/dports/biology/mafft/mafft-7.267-without-extensions/core/ |
H A D | Lalignmm.c | 262 lgth1 = ien-ist+1; 296 klim = lgth1+lgth2; 384 int lgth1, lgth2; in MSalign2m2m_rec() local 416 lgth1 = ien-ist+1; in MSalign2m2m_rec() 429 ttt1[lgth1] = 0; in MSalign2m2m_rec() 579 lasti = lgth1+1; in MSalign2m2m_rec() 779 mp[j] = lgth1-1; in MSalign2m2m_rec() 1079 if( k != lgth1 ) 1284 int lgth1, lgth2; in MSalignmm_rec() local 1329 ttt1[lgth1] = 0; in MSalignmm_rec() [all …]
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H A D | MSalign11.c | 57 lgth1 = strlen( seq1[0] ); in Atracking() 62 for( i=0; i<lgth1; i++ ) in Atracking() 78 mseq1[0] += lgth1+lgth2; in Atracking() 80 mseq2[0] += lgth1+lgth2; in Atracking() 82 iin = lgth1; jin = lgth2; in Atracking() 83 limk = lgth1+lgth2 + 1; in Atracking() 152 for( i=0; i<lgth1-1; i++ ) in backdp() 166 for( i=0; i<lgth1; i++ ) in backdp() 290 int lgth1, lgth2; in MSalign11() local 470 lasti = lgth1+1; in MSalign11() [all …]
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H A D | Galign11.c | 44 for( i=0; i<lgth1; i++ ) in Atracking() 71 ijp[lgth1][lgth2] = +( lgth1 - i ); in Atracking() 87 mseq1[0] += lgth1+lgth2; in Atracking() 95 limk = lgth1+lgth2 + 1; in Atracking() 171 int lgth1, lgth2; in G__align11() local 295 if( lgth1 == 0 ) in G__align11() 305 seq2[0][lgth1] = 0; in G__align11() 306 while( lgth1 ) seq2[0][--lgth1] = *newgapstr; in G__align11() 448 if( tailgp ) lasti = lgth1+1; else lasti = lgth1; in G__align11() 693 int lgth1, lgth2; in G__align11_noalign() local [all …]
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H A D | Salignmm.c | 43 while( lgth1-- ) in imp_match_out_vead_tate_gapmap() 774 ijp[lgth1][lgth2] = +( lgth1 - i ); in Atracking_localhom() 915 ijp[lgth1][lgth2] = +( lgth1 - i ); in Atracking() 1021 int lgth1, lgth2; in A__align() local 1146 if( lgth1 == 0 ) in A__align() 1162 j = lgth1; in A__align() 1477 if( tailgp ) lasti = lgth1+1; else lasti = lgth1; in A__align() 1788 int lgth1, lgth2; in A__align_variousdist() local 1941 if( lgth1 == 0 ) in A__align_variousdist() 1957 j = lgth1; in A__align_variousdist() [all …]
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H A D | MSalignmm.c | 185 lgth1 = ien-ist+1; in Atracking() 213 ijp[lgth1][lgth2] = +( lgth1 - i ); in Atracking() 237 ijp[lgth1][lgth2] = +( lgth1 - i ); in Atracking() 351 int lgth1, lgth2; in MSalignmm_tanni() local 382 lgth1 = ien-ist+1; in MSalignmm_tanni() 386 strncpy( ttt1, seq1[0]+ist, lgth1 ); ttt1[lgth1] = 0; in MSalignmm_tanni() 675 int lgth1, lgth2; in MSalignmm_rec() local 738 ttt1[lgth1] = 0; in MSalignmm_rec() 893 lasti = lgth1+1; in MSalignmm_rec() 1124 firstmp = lgth1; in MSalignmm_rec() [all …]
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H A D | partSalignmm.c | 92 while( lgth1-- ) in part_imp_match_out_vead_tate_gapmap() 701 ijp[lgth1][lgth2] = +( lgth1 - i ); in Atracking_localhom() 847 ijp[lgth1][lgth2] = +( lgth1 - i ); in Atracking() 963 int lgth1, lgth2; in partA__align() local 1083 if( lgth1 == 0 ) in partA__align() 1099 j = lgth1; in partA__align() 1368 if( outgap ) lasti = lgth1+1; else lasti = lgth1; in partA__align() 1651 int lgth1, lgth2; in partA__align_variousdist() local 1796 if( lgth1 == 0 ) in partA__align_variousdist() 1812 j = lgth1; in partA__align_variousdist() [all …]
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H A D | SAalignmm.c | 60 lgth1 = strlen( seq1[0] ); in Atracking() 64 for( i=0; i<lgth1; i++ ) in Atracking() 75 for( i=0; i<lgth1; i++ ) in Atracking() 81 ijp[lgth1][lgth2] = +( lgth1 - i ); in Atracking() 89 iin = lgth1-1; jin = j; in Atracking() 106 mseq1[i] += lgth1+lgth2; in Atracking() 111 mseq2[j] += lgth1+lgth2; in Atracking() 114 iin = lgth1; jin = lgth2; in Atracking() 164 int lgth1, lgth2; in Aalign() local 196 lgth1 = strlen( seq1[0] ); in Aalign() [all …]
