/dports/biology/mmseqs2/MMseqs2-13-45111/src/commons/ |
H A D | MultiParam.cpp | 9 this->nucleotides = nucleotides; in MultiParam() 16 return SSTR(multiparam.nucleotides); in format() 27 nucleotides = INT_MAX; in MultiParam() 33 nucleotides = INT_MAX; in MultiParam() 37 nucleotides = aminoacids; in MultiParam() 46 nucleotides = FLT_MAX; in MultiParam() 52 nucleotides = FLT_MAX; in MultiParam() 56 nucleotides = aminoacids; in MultiParam() 67 this->nucleotides = strdup(nucleotides); in MultiParam() 93 free(nucleotides); in ~MultiParam() [all …]
|
H A D | MultiParam.h | 19 T nucleotides; variable 21 MultiParam(T aminoacids, T nucleotides); 28 nucleotides = value; 39 char* nucleotides; variable 41 MultiParam(const char* aminoacids, const char* nucleotides); 44 nucleotides = strdup(par.nucleotides); in MultiParam() 59 if (nucleotides != NULL) { 60 free(nucleotides); 65 nucleotides = strdup(other.nucleotides);
|
/dports/biology/gmap/gmap-2020-09-12/src/ |
H A D | maxent.c | 99027 if (nucleotides[i] > 0x3) { in hashseq_nucleotides() 99029 i,nucleotides[i],length); in hashseq_nucleotides() 99033 sum = sum*4 + nucleotides[i]; in hashseq_nucleotides() 99104 if (nucleotides[i] > 0x3) { in hashseq_skip_nucleotides() 99106 i,nucleotides[i],length1); in hashseq_skip_nucleotides() 99110 sum = sum*4 + nucleotides[i]; in hashseq_skip_nucleotides() 99115 if (nucleotides[i] > 0x3) { in hashseq_skip_nucleotides() 99117 ,i,nucleotides[i],length2); in hashseq_skip_nucleotides() 99121 sum = sum*4 + nucleotides[i]; in hashseq_skip_nucleotides() 99250 i = nucleotides[DONOR_MODEL_LEFT_MARGIN]*4 + nucleotides[DONOR_MODEL_LEFT_MARGIN + 1]; in score_donor_dinucleotide_nucleotides() [all …]
|
H A D | maxent.h | 17 Maxent_donor_prob_nucleotides (unsigned char *nucleotides); 21 Maxent_donor_logodds_nucleotides (unsigned char *nucleotides); 28 Maxent_acceptor_prob_nucleotides (unsigned char *nucleotides); 32 Maxent_acceptor_logodds_nucleotides (unsigned char *nucleotides);
|
H A D | genome.c | 502 static const char *nucleotides[65536] = variable 9068 memcpy(Buffer,nucleotides[low & 0x0000FFFF],8); in Genome_uncompress_mmap() 9069 memcpy(&(Buffer[8]),nucleotides[low >> 16],8); in Genome_uncompress_mmap() 9071 memcpy(&(Buffer[24]),nucleotides[high >> 16],8); in Genome_uncompress_mmap() 9091 memcpy(Buffer,nucleotides[low & 0x0000FFFF],8); in Genome_uncompress_mmap() 9092 memcpy(&(Buffer[8]),nucleotides[low >> 16],8); in Genome_uncompress_mmap() 9094 memcpy(&(Buffer[24]),nucleotides[high >> 16],8); in Genome_uncompress_mmap() 9187 memcpy(Buffer,nucleotides[low & 0x0000FFFF],8); in Genome_uncompress_memory() 9188 memcpy(&(Buffer[8]),nucleotides[low >> 16],8); in Genome_uncompress_memory() 9210 memcpy(Buffer,nucleotides[low & 0x0000FFFF],8); in Genome_uncompress_memory() [all …]
|
/dports/biology/viennarna/ViennaRNA-2.4.18/src/ViennaRNA/ |
H A D | sequence.c | 69 vc->nucleotides = (vrna_seq_t *)vrna_realloc(vc->nucleotides, in vrna_sequence_add() 72 set_sequence(&(vc->nucleotides[vc->strands]), in vrna_sequence_add() 86 vc->nucleotides[vc->strands - 1].string, in vrna_sequence_add() 298 memmove(vc->nucleotides + i, vc->nucleotides + i + 1, sizeof(vrna_seq_t) * size); in vrna_sequence_remove() 301 vc->nucleotides = in vrna_sequence_remove() 322 free(fc->nucleotides); in vrna_sequence_remove_all() 323 fc->nucleotides = NULL; in vrna_sequence_remove_all() 407 fc->nucleotides = (vrna_seq_t *)vrna_realloc(fc->nucleotides, in vrna_sequence_prepare() 409 fc->nucleotides[0].string = NULL; in vrna_sequence_prepare() 411 fc->nucleotides[0].length = fc->length; in vrna_sequence_prepare() [all …]
|
/dports/biology/fastx-toolkit/fastx_toolkit-0.0.14/src/fastx_trimmer/ |
H A D | fastx_trimmer.c | 123 fastx.nucleotides[keep_last_base] = 0 ; in main() 127 if ( strlen(fastx.nucleotides) < (size_t)keep_first_base ) //sequence too short - remove it in main() 129 for (i=0; i < strlen(fastx.nucleotides)-keep_first_base+1 ; i++) { in main() 130 fastx.nucleotides[i] = fastx.nucleotides[i+keep_first_base-1]; in main() 133 fastx.nucleotides[i] = 0 ; in main() 137 if (strlen(fastx.nucleotides) <= trim_last_bases) in main() 139 i = strlen(fastx.nucleotides) - trim_last_bases; in main() 142 fastx.nucleotides[i] = 0; in main()
