/dports/biology/jalview/jalview/test/jalview/datamodel/ |
H A D | AlignedCodonIteratorTest.java | 69 assertEquals("P", codon.product); in testNext() 70 codon = codons.next(); in testNext() 73 codon = codons.next(); in testNext() 98 codon = codons.next(); in testNext_unmappedPeptide() 101 codon = codons.next(); in testNext_unmappedPeptide() 127 codon = codons.next(); in testNext_incompleteCodon() 152 codon = codons.next(); in testAnother() 155 codon = codons.next(); in testAnother() 158 codon = codons.next(); in testAnother() 182 codon = codons.next(); in testNext_withOffset() [all …]
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/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/libv3/models/codon/ |
H A D | MG_REV.bf | 1 LoadFunctionLibrary("../codon.bf"); 7 /** @module models.codon.MG_REV */ 10 * @name models.codon.MG_REV.ModelDescription 16 codons = models.codon.MapCode(code); 101 * @name models.codon.MG_REV._DefineQ 157 … models.codon.MG_REV.set_branch_length.sub[models.codon.MG_REV.set_branch_length.alpha] = 1; 158 … models.codon.MG_REV.set_branch_length.sub[models.codon.MG_REV.set_branch_length.beta] = 0; 161 … models.codon.MG_REV.set_branch_length.sub[models.codon.MG_REV.set_branch_length.alpha] = 0; 162 … models.codon.MG_REV.set_branch_length.sub[models.codon.MG_REV.set_branch_length.beta] = 1; 221 …messages.log ("models.codon.MG_REV.set_branch_length: " + models.codon.MG_REV.set_branch_length.al… [all …]
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/dports/biology/py-biopython/biopython-1.79/Bio/Data/ |
H A D | CodonTable.py | 246 c1, c2, c3 = codon 294 if {codon[0] for codon in codons}.issuperset(set(meanings)) 299 if {codon[1] for codon in codons}.issuperset(set(meanings)) 304 if {codon[2] for codon in codons}.issuperset(set(meanings)) 312 if codon not in candidates and codon not in codons: 319 for codon in [ 524 codon = codon.replace("T", "U") 533 if "T" in codon: 534 codon = codon.replace("T", "U") 541 if "T" in codon: [all …]
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/dports/biology/ncbi-toolkit/ncbi/algo/blast/core/ |
H A D | blast_util.c | 385 if ((codon[0] | codon[1] | codon[2]) > 15) { in s_CodonToAA() 395 if (codon[0] & mapping[i]) { in s_CodonToAA() 431 Uint1 codon[CODON_LENGTH]; in BLAST_GetTranslation() local 443 codon[0] = nucl_seq[index]; in BLAST_GetTranslation() 444 codon[1] = nucl_seq[index+1]; in BLAST_GetTranslation() 445 codon[2] = nucl_seq[index+2]; in BLAST_GetTranslation() 514 int byte_value, codon=-1; in BLAST_TranslateCompressedSequence() local 642 codon = byte_value & 63; in BLAST_TranslateCompressedSequence() 790 codon = (byte_value & 63); in BLAST_TranslateCompressedSequence() 794 codon = (byte_value >> 2); in BLAST_TranslateCompressedSequence() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/ |
H A D | blast_util.c | 385 if ((codon[0] | codon[1] | codon[2]) > 15) { in s_CodonToAA() 395 if (codon[0] & mapping[i]) { in s_CodonToAA() 431 Uint1 codon[CODON_LENGTH]; in BLAST_GetTranslation() local 443 codon[0] = nucl_seq[index]; in BLAST_GetTranslation() 444 codon[1] = nucl_seq[index+1]; in BLAST_GetTranslation() 445 codon[2] = nucl_seq[index+2]; in BLAST_GetTranslation() 514 int byte_value, codon=-1; in BLAST_TranslateCompressedSequence() local 642 codon = byte_value & 63; in BLAST_TranslateCompressedSequence() 790 codon = (byte_value & 63); in BLAST_TranslateCompressedSequence() 794 codon = (byte_value >> 2); in BLAST_TranslateCompressedSequence() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/ |