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H A D | Dalignmm.c | 83 while( lgth1-- ) 666 ijp[lgth1][lgth2] = +( lgth1 - i ); in Atracking_localhom() 807 ijp[lgth1][lgth2] = +( lgth1 - i ); in Atracking() 2715 int lgth1, lgth2; in D__align() local 2870 if( lgth1 == 0 ) in D__align() 2886 j = lgth1; in D__align() 3063 int ll1 = lgth1; in D__align() 3486 if( tailgp ) lasti = lgth1+1; else lasti = lgth1; in D__align() 4740 if( lgth1 == 0 ) in D__align_variousdist() 4756 j = lgth1; in D__align_variousdist() [all …]
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H A D | Lalign11.c | 102 lgth1 = strlen( seq1[0] ); in Ltracking() 106 for( i=0; i<lgth1; i++ ) in Ltracking() 121 mseq1[0] += lgth1+lgth2; in Ltracking() 123 mseq2[0] += lgth1+lgth2; in Ltracking() 126 limk = lgth1+lgth2; in Ltracking() 214 int lgth1, lgth2; in L__align11() local 303 warpbase = lgth1 + lgth2; in L__align11() 415 for( i=0; i<lgth1; i++ ) in L__align11() 438 lasti = lgth1+1; in L__align11() 754 int lgth1, lgth2; in L__align11_noalign() local [all …]
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H A D | rna.c | 340 int lgth1 = strlen( seq1[0] ); local 352 useq1 = AllocateCharMtx( nseq1, lgth1+10 ); 354 oseq1 = AllocateCharMtx( nseq1, lgth1+10 ); 356 oseq1r = AllocateCharMtx( nseq1, lgth1+10 ); 358 odir1 = AllocateCharVec( lgth1+10 ); 365 map = AllocateFloatMtx( lgth1, lgth2 ); 366 impmtx2 = AllocateFloatMtx( lgth1, lgth2 ); 367 tbppmtx = AllocateFloatMtx( lgth1, lgth2 ); 377 for( i=0; i<lgth1; i++ ) 390 utot( nseq1, lgth1, oseq1 ); [all …]
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H A D | genalign11.c | 41 lgth1 = strlen( seq1[0] ); in gentracking() 45 for( i=0; i<lgth1; i++ ) in gentracking() 51 for( i=0; i<lgth1+1; i++ ) in gentracking() 62 mseq1[0] += lgth1+lgth2; in gentracking() 64 mseq2[0] += lgth1+lgth2; in gentracking() 67 limk = lgth1+lgth2; in gentracking() 119 int lgth1, lgth2; in genL__align11() local 207 lgth1 = strlen( seq1[0] ); in genL__align11() 313 for( i=0; i<lgth1; i++ ) in genL__align11() 337 for( i=0; i<lgth1+1; i++ ) in genL__align11() [all …]
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H A D | suboptalign11.c | 57 lgth1 = strlen( seq1[0] ); in gentracking() 60 mspt1 = res1 + lgth1+lgth2; in gentracking() 62 mspt2 = res2 + lgth1+lgth2; in gentracking() 66 limk = lgth1+lgth2; in gentracking() 104 limk = lgth1+lgth2; in gentracking() 136 int lgth1, lgth2; in suboptalign11() local 205 lgth1 = strlen( seq1[0] ); in suboptalign11() 315 for( i=0; i<lgth1; i++ ) in suboptalign11() 340 for( i=0; i<lgth1+1; i++ ) in suboptalign11() 372 lasti = lgth1+1; in suboptalign11() [all …]
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H A D | rnatest.c | 426 lgth1 = strlen( seq[0] ); in main() 427 for( i=0; i<lgth1; i++ ) in main()
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H A D | functions.h | 132 extern void imp_match_init_strictD( double *imp, int clus1, int clus2, int lgth1, int lgth2, char *… 133 extern void imp_match_init( double *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, c… 150 extern void part_imp_match_init_strict( double *imp, int clus1, int clus2, int lgth1, int lgth2, ch… 151 extern void part_imp_match_init( double *imp, int clus1, int clus2, int lgth1, int lgth2, char **se… 310 extern void imp_match_init_strict( double *imp, int clus1, int clus2, int lgth1, int lgth2, char **…
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