| /dports/biology/mafft/mafft-7.267-without-extensions/core/ |
| H A D | iteration.c | 103 static char *mseq1, **mseq2 = NULL; in iteration() local
140 if( mseq2 == NULL ) in iteration()
143 AllocateTmpSeqs( &mseq2, &mseq1, alloclen ); in iteration()
257 gappick( locnjob, s, aseq, mseq2, eff, effarr ); in iteration()
268 FreeTmpSeqs( mseq2, mseq1 ); in iteration()
271 AllocateTmpSeqs( &mseq2, &mseq1, alloclen ); in iteration()
278 strcpy( mseq1, mseq2[locnjob-1] ); in iteration()
282 for( i=locnjob-2; i>=s; i-- ) strcpy( mseq2[i+1], mseq2[i] ); in iteration()
283 strcpy( mseq2[s], mseq1 ); in iteration()
301 identity = !strcmp( mseq2[s], aseq[s] ); in iteration()
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| H A D | MSalign11.c | 22 *--mseq2[0] = *gap; in extendmseq()
33 *--mseq2[0] = seq2[0][j]; in extendmseq()
80 mseq2[0] += lgth1+lgth2; in Atracking()
81 *mseq2[0] = 0; in Atracking()
102 *--mseq2[0] = *gap; in Atracking()
266 *--mseq2[0] = 'u'; in backdp()
316 static char **mseq2; in MSalign11() local
400 mseq2[0] = mseq[1]; in MSalign11()
614 *mseq2[0] = 0; in MSalign11()
637 mseq2[0] = mseq[1]; in MSalign11()
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| H A D | pairlocalalign.c | 281 strcpy( *mseq2, aln2 ); in recallpairfoldalign()
1242 strcpy( ori2, *mseq2 ); in recalllara()
1248 strcpy( *mseq2, com ); in recalllara()
1315 t2u( *mseq2 ); in calldafs_giving_bpp()
1329 write1seq( fp, *mseq2 ); in calldafs_giving_bpp()
1432 t2u( *mseq2 ); in callmxscarna_giving_bpp()
2011 free( mseq2 ); in athread()
2061 mseq2[0] = aseq[1]; in athread()
2575 mseq2[0] = aseq[1]; in pairalign()
2926 char **mseq1, **mseq2; in main() local
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| H A D | tditeration.c | 256 char **mseq1, char **mseq2, in freelocalarrays() argument
295 free( mseq2 ); in freelocalarrays()
369 char **mseq1, **mseq2; in athread() local
450 mseq2 = AllocateCharMtx( locnjob, 0 ); in athread()
529 mseq1, mseq2, in athread()
646 mseq1, mseq2, in athread()
691 mseq1, mseq2, in athread()
844 commongappick( clus2, mseq2 ); in athread()
1267 static char **mseq1, **mseq2; local
1327 mseq2 = AllocateCharMtx( locnjob, 0 );
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| H A D | makedirectionlist.c | 334 char **mseq1, **mseq2; in directionthread() local
340 mseq2 = AllocateCharMtx( 1, 0 ); in directionthread()
377 mseq2[0] = seq[j]; in directionthread()
387 free( mseq2 ); in directionthread()
513 gappick0( mseq2[0], seq[i] ); in main()
522 strcpy( mseq2[0], seq[i] ); in main()
528 strcpy( mseq2[0], seq[i] ); in main()
541 sreverse( seq[i], mseq2[0] ); in main()
550 strcpy( seq[i], mseq2[0] ); in main()
560 FreeCharMtx( mseq2 ); in main()
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| H A D | SAalignmm.c | 51 char **mseq1, char **mseq2, in Atracking() argument
111 mseq2[j] += lgth1+lgth2; in Atracking()
112 *mseq2[j] = 0; in Atracking()
135 *--mseq2[j] = *gap; in Atracking()
144 *--mseq2[j] = seq2[j][jfi+l]; in Atracking()
151 *--mseq2[j] = seq2[j][jfi]; in Atracking()
178 static TLS char **mseq2; in Aalign() local
193 mseq2 = AllocateCharMtx( njob, 1 ); /* by J. Thompson */ in Aalign()
253 for( j=0; j<jcyc; j++ ) mseq2[j] = mseq[icyc+j]; in Aalign()
363 Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc ); in Aalign()
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| H A D | genalign11.c | 64 mseq2[0] += lgth1+lgth2; in gentracking()
65 *mseq2[0] = 0; in gentracking()
83 *--mseq2[0] = *gap; in gentracking()
90 *--mseq2[0] = seq2[0][jfi+l]; in gentracking()
96 *--mseq2[0] = seq2[0][jfi]; in gentracking()
142 static TLS char **mseq2; in genL__align11() local
171 free( mseq2 ); in genL__align11()
203 mseq2 = AllocateCharMtx( njob, 0 ); in genL__align11()