H A D | blast_util.c | 385 if ((codon[0] | codon[1] | codon[2]) > 15) { in s_CodonToAA() 395 if (codon[0] & mapping[i]) { in s_CodonToAA() 431 Uint1 codon[CODON_LENGTH]; in BLAST_GetTranslation() local 443 codon[0] = nucl_seq[index]; in BLAST_GetTranslation() 444 codon[1] = nucl_seq[index+1]; in BLAST_GetTranslation() 445 codon[2] = nucl_seq[index+2]; in BLAST_GetTranslation() 514 int byte_value, codon=-1; in BLAST_TranslateCompressedSequence() local 642 codon = byte_value & 63; in BLAST_TranslateCompressedSequence() 790 codon = (byte_value & 63); in BLAST_TranslateCompressedSequence() 794 codon = (byte_value >> 2); in BLAST_TranslateCompressedSequence() [all …]
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/dports/biology/biolibc/biolibc-0.2.1/ |
H A D | orf.c | 57 long bl_next_start_codon(FILE *rna_stream, char codon[4]) in bl_next_start_codon() 66 codon[0] = codon[3] = '\0'; in bl_next_start_codon() 85 codon[0] = ch1; codon[1] = ch2; codon[2] = ch3; in bl_next_start_codon() 154 long bl_next_stop_codon(FILE *rna_stream, char codon[4]) in bl_next_stop_codon() 163 codon[0] = codon[3] = '\0'; in bl_next_stop_codon() 183 codon[0] = ch1; codon[1] = ch2; codon[2] = ch3; in bl_next_stop_codon() 196 codon[0] = ch1; codon[1] = ch2; codon[2] = ch3; in bl_next_stop_codon()
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/dports/biology/wise/wise2.4.1/src/dynlibsrc/ |
H A D | codon.dy | 113 codon c; 144 ct r codon table 164 ct r codon table 176 ct r codon table 189 ct r codon table 220 Tells you if this codon is a real codon 271 maps a 0-63 codon to a 0-123 codon. Suprisingly useful. 290 maps a 0-125 codon to a 0-63 codon. 294 c r codon 0-125 402 Reverses codon. Takes a forward codon number and [all …]
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H A D | codon.pod | 102 returns amino acid for this codon number (NB codon numbers 0-125) 107 Argument c [READ ] codon number [codon] 120 Argument c [READ ] codon number [codon] 130 in this codon table 198 Tells you if this codon is a real codon 210 maps a 0-63 codon to a 0-123 codon. Suprisingly useful. 222 maps a 0-125 codon to a 0-63 codon. 228 Argument c [READ ] codon 0-125 [codon] 240 Argument c [READ ] codon number 0-124 [codon] 257 Argument c [READ ] codon number [codon] [all …]
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H A D | codon.h | 16 typedef short int codon; typedef 127 aa Wise2_aminoacid_from_codon(CodonTable * ct,codon c); 143 int Wise2_aminoacid_no_from_codon(CodonTable * ct,codon c); 159 boolean Wise2_is_stop_codon(codon c,CodonTable * ct); 217 codon Wise2_codon_from_base4_codon(int c); 233 int Wise2_base4_codon_from_codon(codon c); 247 boolean Wise2_has_random_bases(codon c); 269 codon Wise2_permute_possible_random_bases(codon c,base one,base two,base three); 302 codon Wise2_reverse_codon(codon c); 319 base Wise2_base_from_codon(codon c,int pos); [all …]
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H A D | codon.tex | 1 \section{codon} section in File Documentation 22 Tells you if this codon is a real codon 36 maps a 0-63 codon to a 0-123 codon. Suprisingly useful. 47 \item[c] [READ ] codon 0-125 [codon] 50 maps a 0-125 codon to a 0-63 codon. 64 \item[c] [READ ] codon number 0-124 [codon] 78 \item[c] [READ ] codon number [codon] 82 \item[returns] [UNKN ] codon number [codon] 315 \item[c] [READ ] codon number [codon] 318 returns amino acid for this codon number (NB codon numbers 0-125) [all …]
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H A D | codon_api.h | 95 aa Wise2_aminoacid_from_codon( Wise2_CodonTable * ct,codon c); 109 boolean Wise2_is_stop_codon( codon c,Wise2_CodonTable * ct); 215 codon Wise2_codon_from_base4_codon( int c); 229 int Wise2_base4_codon_from_codon( codon c); 241 boolean Wise2_has_random_bases( codon c); 261 codon Wise2_permute_possible_random_bases( codon c,base one,base two,base three); 276 base Wise2_base_from_codon( codon c,int pos); 293 codon Wise2_codon_from_seq( char * seq);
