haplo_train.c File Reference

Trains a set of Y-STR haplotype label classifiers. More...

#include <config.h>
#include <stdlib.h>
#include <stdio.h>
#include <assert.h>
#include <string.h>
#include <errno.h>
#include <jwsc/base/error.h>
#include <jwsc/base/option.h>
#include <jwsc/vector/vector.h>
#include <jwsc/matrix/matrix.h>
#include <jwsc/matblock/matblock.h>
#include "haplo_groups.h"
#include "options.h"
#include "input.h"
#include "nb_freq.h"
#include "nb_gauss.h"
#include "nb_gmm.h"
#include "mv_gmm.h"
#include "mv_mmm.h"
#include "nearest.h"

Go to the source code of this file.

Defines
#define	NUM_SVM_OPTS   0
#define	NUM_WEKA_OPTS   0
#define	NUM_OPTS_NO_ARG   0 + NUM_SHARED_OPTS_NO_ARG
#define	NUM_OPTS_WITH_ARG   14 + NUM_SVM_OPTS + NUM_WEKA_OPTS + NUM_SHARED_OPTS_WITH_ARG
#define	LABEL_COL   1
#define	DATA_OUT_DIRNAME   0
Functions
uint32_t	get_num_opts_no_arg ()
	Returns the number of options not taking an argument.
uint32_t	get_num_opts_with_arg ()
	Returns the number of options taking an argument.
void	print_usage ()
	Prints the program usage to stderr.
Error *	process_data_out_dir_opt (Option_arg arg)
	Process the 'data-out-dir' program option.
static void	init_train_options (void)
	Initializes the haplo-train program options.
int	main (int argc, const char **argv)
	Main function for the haplo-train program.
Variables
Option_no_arg	opts_no_arg [NUM_OPTS_NO_ARG]
	Program options not taking an argument.
Option_with_arg	opts_with_arg [NUM_OPTS_WITH_ARG]
	Program options taking an argument.
const char *	data_out_dirname
	Director to put the generated training data.

---

Detailed Description

Trains a set of Y-STR haplotype label classifiers.

Author:

Joseph Schlecht

License:

Creative Commons BY-NC-SA 3.0

Classifier types include

1. Naive Bayes non-parametric marker frequency model
2. Naive Bayes Gaussian model
3. Naive Bayes Gaussian mixture model
4. Multivariate Gaussian mixture model
5. Multivariate multinomial mixture model
6. Support Vector Machines
7. Weka PART and J48
8. Nearest neighbor

Definition in file haplo_train.c.

---

Define Documentation

#define NUM_SVM_OPTS   0

Definition at line 260 of file haplo_train.c.

#define NUM_WEKA_OPTS   0

Definition at line 266 of file haplo_train.c.

#define NUM_OPTS_NO_ARG   0 + NUM_SHARED_OPTS_NO_ARG

Definition at line 269 of file haplo_train.c.

#define NUM_OPTS_WITH_ARG   14 + NUM_SVM_OPTS + NUM_WEKA_OPTS + NUM_SHARED_OPTS_WITH_ARG

Definition at line 270 of file haplo_train.c.

#define LABEL_COL   1

Definition at line 273 of file haplo_train.c.

#define DATA_OUT_DIRNAME   0

Definition at line 274 of file haplo_train.c.

---

Function Documentation

uint32_t get_num_opts_no_arg

(

)

Returns the number of options not taking an argument.

Definition at line 288 of file haplo_train.c.

uint32_t get_num_opts_with_arg

(

)

Returns the number of options taking an argument.

Definition at line 294 of file haplo_train.c.

void print_usage

(

void

)

Prints the program usage to stderr.

Definition at line 300 of file haplo_train.c.

Error* process_data_out_dir_opt

(

Option_arg

arg

)

Process the 'data-out-dir' program option.

Definition at line 308 of file haplo_train.c.

static void init_train_options

(

void

)

[static]

Initializes the haplo-train program options.

Definition at line 320 of file haplo_train.c.

int main	(	int	argc,
		const char **	argv
	)

Main function for the haplo-train program.

Definition at line 463 of file haplo_train.c.

---

Variable Documentation

Option_no_arg opts_no_arg[NUM_OPTS_NO_ARG]

Program options not taking an argument.

Definition at line 278 of file haplo_train.c.

Option_with_arg opts_with_arg[NUM_OPTS_WITH_ARG]

Program options taking an argument.

Definition at line 281 of file haplo_train.c.

const char* data_out_dirname

Director to put the generated training data.

Definition at line 284 of file haplo_train.c.