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Searched refs:lgth1 (Results 1 – 14 of 14) sorted by relevance

/dports/biology/mafft/mafft-7.267-without-extensions/core/
H A DLalignmm.c262 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()
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H A DMSalign11.c57 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()
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H A DGalign11.c44 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
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H A DSalignmm.c43 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()
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H A DMSalignmm.c185 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()
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H A DpartSalignmm.c92 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()
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H A DSAalignmm.c60 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()
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H A DDalignmm.c83 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()
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H A DLalign11.c102 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
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H A Drna.c340 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 );
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H A Dgenalign11.c41 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()
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H A Dsuboptalign11.c57 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()
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H A Drnatest.c426 lgth1 = strlen( seq[0] ); in main()
427 for( i=0; i<lgth1; i++ ) in main()
H A Dfunctions.h132 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 **…