| Bsoft 2.0.5 Bernard's software package

seq_align.h
Go to the documentation of this file.
1
9 #include "rwmolecule.h"
10 #include "rwresprop.h"
11 #include "Matrix.h"
12
13 // Function prototypes
14 long seq_pair_align(Bmolecule* mol1, Bmolecule* mol2, double gapopen,
15 double gapextend, Bresidue_matrix* simat);
16 int seq_find_best_offset(Bmolecule* mol1, Bmolecule* mol2,
17 long& nres, Bresidue_matrix* simat);
18 Matrix seq_dot_plot(Bmolecule* mol1, Bmolecule* mol2, Bresidue_matrix* simat);
19 Matrix seq_dot_plot_mov_avg(Matrix dot_plot, int window);
20 int seq_dot_plot_interpret(Matrix dot_plot);
21 double seq_dot_plot_best_segments(Matrix dot_plot);
22 int seq_show_segments(Bmolecule* mol1, Bmolecule* mol2, double threshold, Matrix dot_plot);
23
seq_dot_plot_mov_avg
Matrix seq_dot_plot_mov_avg(Matrix dot_plot, int window)
Calculates a moving average along the diagonals of a dot plot.
Definition: seq_align.cpp:168
rwresprop.h
Header file for reading residue property files.
seq_dot_plot_best_segments
double seq_dot_plot_best_segments(Matrix dot_plot)
Finding the best segments in a dot plot.
Definition: seq_align.cpp:265
Matrix.h
Generalized matrix class.
seq_dot_plot
Matrix seq_dot_plot(Bmolecule *mol1, Bmolecule *mol2, Bresidue_matrix *simat)
Calculates a dot plot for two sequences.
Definition: seq_align.cpp:137
seq_find_best_offset
int seq_find_best_offset(Bmolecule *mol1, Bmolecule *mol2, long &nres, Bresidue_matrix *simat)
Finds the best offset for aligning two sequences without gaps.
Definition: seq_align.cpp:94
rwmolecule.h
Header file for reading reflection files.
seq_dot_plot_interpret
int seq_dot_plot_interpret(Matrix dot_plot)
Finds the row and column maxima in a dot plot.
Definition: seq_align.cpp:214
seq_pair_align
long seq_pair_align(Bmolecule *mol1, Bmolecule *mol2, double gapopen, double gapextend, Bresidue_matrix *simat)
Aligns two sequences.
Definition: seq_align.cpp:34
Bresidue_matrix
Definition: rwresprop.h:44
Bmolecule
Definition: rwmolecule.h:107
Matrix
Definition: Matrix.h:21
seq_show_segments
int seq_show_segments(Bmolecule *mol1, Bmolecule *mol2, double threshold, Matrix dot_plot)
Finds the best offset for aligning two sequences without gaps.
Definition: seq_align.cpp:324