Home
last modified time | relevance | path

Searched refs:aminoacid_from_seq (Results 1 – 25 of 31) sorted by relevance

12

/dports/biology/wise/wise2.4.1/src/models/
H A Devopairwise.c63 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()
H A Dgenedisplay.c225 …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()
H A Dalignwise.c34 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()
H A Dpseudowise.c85 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()
H A Dgenedisplay.dy218 …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);
H A Dsywise.c121 …bel,alc->alu[0]->start+1,alc->alu[1]->start+1,seq1,aminoacid_from_seq(ct,seq1),seq2,aminoacid_from… in show_score_sequence()
H A Dgenewisemodel.dy466 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);
H A Damplimer_resolver.c97 out->seq[j] = aminoacid_from_seq(ct,swapped->seq+i); in translate_swapped()
H A Dgenewisemodel.c476 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()
H A Dgenomewise.c189 …%c%c %c\n",gen->seq[cstart],gen->seq[cstart+1],gen->seq[cstart+2],aminoacid_from_seq(ct,gen->seq+… in debug_genomewise()
H A Destwrap.c410 fputc(aminoacid_from_seq(ct,seq->seq+alc->alu[i]->start+1),ofp); in write_mul_estwise_AlnBlock()
H A Dgenewisehsp.dy112 temp_seq[j] = aminoacid_from_seq(ct,dna->seq+i);
/dports/biology/wise/wise2.4.1/src/dynlibsrc/
H A Dcodon.c123 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()
H A Dcodon.dy30 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) ) {
H A Dcodon.h113 #define aminoacid_from_seq Wise2_aminoacid_from_seq macro
H A Dsequence_codon.c146 out->seq[j] = aminoacid_from_seq(ct,dna->seq+i); in translate_Sequence()
H A Dcodon.tex281 \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)}
H A Dcodon.xs26 aminoacid_from_seq(ct,seq)
H A Dtranslation.c97 seq->seq[j] = aminoacid_from_seq(ct,cd->baseseq->seq+i); in get_Protein_from_Translation()
H A Dcodon.pod82 =item aminoacid_from_seq
84 &Wise2::CodonTable::aminoacid_from_seq(ct,seq)
H A Dpairbase.c647 …fprintf(ofp,"%9d %s[%c] %s[%c] : %d\n",i,seq1,aminoacid_from_seq(ct,seq1),seq2,aminoacid_from_seq(… in show_PairBaseCodonModelScore()
H A Dtranslation.dy125 seq->seq[j] = aminoacid_from_seq(ct,cd->baseseq->seq+i);
H A Dpairbase.dy549 …fprintf(ofp,"%9d %s[%c] %s[%c] : %d\n",i,seq1,aminoacid_from_seq(ct,seq1),seq2,aminoacid_from_seq(…
H A Dsequence_codon.dy145 out->seq[j] = aminoacid_from_seq(ct,dna->seq+i);
/dports/biology/wise/wise2.4.1/src/perl/scripts/
H A Dprotestwise.pl111 $temp = $ct->aminoacid_from_seq($dnatemp);

12