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H A D | codon.c | 58 codon c; in read_CodonTable() 266 codon codon_from_base4_codon(int c) in codon_from_base4_codon() 324 boolean has_random_bases(codon c) in has_random_bases() 359 codon permute_possible_random_bases(codon c,base one,base two,base three) in permute_possible_random_bases() 430 codon reverse_codon(codon c) in reverse_codon() 501 codon codon_from_seq(char * seq) in codon_from_seq() 669 char codon[3]; in four_fold_sites_CodonTable() local 675 codon[0] = seq[0]; in four_fold_sites_CodonTable() 676 codon[1] = seq[1]; in four_fold_sites_CodonTable() 677 codon[2] = seq[2]; in four_fold_sites_CodonTable() [all …]
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/dports/biology/py-biopython/biopython-1.79/Bio/SeqUtils/ |
H A D | CodonUsage.py | 115 for codon in codons: 116 total += self.codon_count[codon] 119 for codon in codons: 125 for codon_index, codon in enumerate(codons): 145 codon = dna_sequence[i : i + 3] 146 if codon in self.index: 148 if codon not in ["ATG", "TGG"]: 152 elif codon not in ["TGA", "TAA", "TAG"]: 173 codon = dna_sequence[i : i + 3] 174 if codon in self.codon_count: [all …]
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/dports/biology/wise/wise2.4.1/src/HMMer2/ |
H A D | translate.c | 51 int codon; /* index for codon */ in Translate() local 66 codon = 0; in Translate() 69 codon *= 4; in Translate() 72 case 'C': case 'c': codon += 1; break; in Translate() 73 case 'G': case 'g': codon += 2; break; in Translate() 74 case 'T': case 't': codon += 3; break; in Translate() 75 case 'U': case 'u': codon += 3; break; in Translate() 76 default: codon = 64; break; in Translate() 78 if (codon == 64) break; in Translate() 81 strcpy(aaptr, code[codon]); in Translate() [all …]
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/dports/biology/clustal-omega/clustal-omega-1.2.4/src/squid/ |
H A D | translate.c | 52 int codon; /* index for codon */ in Translate() local 67 codon = 0; in Translate() 70 codon *= 4; in Translate() 73 case 'C': case 'c': codon += 1; break; in Translate() 74 case 'G': case 'g': codon += 2; break; in Translate() 75 case 'T': case 't': codon += 3; break; in Translate() 76 case 'U': case 'u': codon += 3; break; in Translate() 77 default: codon = 64; break; in Translate() 79 if (codon == 64) break; in Translate() 82 strcpy(aaptr, code[codon]); in Translate() [all …]
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/dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-v0.3.1/src/ |
H A D | tightString.c | 213 Codon codon; in readTightString() local 225 codon = tString->sequence[index]; in readTightString() 233 codon = tString->sequence[index]; in readTightString() 257 return (codon & 192) >> 6; in getNucleotide() 259 return (codon & 48) >> 4; in getNucleotide() 261 return (codon & 12) >> 2; in getNucleotide() 263 return (codon & 3); in getNucleotide() 293 Codon codon; in getNucleotideChar() local 301 return readNucleotide((codon & 48) >> 4); in getNucleotideChar() 305 return readNucleotide((codon & 3)); in getNucleotideChar() [all …]
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/dports/biology/velvet/velvet_1.2.10/src/ |
H A D | tightString.c | 185 Codon codon; in readTightString() local 197 codon = tString->sequence[index]; in readTightString() 205 codon = tString->sequence[index]; in readTightString() 229 return (codon & 192) >> 6; in getNucleotide() 231 return (codon & 48) >> 4; in getNucleotide() 233 return (codon & 12) >> 2; in getNucleotide() 235 return (codon & 3); in getNucleotide() 265 Codon codon; in getNucleotideChar() local 273 return readNucleotide((codon & 48) >> 4); in getNucleotideChar() 275 return readNucleotide((codon & 12) >> 2); in getNucleotideChar() [all …]
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/dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-1.2.01/Velvet-1.1.06/ |
