| Bsoft 2.0.5 Bernard's software package

seq_util.h
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1
9 #include "Bstring.h"
10 #include "rwmolecule.h"
11
12 // Function prototypes
13 int seq_show(Bmolgroup* molgroup);
14 int seq_mass(Bmolgroup* molgroup);
15 vector<double> seq_elements(Bmolgroup* molgroup, Bstring& paramfile);
16 int seq_complement_all(Bmolgroup* molgroup);
17 int seq_translate_all(Bmolgroup* molgroup, int frame, Bstring& gcname);
18 long seq_find_dna(Bmolgroup* molgroup, Bstring& seq);
19 long seq_find_protein(Bmolgroup* molgroup, Bstring& seq);
20 Bstring seq_find_protein_in_dna(Bmolgroup* molgroup, Bstring& seq, int seqlenmin, int seqlenmax,
21 int side1, int side2, double threshold, Bstring& gcfile);
22 int getcode3(char c, char* cod);
23 char getcode1(char* acode);
24 int complement_sequence(Bstring& nucseq);
25 char get_complement(char nuc);
26 Bstring sequence_translate(Bstring& nucseq, long frame, Bstring& gencode);
27
seq_mass
int seq_mass(Bmolgroup *molgroup)
Shows the masses of all molecular sequences.
Definition: seq_util.cpp:131
sequence_translate
Bstring sequence_translate(Bstring &nucseq, long frame, Bstring &gencode)
Translates a nucleotide sequence to a protein sequence.
Definition: seq_util.cpp:593
seq_show
int seq_show(Bmolgroup *molgroup)
Shows all molecular sequences.
Definition: seq_util.cpp:81
getcode3
int getcode3(char c, char *cod)
Converts a one-letter amino acid designation to the three-letter equivalent.
Definition: seq_util.cpp:510
rwmolecule.h
Header file for reading reflection files.
Bmolgroup
Definition: rwmolecule.h:170
seq_find_protein
long seq_find_protein(Bmolgroup *molgroup, Bstring &seq)
Finds an amino acid sequence.
Definition: seq_util.cpp:356
seq_find_dna
long seq_find_dna(Bmolgroup *molgroup, Bstring &seq)
Finds a nucleotide sequence.
Definition: seq_util.cpp:314
seq_elements
vector< double > seq_elements(Bmolgroup *molgroup, Bstring &paramfile)
Shows the elemental composition of all molecular sequences.
Definition: seq_util.cpp:176
seq_complement_all
int seq_complement_all(Bmolgroup *molgroup)
Complements all nucleotide sequences.
Definition: seq_util.cpp:265
get_complement
char get_complement(char nuc)
Get the Watson-Crick complement of a nucleotide base.
Definition: seq_util.cpp:570
seq_find_protein_in_dna
Bstring seq_find_protein_in_dna(Bmolgroup *molgroup, Bstring &seq, int seqlenmin, int seqlenmax, int side1, int side2, double threshold, Bstring &gcfile)
Finds the coding region for an amino acid sequence.
Definition: seq_util.cpp:394
Bstring
Definition: Bstring.h:29
seq_translate_all
int seq_translate_all(Bmolgroup *molgroup, int frame, Bstring &gcname)
Translates all nucleotide sequences to protein sequences.
Definition: seq_util.cpp:289
Bstring.h
Header file for the string class.
getcode1
char getcode1(char *acode)
Converts a three-letter amino acid designation to the one-letter equivalent.
Definition: seq_util.cpp:531
complement_sequence
int complement_sequence(Bstring &nucseq)
Complements a nucleotide sequence in place.
Definition: seq_util.cpp:550