278 mseq2[0] = mseq[1]; in genL__align11()
597 strcpy( seq2[0], mseq2[0] ); in genL__align11()
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| H A D | Galign11.c | 89 mseq2[0] += lgth1+lgth2; in Atracking()
90 *mseq2[0] = 0; in Atracking()
123 *--mseq2[0] = *gap; in Atracking()
130 *--mseq2[0] = seq2[0][l]; in Atracking()
141 *--mseq2[0] = *gap; in Atracking()
148 *--mseq2[0] = seq2[0][jfi+l]; in Atracking()
154 *--mseq2[0] = seq2[0][jfi]; in Atracking()
199 static TLS char **mseq2 = NULL; in G__align11() local
228 if( mseq2 ) free( mseq2 ); mseq2 = NULL; in G__align11()
383 mseq2[0] = mseq[1]; in G__align11()
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| H A D | disttbfast.c | 903 char **mseq1, **mseq2; in treebasethread() local
928 mseq2 = AllocateCharMtx( njob, 0 ); in treebasethread()
967 free( mseq2 ); in treebasethread()
1074 if( strlen( mseq2[j] ) != len2 ) in treebasethread()
1432 commongappick( clus2, mseq2 ); in treebase()
1433 len2nocommongap = strlen( mseq2[0] ); in treebase()
1648 eq2dash( mseq2[i] ); in treebase()
1836 char **mseq1 = NULL, **mseq2 = NULL; in disttbfast() local
1981 mseq2 = AllocateCharMtx( njob, 0 ); in disttbfast()
2972 free( mseq2 ); in disttbfast()
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| H A D | tbfast.c | 540 char **mseq1, **mseq2; in treebasethread() local
561 mseq2 = AllocateCharMtx( njob, 0 ); in treebasethread()
627 free( mseq2 ); in treebasethread()
1057 findcommongaps( clus2, mseq2, gapmap ); in treebase()
1058 commongappick( clus2, mseq2 ); in treebase()
1059 len2nocommongap = strlen( mseq2[0] ); in treebase()
1244 for( i=0; i<clus2; i++ ) eq2dash( mseq2[i] ); in treebase()
1247 eq2dashmatometehayaku( mseq2, clus2 ); in treebase()
1372 static char **mseq1, **mseq2; in main() local
1456 mseq2 = AllocateCharMtx( njob, 0 ); in main()
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| H A D | mafft-profile.c | 179 …q2, char **name, int *nlen, char **seq, char **aseq, char **mseq1, char **mseq2, int ***topol, dou… in GroupAlign() argument
225 clus2 = conjuctionforgaln( nseq1, njob, aseq, mseq2, effarr2, effarr, name, name2, indication2 ); in GroupAlign()
239 commongappick( nseq2, mseq2 ); in GroupAlign()
249 …pscore = Falign_udpari_long( NULL, NULL, n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, N… in GroupAlign()
251 …pscore = Falign( NULL, NULL, n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, NULL, NULL, c… in GroupAlign()
256 …pscore = MSalignmm( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen… in GroupAlign()
258 …pscore = A__align( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen,… in GroupAlign()
312 static char **mseq1, **mseq2; in main() local
362 mseq2 = AllocateCharMtx( njob, 1 ); in main()
478 GroupAlign( nseq1, nseq2, name, nlen, seq, aseq, mseq1, mseq2, topol, len, eff, alloclen ); in main()
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| H A D | Lalign11.c | 123 mseq2[0] += lgth1+lgth2; in Ltracking()
124 *mseq2[0] = 0; in Ltracking()
156 *--mseq2[0] = *gap; in Ltracking()
163 *--mseq2[0] = seq2[0][l]; in Ltracking()
175 *--mseq2[0] = *gap; in Ltracking()
182 *--mseq2[0] = seq2[0][jfi+l]; in Ltracking()
190 *--mseq2[0] = seq2[0][jfi]; in Ltracking()
233 static TLS char **mseq2; in L__align11() local
274 free( mseq2 ); in L__align11()
383 mseq2[0] = mseq[1]; in L__align11()
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| H A D | MSalignmm.c | 754 mseq2[i][0] = 0; in MSalignmm_rec()
1536 mseq2[j][len+l] = 0; in MSalignmm_rec()
1557 mseq2[j][len+l] = 0; in MSalignmm_rec()
1655 char **mseq2 in freearrays() argument
1669 FreeCharMtx( mseq2 ); in freearrays()
1681 char **mseq2; in MSalignmm() local
2362 mseq2[i][0] = 0; in MSalignmm_rec_variousdist()
3175 mseq2[j][len+l] = 0; in MSalignmm_rec_variousdist()
