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| H A D | tditeration.c | 255 double *effarr, double *effarrforlocalhom, double *effarr1, double *effarr2, in freelocalarrays() argument
292 free( effarr1 ); in freelocalarrays()
372 double *effarr1, *effarr2, *effarr1_kozo, *effarr2_kozo; in athread() local
447 effarr1 = AllocateDoubleVec( locnjob ); in athread()
528 effarr, effarrforlocalhom, effarr1, effarr2, in athread()
645 effarr, effarrforlocalhom, effarr1, effarr2, in athread()
690 effarr, effarrforlocalhom, effarr1, effarr2, in athread()
1258 static double *effarr1 = NULL; local
1324 effarr1 = AllocateDoubleVec( locnjob );
1621 effarr1[0] = 1.0;
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| H A D | mafft-profile.c | 187 double *effarr1 = NULL; in GroupAlign() local
201 if( effarr1 == NULL ) in GroupAlign()
207 effarr1 = AllocateDoubleVec( njob ); in GroupAlign()
224 clus1 = conjuctionforgaln( 0, nseq1, aseq, mseq1, effarr1, effarr, name, name1, indication1 ); 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()
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| H A D | tbfast.c | 547 double *effarr1 = NULL; in treebasethread() local
575 effarr1 = AllocateDoubleVec( njob ); in treebasethread()
629 free( effarr1 ); in treebasethread()
733 …clus1 = fastconjuction_noname( topol[l][0], localcopy, mseq1, effarr1, effarr, indication1, minimu… in treebasethread()
820 …if( rnakozo ) imp_rna( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, NULL, N… in treebasethread()
853 pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen ); in treebasethread()
923 double *effarr1 = NULL; in treebase() local
951 effarr1 = AllocateDoubleVec( njob ); in treebase()
1041 …clus1 = fastconjuction_noname( topol[l][0], aseq, mseq1, effarr1, effarr, indication1, minimumweig… in treebase()
1181 pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen ); in treebase()
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| H A D | disttbfast.c | 911 double *effarr1 = NULL; in treebasethread() local
931 effarr1 = AllocateDoubleVec( njob ); in treebasethread()
969 free( effarr1 ); in treebasethread()
1162 pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen ); in treebasethread()
1306 double *effarr1 = NULL; in treebase() local
1329 if( effarr1 == NULL ) in treebase()
1331 effarr1 = AllocateDoubleVec( njob ); in treebase()
1554 pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen ); in treebase()
1731 free( effarr1 ); in treebase()
1740 effarr1 = NULL; in treebase()
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| H A D | getlag.c | 170 static double *effarr1 = NULL; in treebase() local
184 effarr1 = AllocateDoubleVec( njob ); in treebase()
218 clus1 = conjuction( pair, s1, aseq, mseq1, effarr1, effarr, name, name1, indication1 ); in treebase()
233 for( i=0; i<clus1; i++ ) fprintf( stderr, "STEP%d-eff for mseq1-%d %f\n", l+1, i, effarr1[i] ); in treebase()
246 …pscore = Fgetlag( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen ); in treebase()
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| H A D | multi2hat3s.c | 141 static double *effarr1 = NULL; in pairalign() local
166 if( effarr1 == NULL ) in pairalign()
168 effarr1 = AllocateDoubleVec( njob ); in pairalign()
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| H A D | pair2hat3s.c | 153 static double *effarr1 = NULL; in pairalign() local
181 if( effarr1 == NULL ) in pairalign()
183 effarr1 = AllocateDoubleVec( njob ); in pairalign()
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| H A D | tddis.c | 291 void mseqcat( char **seq1, char **seq2, double **eff, double *effarr1, double *effarr2, char name1[… in mseqcat() argument
298 for( i=0; i<clus1; i++ ) for( j=0; j<clus1; j++ ) eff[i][j] = effarr1[i]* effarr1[j]; in mseqcat()
299 …for( i=0; i<clus1; i++ ) for( j=clus1; j<clus1+clus2; j++ ) eff[i][j] = effarr1[i]* effarr2[j-clus… in mseqcat()
300 …for( i=clus1; i<clus1+clus2; i++ ) for( j=0; j<clus1; j++ ) eff[i][j] = effarr2[i-clus1] * effarr1… in mseqcat()
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| H A D | pairlocalalign.c | 1937 double *effarr1; in athread() local
1962 effarr1 = AllocateDoubleVec( 1 ); in athread()
2008 free( effarr1 ); in athread()
2058 effarr1[0] = 1.0; in athread()
2082 …pscore = Falign( NULL, NULL, n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, NULL, NULL, 1… in athread()
2240 pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen ); in athread()
2337 double *effarr1; in pairalign() local
2396 effarr1 = AllocateDoubleVec( njob ); in pairalign()
2572 effarr1[0] = 1.0; in pairalign()
2745 pscore = Aalign( mseq1, mseq2, effarr1, effarr2, 1, 1, alloclen ); in pairalign()
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| H A D | addsingle.c | 1159 double *effarr1 = NULL; in treebase() local
1185 effarr1 = AllocateDoubleVec( nseq ); in treebase()
1274 …clus1 = fastconjuction_noname_kozo( topol[l][0], aseq, mseq1, effarr1, effarr, effarr1_kozo, effar… in treebase()
1279 clus1 = fastconjuction_noname( topol[l][0], aseq, mseq1, effarr1, effarr, indication1, 0.0 ); in treebase()
1396 …ULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, effarr1… in treebase()
1397 …if( rnakozo ) imp_rna( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, NULL, N… in treebase()
1412 …pscore = Falign_udpari_long( NULL, NULL, n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, N… in treebase()
1415 …pscore = Falign( NULL, NULL, n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, NULL, NULL, c… in treebase()
1424 pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen ); in treebase()
1428 …pscore = MSalignmm( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *allocle… in treebase()
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| H A D | splittbfast.c | 935 static double *effarr1 = NULL; in pairalign() local
947 if( effarr1 == NULL ) in pairalign()
950 effarr1 = AllocateDoubleVec( nseq ); in pairalign()
973 clus1 = fastconjuction_noname( mem1, seq, mseq1, effarr1, weight, indication1, 0.0 ); in pairalign()
976 clus1 = fastconjuction_noweight( mem1, seq, mseq1, effarr1, indication1 ); in pairalign()
1019 …pscore = Falign_udpari_long( NULL, NULL, n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, N… in pairalign()
1024 …pscore = Falign( NULL, NULL, n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, NULL, NULL, c… in pairalign()
1034 pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen ); in pairalign()
1039 …pscore = MSalignmm( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *allocle… in pairalign()
1050 …pscore = A__align( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen… in pairalign()
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| H A D | pairash.c | 1033 static double *effarr1 = NULL; in pairalign() local
1061 if( effarr1 == NULL ) in pairalign()
1064 effarr1 = AllocateDoubleVec( njob ); in pairalign()
1117 clus1 = conjuctionfortbfast_old( pair, i, aseq, mseq1, effarr1, effarr, indication1 ); in pairalign()
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| H A D | functions.h | 76 extern void mseqcat( char **seq1, char **seq2, double **eff, double *effarr1, double *effarr2, char…
144 extern double translate_and_Calign( char **mseq1, char **mseq2, double *effarr1, double *effarr2, i…
298 extern void foldalignedrna( int clus1, int clus2, char **mseq1, char **mseq2, double *effarr1, doub…
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