/dports/biology/wise/wise2.4.1/src/models/ |
H A D | evopairwise.c | 63 ref_aa = aminoacid_from_seq(ct,ref); in logl_negative_selection() 64 diff_aa = aminoacid_from_seq(ct,diff); in logl_negative_selection() 101 ref_aa = aminoacid_from_seq(ct,ref); in logl_positive_selection() 102 diff_aa = aminoacid_from_seq(ct,diff); in logl_positive_selection() 165 if( aminoacid_from_seq(ct,ref->seq+i) != aminoacid_from_seq(ct,diff->seq+i)) { in show_verbose_evo()
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H A D | genedisplay.c | 225 …write_codon_match(btp,'-',' ',alc->alu[1]->start+1,aminoacid_from_seq(ct,dna->seq+alc->alu[1]->sta… in protdna_btc_display() 228 …write_codon_match(btp,'~',' ',alc->alu[1]->start+1,aminoacid_from_seq(ct,dna->seq+alc->alu[1]->sta… in protdna_btc_display() 230 …]->end],alc->alu[0]->score[0],aminoacid_from_seq(ct,dna->seq+alc->alu[1]->start+1)),alc->alu[1]->s… in protdna_btc_display() 336 transc = aminoacid_from_seq(ct,dnatemp); in protdna_btc_display()
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H A D | alignwise.c | 34 aminoacid_from_seq(ct,gen->seq+alc->alu[1]->start+1),alc->alu[1]->start+1 in show_Gene_debug() 46 aminoacid_from_seq(ct,seq), in show_Gene_debug()
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H A D | pseudowise.c | 85 aa = aminoacid_from_seq(ct,gen->seq+gen_pos); in pseudo_gene_assessment() 129 if( pep->seq[i] != aminoacid_from_seq(ct,cdna->seq+(i*3)) ) { in check_pep_cdna_synchrony()
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H A D | genedisplay.dy | 218 …write_codon_match(btp,'-',' ',alc->alu[1]->start+1,aminoacid_from_seq(ct,dna->seq+alc->alu[1]->sta… 221 …write_codon_match(btp,'~',' ',alc->alu[1]->start+1,aminoacid_from_seq(ct,dna->seq+alc->alu[1]->sta… 223 …]->end],alc->alu[0]->score[0],aminoacid_from_seq(ct,dna->seq+alc->alu[1]->start+1)),alc->alu[1]->s… 329 transc = aminoacid_from_seq(ct,dnatemp);
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H A D | sywise.c | 121 …bel,alc->alu[0]->start+1,alc->alu[1]->start+1,seq1,aminoacid_from_seq(ct,seq1),seq2,aminoacid_from… in show_score_sequence()
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H A D | genewisemodel.dy | 466 buffer[i++] = aminoacid_from_seq(ct,dna->seq+col->alu[position_in_aln]->start+1); 482 buffer[i++] = aminoacid_from_seq(ct,tempseq); 483 /* buffer[i++] = aminoacid_from_seq(ct,dna->seq+col->alu[position_in_aln]->start+6);*/ 495 buffer[i++] = aminoacid_from_seq(ct,tempseq); 496 /*buffer[i++] = aminoacid_from_seq(ct,dna->seq+col->alu[position_in_aln]->start+5);*/ 508 buffer[i++] = aminoacid_from_seq(ct,dna->seq+col->alu[position_in_aln]->start+3);
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H A D | amplimer_resolver.c | 97 out->seq[j] = aminoacid_from_seq(ct,swapped->seq+i); in translate_swapped()
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H A D | genewisemodel.c | 476 buffer[i++] = aminoacid_from_seq(ct,dna->seq+col->alu[position_in_aln]->start+1); in Protein_from_GeneWise_AlnColumn() 492 buffer[i++] = aminoacid_from_seq(ct,tempseq); in Protein_from_GeneWise_AlnColumn() 505 buffer[i++] = aminoacid_from_seq(ct,tempseq); in Protein_from_GeneWise_AlnColumn() 518 buffer[i++] = aminoacid_from_seq(ct,dna->seq+col->alu[position_in_aln]->start+3); in Protein_from_GeneWise_AlnColumn()
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H A D | genomewise.c | 189 …%c%c %c\n",gen->seq[cstart],gen->seq[cstart+1],gen->seq[cstart+2],aminoacid_from_seq(ct,gen->seq+… in debug_genomewise()
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H A D | estwrap.c | 410 fputc(aminoacid_from_seq(ct,seq->seq+alc->alu[i]->start+1),ofp); in write_mul_estwise_AlnBlock()
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H A D | genewisehsp.dy | 112 temp_seq[j] = aminoacid_from_seq(ct,dna->seq+i);
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/dports/biology/wise/wise2.4.1/src/dynlibsrc/ |
H A D | codon.c | 123 aa aminoacid_from_seq(CodonTable * ct,char * seq) in aminoacid_from_seq() function 679 aa = aminoacid_from_seq(ct,codon); in four_fold_sites_CodonTable() 686 if( aa != aminoacid_from_seq(ct,codon) ) { in four_fold_sites_CodonTable()
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H A D | codon.dy | 30 func aminoacid_from_seq 168 aa aminoacid_from_seq(CodonTable * ct,char * seq) 592 aa = aminoacid_from_seq(ct,codon); 599 if( aa != aminoacid_from_seq(ct,codon) ) {
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H A D | codon.h | 113 #define aminoacid_from_seq Wise2_aminoacid_from_seq macro
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H A D | sequence_codon.c | 146 out->seq[j] = aminoacid_from_seq(ct,dna->seq+i); in translate_Sequence()
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H A D | codon.tex | 281 \subsubsection{aminoacid_from_seq} subsubsection 285 \item[Perl] {\tt &Wise2::CodonTable::aminoacid_from_seq (ct,seq)} 287 \item[Perl-OOP call] {\tt $obj->aminoacid_from_seq(seq)}
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H A D | codon.xs | 26 aminoacid_from_seq(ct,seq)
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H A D | translation.c | 97 seq->seq[j] = aminoacid_from_seq(ct,cd->baseseq->seq+i); in get_Protein_from_Translation()
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H A D | codon.pod | 82 =item aminoacid_from_seq 84 &Wise2::CodonTable::aminoacid_from_seq(ct,seq)
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H A D | pairbase.c | 647 …fprintf(ofp,"%9d %s[%c] %s[%c] : %d\n",i,seq1,aminoacid_from_seq(ct,seq1),seq2,aminoacid_from_seq(… in show_PairBaseCodonModelScore()
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H A D | translation.dy | 125 seq->seq[j] = aminoacid_from_seq(ct,cd->baseseq->seq+i);
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H A D | pairbase.dy | 549 …fprintf(ofp,"%9d %s[%c] %s[%c] : %d\n",i,seq1,aminoacid_from_seq(ct,seq1),seq2,aminoacid_from_seq(…
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H A D | sequence_codon.dy | 145 out->seq[j] = aminoacid_from_seq(ct,dna->seq+i);
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/dports/biology/wise/wise2.4.1/src/perl/scripts/ |
H A D | protestwise.pl | 111 $temp = $ct->aminoacid_from_seq($dnatemp);
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