| Bsoft 2.0.5 Bernard's software package

seq_analysis.h
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1
9 #include "rwmolecule.h"
10 #include "rwresprop.h"
11 #include "rwimg.h"
12 #include "Complex.h"
13 #include "utilities.h"
14
15 // Function prototypes
16 Bimage* seq_aligned_identity(Bmolgroup* molgroup);
17 Bimage* seq_aligned_similarity(Bmolgroup* molgroup, double threshold, Bresidue_matrix* simat);
18 char* seq_aligned_profile(Bmolgroup* molgroup);
19 int seq_aligned_information(Bmolgroup* molgroup, int window, Bstring& psfile);
20 int seq_aligned_hydrophobicity(Bmolgroup* molgroup,
21 int window, double threshold, Bstring& hphobfile, Bstring& psfile);
22 Complex<float>* seq_frequency_analysis(int length, int win, int start, int end, double* data);
23 Bimage* seq_correlated_mutation(Bmolgroup* molgroup,
24 int refseqnum, double cutoff, Bstring& simfile);
rwresprop.h
Header file for reading residue property files.
seq_aligned_similarity
Bimage * seq_aligned_similarity(Bmolgroup *molgroup, double threshold, Bresidue_matrix *simat)
Calculates the pairwise similarities between aligned sequences.
Definition: seq_analysis.cpp:119
utilities.h
Header file for general utilities.
seq_correlated_mutation
Bimage * seq_correlated_mutation(Bmolgroup *molgroup, int refseqnum, double cutoff, Bstring &simfile)
Correlated mutation analysis of an alignment.
Definition: seq_analysis.cpp:676
Complex.h
Class for complex numbers.
seq_aligned_profile
char * seq_aligned_profile(Bmolgroup *molgroup)
Generates a PROSITE format profile from an aligned set of sequences.
Definition: seq_analysis.cpp:197
Bimage
General image parameter class.
Definition: Bimage.h:163
rwmolecule.h
Header file for reading reflection files.
Bmolgroup
Definition: rwmolecule.h:170
seq_aligned_hydrophobicity
int seq_aligned_hydrophobicity(Bmolgroup *molgroup, int window, double threshold, Bstring &hphobfile, Bstring &psfile)
Calculates the average hydrophobicity at every position in an alignment.
Definition: seq_analysis.cpp:456
length
double length(vector< T > v)
Definition: Vector3.h:528
seq_aligned_identity
Bimage * seq_aligned_identity(Bmolgroup *molgroup)
Calculates the pairwise identities between aligned sequences.
Definition: seq_analysis.cpp:43
seq_aligned_information
int seq_aligned_information(Bmolgroup *molgroup, int window, Bstring &psfile)
Calculates the sequence logo representation for an alignment.
Definition: seq_analysis.cpp:302
Bresidue_matrix
Definition: rwresprop.h:44
seq_frequency_analysis
Complex< float > * seq_frequency_analysis(int length, int win, int start, int end, double *data)
Fourier transforms a vector for frequency analysis.
Definition: seq_analysis.cpp:596
Complex
Definition: Complex.h:23
Bstring
Definition: Bstring.h:29
rwimg.h
Header file for 2D and 3D image I/O.