3294 char **mseq2 in freearrays_variousdist() argument
3308 FreeCharMtx( mseq2 ); in freearrays_variousdist()
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| H A D | pairash.c | 397 readtmalign( fp, *mseq1, *mseq2, equiv ); in calltmalign()
404 value = (double)naivepairscore11( *mseq1, *mseq2, penalty ); in calltmalign()
502 readrash( fp, *mseq1, *mseq2, equiv ); in callrash()
510 value = (double)naivepairscore11( *mseq1, *mseq2, penalty ); in callrash()
1118 clus2 = conjuctionfortbfast_old( pair, j, aseq, mseq2, effarr2, effarr, indication2 ); in pairalign()
1141 pscore = callrash( i, j, mseq1, mseq2, equiv, strfiles[i], strfiles[j], alloclen ); in pairalign()
1183 gappick0( seq[j], mseq2[0] ); in pairalign()
1189 gappick0( seq[j], mseq2[0] ); in pairalign()
1318 static char **mseq1, **mseq2; in main() local
1362 preparetmalign( infp, &strfiles, &chainids, &seq, &mseq1, &mseq2, &equiv, &alloclen ); in main()
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| H A D | partSalignmm.c | 731 mseq2[j] += lgth1+lgth2; in Atracking_localhom()
732 *mseq2[j] = 0; in Atracking_localhom()
765 *--mseq2[j] = *gap; in Atracking_localhom()
787 *--mseq2[j] = *gap; in Atracking_localhom()
878 *mseq2[j] = 0; in Atracking()
910 *--mseq2[j] = *gap; in Atracking()
932 *--mseq2[j] = *gap; in Atracking()
982 static TLS char **mseq2; in partA__align() local
1037 free( mseq2 ); in partA__align()
1670 static TLS char **mseq2; in partA__align_variousdist() local
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| H A D | addfunctions.c | 451 char **mseq2, **mseq0, **mseq1; in insertnewgaps() local
524 mseq2 = AllocateCharMtx( ngroup2, alloclen ); in insertnewgaps()
550 for( i=0; i<ngroup2; i++ ) mseq2[i][0] = 0; in insertnewgaps()
669 FreeCharMtx( mseq2 ); in insertnewgaps()
682 char **mseq2, **mseq0, **mseq1; in insertnewgaps_bothorders() local
768 mseq2 = AllocateCharMtx( ngroup2, alloclen ); in insertnewgaps_bothorders()
814 for( i=0; i<ngroup2; i++ ) mseq2[i][0] = 0; in insertnewgaps_bothorders()
858 reporterr( "mseq2[0] = %s\n", mseq2[0] ); in insertnewgaps_bothorders()
938 reporterr( "mseq2[0] = %s\n", mseq2[0] ); in insertnewgaps_bothorders()
967 reporterr( "mseq2[0] = %s\n", mseq2[0] ); in insertnewgaps_bothorders()
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| H A D | getlag.c | 157 void treebase( char **name, int nlen[M], char **seq, char **aseq, char **mseq1, char **mseq2, doubl… in treebase() argument
219 clus2 = conjuction( pair, s2, aseq, mseq2, effarr2, effarr, name, name2, indication2 ); in treebase()
246 …pscore = Fgetlag( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen ); in treebase()
330 static char **mseq1, **mseq2; in main() local
352 mseq2 = AllocateCharMtx( njob, 0 ); in main()
449 treebase( name, nlen, bseq, aseq, mseq1, mseq2, pscore, topol, len, eff, alloclen ); in main()
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| H A D | Lalignmm.c | 445 mseq2[i][0] = 0; in MSalign2m2m_rec()
447 strcat( mseq2[i], "-" ); in MSalign2m2m_rec()
460 for( i=0; i<jcyc; i++ ) aseq2[i] = mseq2[i]; in MSalign2m2m_rec()
1345 mseq2[i][0] = 0; in MSalignmm_rec()
1347 strcat( mseq2[i], "-" ); in MSalignmm_rec()
2169 char **mseq2; in Lalignmm_hmout() local
2201 mseq2 = AllocateCharMtx( jcyc, ll1+ll2 ); in Lalignmm_hmout()
2337 FreeCharMtx( mseq2 ); in Lalignmm_hmout()
2372 char **mseq2; in Lalign2m2m_hmout() local
2398 mseq2 = AllocateCharMtx( jcyc, ll1+ll2 ); in Lalign2m2m_hmout()
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| H A D | suboptalign11.c | 40 char **mseq1, char **mseq2, in gentracking() argument
121 strcpy( mseq2[0], mspt2 ); in gentracking()
159 static char **mseq2; in suboptalign11() local
266 mseq2 = AllocateCharMtx( njob, ll1+ll2 ); in suboptalign11()