H A D | tightString.c | 192 Codon codon; in readTightString() local 204 codon = tString->sequence[index]; in readTightString() 212 codon = tString->sequence[index]; in readTightString() 236 return (codon & 192) >> 6; in getNucleotide() 238 return (codon & 48) >> 4; in getNucleotide() 240 return (codon & 12) >> 2; in getNucleotide() 242 return (codon & 3); in getNucleotide() 272 Codon codon; in getNucleotideChar() local 280 return readNucleotide((codon & 48) >> 4); in getNucleotideChar() 282 return readNucleotide((codon & 12) >> 2); in getNucleotideChar() [all …]
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/dports/biology/py-hits/hits-0.1/hits/ |
H A D | genetic_code.py | 7 def codon_sorting_key(codon): argument 8 return [nucleotide_to_index[b] for b in codon] 20 codon_to_index = {codon: i for i, codon in enumerate(all_codons)} 23 for codon in all_codons: 24 amino_acid = full_forward_table[codon] 26 full_back_table[amino_acid] = [codon] 28 full_back_table[amino_acid].append(codon) 34 for i, codon in enumerate(full_back_table[amino_acid]): 35 codon_to_amino_acid_and_index[codon] = (amino_acid, i) 99 for codon in anticodon_to_codons[anticodon]: [all …]
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/dports/biology/biolibc/biolibc-0.2.1/Man/ |
H A D | bl_next_start_codon.3 | 17 long bl_next_start_codon(FILE *rna_stream, char codon[4]) 23 codon 4-character buffer to receive codon sequence 24 Set to "" if no codon found 36 codon). For example, givent the following input: 47 or EOF if no codon is found. 54 char codon[4]; 58 printf("Start codon at %lu.n", pos); 59 if ( (pos = next_stop_codon(stdin, codon)) != EOF ) 60 printf("Stop codon %s at %lu.n", codon, pos); 62 puts("No stop codon found."); [all …]
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H A D | bl_next_stop_codon.3 | 17 long bl_next_stop_codon(FILE *rna_stream, char codon[4]) 23 codon 4-character buffer to receive codon sequence 24 Set to "" if no codon found 36 codon). For example, givent the following input: 47 or EOF if no codon is found. 54 char codon[4]; 58 printf("Start codon at %lu.n", pos); 59 if ( (pos = next_stop_codon(stdin, codon)) != EOF ) 60 printf("Stop codon %s at %lu.n", codon, pos); 62 puts("No stop codon found."); [all …]
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/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/libv3/tasks/ |
H A D | genetic_code.bf | 107 lfunction genetic_code.partition_codon(codon) { 110 codon$16, (codon % 16) $4, codon % 4 141 for (codon = 0; codon < 64; codon += 1) { 142 if (genCode[codon] == stop_code) { 145 aa1 = genCode [codon]; 172 * @returns returns ordered codon to amino acid map 191 * @returns whether or not the codon is a stop codon 193 lfunction genetic_code.IsStop(codon, code) { 276 for (codon = 0; codon < 64; codon += 1) { 279 if (genCode[codon] == stop_code) { [all …]
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/dports/biology/emboss/EMBOSS-6.6.0/emboss/ |
H A D | chips.c | 39 AjPCod codon; in main() local 57 codon = ajCodNewCodenum(0); in main() 68 ajCodSetTripletsS(codon,substr,&ccnt); in main() 71 ajCodCalcUsage(codon,ccnt); in main() 72 td = ajCodCalcNc(codon); in main() 76 ajCodClearData(codon); in main() 82 ajCodCalcUsage(codon,ccnt); in main() 83 td = ajCodCalcNc(codon); in main() 91 ajCodDel(&codon); in main()
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H A D | cusp.c | 39 AjPCod codon; in main() local 53 codon = ajCodNewCodenum(0); in main() 54 ajCodSetNameS(codon, ajFileGetPrintnameS(outf)); in main() 61 ajCodSetTripletsS(codon,substr,&ccnt); in main() 64 ajCodCalcUsage(codon,ccnt); in main() 66 ajCodSetDescC(codon, "CUSP codon usage file"); in main() 67 ajCodWrite(codon, outf); in main() 71 ajCodDel(&codon); in main()
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