|
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/sequences/ |
H A D | assignment_3_solution.cpp | 9 String<Dna5> nucleotides = "AGTCGTGNNANCT"; in main() local 13 for (unsigned i = 0; i < length(nucleotides); ++i){ in main() 14 if (nucleotides[i] < 'G') in main() 15 appendValue(lesser, nucleotides[i]); in main() 16 else if (nucleotides[i] > 'G') in main() 17 appendValue(greater, nucleotides[i]); in main()
|
H A D | assignment_3.cpp | 9 String<Dna5> nucleotides = "AGTCGTGNNANCT"; in main() local 13 for (unsigned i = 0; i < length(nucleotides); ++i) in main() 15 appendValue(selected, nucleotides[i]); in main()
|
H A D | assignment_3_solution.cpp.stdout | 1 Lesser nucleotides: ACAC 2 Greater nucleotides: TTNNNT
|
/dports/biology/fastx-toolkit/fastx_toolkit-0.0.14/src/fastx_reverse_complement/ |
H A D | fastx_reverse_complement.c | 77 int length = strlen(pFASTX->nucleotides); in reverse_complement_fastx() 83 pFASTX->nucleotides[i] = reverse_complement_base ( pFASTX->nucleotides[i] ) ; in reverse_complement_fastx() 89 temp_nuc = pFASTX->nucleotides[i] ; in reverse_complement_fastx() 90 pFASTX->nucleotides[i] = pFASTX->nucleotides[j] ; in reverse_complement_fastx() 91 pFASTX->nucleotides[j] = temp_nuc; in reverse_complement_fastx()
|
/dports/biology/py-biopython/biopython-1.79/Bio/SeqIO/ |
H A D | NibIO.py | 114 nucleotides = indices.translate(table) 115 sequence = Seq(nucleotides) 149 nucleotides = bytes(sequence) 155 nucleotides += suffix 156 if not set(nucleotides).issubset(b"ACGTNacgtn"): 158 indices = nucleotides.translate(table)
|
/dports/biology/fastx-toolkit/fastx_toolkit-0.0.14/src/libfastx/ |
H A D | fastx.c | 122 if (strlen(ascii_quality_scores) != strlen(pFASTX->nucleotides)) in convert_ascii_quality_score_line() 124 strlen(ascii_quality_scores), strlen(pFASTX->nucleotides), in convert_ascii_quality_score_line() 163 if (index != strlen(pFASTX->nucleotides)) { in convert_numeric_quality_score_line() 165 index, strlen(pFASTX->nucleotides), pFASTX->input_line_number ); in convert_numeric_quality_score_line() 354 if (fgets(pFASTX->nucleotides, MAX_SEQ_LINE_LENGTH, pFASTX->input) == NULL) in fastx_read_next_record() 358 chomp(pFASTX->nucleotides); in fastx_read_next_record() 361 if (strlen(pFASTX->nucleotides)==0) in fastx_read_next_record() 366 pFASTX->nucleotides,pFASTX->input_line_number); in fastx_read_next_record() 382 if (strlen(temp_qual) == strlen(pFASTX->nucleotides)) { in fastx_read_next_record() 455 rc = fprintf(pFASTX->output, "%s\n", pFASTX->nucleotides); in fastx_write_record() [all …]
|
/dports/biology/fastx-toolkit/fastx_toolkit-0.0.14/src/fasta_nucleotide_changer/ |
H A D | fasta_nucleotide_changer.c | 103 for (i=0; i < strlen(fastx.nucleotides) ; i++) { in main() 104 if ( fastx.nucleotides[i] == nuc_to ) { in main() 108 if ( fastx.nucleotides[i] == nuc_from ) { in main() 109 fastx.nucleotides[i] = nuc_to ; in main()
|
/dports/biology/fastx-toolkit/fastx_toolkit-0.0.14/src/fastx_clipper/ |
H A D | fastx_clipper.cpp | 262 std::string query = std::string(fastx.nucleotides) + std::string( strlen(adapter), 'N' ); in main() 263 std::string target= std::string( strlen(fastx.nucleotides), 'N' ) + std::string(adapter); in main() 265 std::string query = std::string(fastx.nucleotides) ; in main() 285 fastx.nucleotides[i] = 0 ; in main() 296 if (strlen(fastx.nucleotides) < min_length) { // too-short sequence ? in main() 311 …if ( (discard_unknown_bases && strchr(fastx.nucleotides,'N')!=NULL ) ) { // contains unknown bases… in main()
|
/dports/biology/fastx-toolkit/fastx_toolkit-0.0.14/src/fastx_artifacts_filter/ |
H A D | fastx_artifacts_filter.c | 70 if (fastx->nucleotides[i]==0) in artifact_sequence() 74 switch(fastx->nucleotides[i]) in artifact_sequence() 93 __LINE__, fastx->nucleotides[i], i ) ; in artifact_sequence()
