 cpmxpd[count][j] = cpmx2[l][j];
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| H A D | genalign11.c | 33 double **cpmx1, double **cpmx2, in gentracking() argument
145 static TLS double **cpmx2; in genL__align11() local
186 FreeFloatMtx( cpmx2 ); in genL__align11()
230 FreeFloatMtx( cpmx2 ); in genL__align11()
259 cpmx2 = AllocateFloatMtx( nalphabets, ll2+2 ); in genL__align11()
584 …gentracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijpi, ijpj, off1pt, … in genL__align11()
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| H A D | partSalignmm.c | 450 if( cpmx2[l][j] ) in match_calc()
452 cpmxpd[j][count] = cpmx2[l][j]; in match_calc()
499 if( cpmx2[l][j] ) in match_calc()
501 cpmxpd[count][j] = cpmx2[l][j]; in match_calc()
588 if( cpmx2[l][j] ) in match_calc_add()
590 cpmxpd[j][count] = cpmx2[l][j]; in match_calc_add()
639 if( cpmx2[l][j] ) in match_calc_add()
641 cpmxpd[count][j] = cpmx2[l][j]; in match_calc_add()
989 static TLS double **cpmx2; in partA__align() local
1056 FreeFloatMtx( cpmx2 ); in partA__align()
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| H A D | suboptalign11.c | 41 double **cpmx1, double **cpmx2, in gentracking() argument
161 static double **cpmx2; in suboptalign11() local
233 FreeFloatMtx( cpmx2 ); in suboptalign11()
260 cpmx2 = AllocateFloatMtx( nalphabets, ll2+2 ); in suboptalign11()
644 …resf = gentracking( used, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijpi, ijpj, off1pt, off2pt, shur… in suboptalign11()
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