644 …resf = gentracking( used, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijpi, ijpj, off1pt, off2pt, shur… in suboptalign11()
646 …putlocalhom3( mseq1[0], mseq2[0], lhmpt, *off1pt, *off2pt, (int)shuryo[k].wm, strlen( mseq1[0] ) ); in suboptalign11()
650 fprintf( stderr, ">\n%s\n", mseq2[0] ); in suboptalign11()
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| H A D | mltaln9.c | 135 char *mseq1, *mseq2;
147 mseq2 = seq2[j];
197 char *mseq1, *mseq2; in intergroup_score_consweight() local
212 mseq2 = seq2[j]; in intergroup_score_consweight()
262 char *mseq1, *mseq2; in intergroup_score_gapnomi() local
277 mseq2 = seq2[j]; in intergroup_score_gapnomi()
328 char *mseq1, *mseq2; in intergroup_score_multimtx() local
349 mseq2 = seq2[j]; in intergroup_score_multimtx()
425 mseq2 = seq2[j]; in intergroup_score_dynmtx()
500 mseq2 = seq2[j]; in intergroup_score()
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| H A D | Salignmm.c | 743 char **mseq1, char **mseq2, in Atracking_localhom() argument
882 char **mseq1, char **mseq2, in Atracking() argument
1044 static TLS char **mseq2; in A__align() local
1099 free( mseq2 ); in A__align()
1212 mseq2 = AllocateCharMtx( njob, 0 ); in A__align()
1305 mseq2[j] = mseq[icyc+j]; in A__align()
1759 for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] ); in A__align()
1811 static TLS char **mseq2; in A__align_variousdist() local
1864 free( mseq2 ); in A__align_variousdist()
2004 mseq2 = AllocateCharMtx( njob, 0 ); in A__align_variousdist()
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| H A D | addsingle.c | 1295 findcommongaps( clus2, mseq2, gapmap ); in treebase()
1296 commongappick( clus2, mseq2 ); in treebase()
1297 len2nocommongap = strlen( mseq2[0] ); in treebase()
1396 …imp_match_init_strict( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, e… in treebase()
1424 pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen ); in treebase()
1453 fprintf( stderr, "%s\n", mseq2[i] ); in treebase()
1463 adjustgapmap( strlen( mseq2[0] )-len2nocommongap+len2, gapmap, mseq2[0] ); in treebase()
1465 findnewgaps( clus2, 0, mseq2, gaplen ); in treebase()
1549 char **mseq1 = NULL, **mseq2 = NULL; in addsinglethread() local
1603 mseq2 = AllocateCharMtx( njob, 0 ); in addsinglethread()
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| H A D | rnatest.c | 329 static char **mseq1, **mseq2; in main() local
373 mseq2 = AllocateCharMtx( njob, 0 ); in main()
443 pairalign( name, nlen, bseq, aseq, mseq1, mseq2, eff, alloclen ); in main()
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| H A D | splittbfast.c | 937 static char **mseq1, **mseq2; in pairalign() local
955 mseq2 = AllocateCharMtx( nseq, 0 ); in pairalign()
974 clus2 = fastconjuction_noname( mem2, seq, mseq2, effarr2, weight, indication2, 0.0 ); in pairalign()
977 clus2 = fastconjuction_noweight( mem2, seq, mseq2, effarr2, indication2 ); in pairalign()
1034 pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen ); in pairalign()
1045 pscore = G__align11( n_dis_consweight_multi, mseq1, mseq2, *alloclen, outgap, outgap ); in pairalign()
1201 static char **mseq2 = NULL; in splitseq_mq() local
1213 mseq2 = AllocateCharMtx( 1, palloclen ); in splitseq_mq()
1412 gappick0( mseq2[0], seq[scores[i].numinseq] ); in splitseq_mq()
1677 gappick0( mseq2[0], seq[scores[picks[i]].numinseq] ); in splitseq_mq()
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| H A D | tddis.c | 59 char *mseq1, *mseq2; in score_calc() local
67 mseq2 = seq[j]; in score_calc()
72 if( mseq1[k] == '-' && mseq2[k] == '-' ) continue; in score_calc()
74 tmpscore += amino_dis[(int)mseq1[k]][(int)mseq2[k]]; in score_calc()
84 if( mseq2[k] == '-' ) in score_calc()
87 while( mseq2[++k] == '-' ) in score_calc()
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