|
/dports/biology/emboss/EMBOSS-6.6.0/emboss/acd/ |
H A D | fuzznuc.acd | 27 help: "The standard IUPAC one-letter codes for the nucleotides are 31 Ambiguities are indicated by listing the acceptable nucleotides 35 brackets '{ }' the nucleotides that are not accepted at a given 36 position. For example: {AG} stands for any nucleotides except A
|
/dports/biology/viennarna/ViennaRNA-2.4.18/tests/data/ |
H A D | rnafold_hc.cmds | 4 # Force the first 3 nucleotides to be paired 7 # Prohibit nucleotides 6 to 15 from base pairing
|
/dports/biology/viennarna/ViennaRNA-2.4.18/doc/latex/ |
H A D | group__struct__utils__wuss.tex | 13 This notation allows for a fine-\/grained annotation of base pairs and unpaired nucleotides, includ… 18 …Unpaired nucleotides that constitute the hairpin loop are indicated by underscores, {\ttfamily \+\… 26 Unpaired nucleotides in multibranch loops are indicated by commas {\ttfamily ,}. 30 …Single stranded nucleotides in the exterior loop, i.\+e. not enclosed by any other pair are denote… 40 …tions usually ignore pseudo-\/knots entirely treating them as unpaired nucleotides, if not stated … 74 …reats pseudo-\/knots annotated by matching pairs of upper/lowercase letters as unpaired nucleotides
|
/dports/biology/fastx-toolkit/fastx_toolkit-0.0.14/src/fastq_quality_filter/ |
H A D | fastq_quality_filter.c | 118 for (i=0; i< strlen(fastx->nucleotides); i++) { in get_percentile_quality() 143 fprintf(stderr, "%s\n", fastx.nucleotides ) ; in main() 144 for (i=0; i<strlen(fastx.nucleotides); i++) { in main()
|
/dports/biology/vsearch/vsearch-2.17.1/src/ |
H A D | db.cc | 68 static uint64_t nucleotides = 0; variable 85 nucleotides = new_nucleotides; in db_setinfo() 133 nucleotides = 0; in db_read() 232 nucleotides += sequencelength; in db_read() 363 return nucleotides; in db_getnucleotidecount()
|
/dports/science/lammps/lammps-stable_29Sep2021/src/CG-DNA/ |
H A D | README.md | 77 pair_oxdna_excv.cpp: excluded volume interaction between the nucleotides 79 pair_oxdna_stk.cpp: stacking interaction between consecutive nucleotides 83 nucleotides on different strands, e.g. A-T and C-G 85 pair_oxdna_xstk.cpp: cross-stacking interaction between nucleotides 87 pair_oxdna_coaxstk.cpp: coaxial stacking interaction between nucleotides
|
/dports/biology/mothur/mothur-1.46.1/source/clearcut/ |
H A D | distclearcut.cpp | 386 long int nucleotides; in NJ_DNA_k2p_correction() local 401 NJ_DNA_count_tt(alignment, i, j, &transitions, &transversions, &nucleotides); in NJ_DNA_k2p_correction() 403 if(!nucleotides) { /* sequences have no non-ambiguous overlap in alignment */ in NJ_DNA_k2p_correction() 407 P = (float)transitions / (float)nucleotides; in NJ_DNA_k2p_correction() 408 Q = (float)transversions / (float)nucleotides; in NJ_DNA_k2p_correction()
|
/dports/biology/fastx-toolkit/fastx_toolkit-0.0.14/src/fastx_renamer/ |
H A D | fastx_renamer.c | 92 strncpy(fastx.name, fastx.nucleotides, sizeof(fastx.name)); in main() 93 strncpy(fastx.name2, fastx.nucleotides, sizeof(fastx.name2)); in main()
|
/dports/biology/viennarna/ViennaRNA-2.4.18/doc/refman.include/ |
H A D | io_formats.dox | 134 For particular nucleotides that are forced to pair, the following @p [ORIENTATION] flags 142 Sequence positions of nucleotides/base pairs are @f$ 1- @f$ based and consist of three 153 Enforces the set of @f$ k @f$ consecutive nucleotides starting at 165 Prohibit a set of @f$ k @f$ consecutive nucleotides to participate 167 @p [WHERE] allows to force the nucleotides to appear within the loop of 175 -# @b "Prohibiting two ranges of nucleotides to pair with each other":\n 184 …This command enforces nucleotides to be unpaired similar to @em prohibiting nucleotides to be pair… 185 as described above. It too marks the corresponding nucleotides to be unpaired, however, 186 the @p [WHERE] flag can be used to enforce specfic loop types the nucleotides must appear in. 212 consecutive nucleotides, starting at position @f$ i @f$. The pseudo free energy is [all …]
|