haplo_groups.h File Reference

Provides a mapping between haplo groups and their sequential ordering. More...

#include <config.h>
#include <stdlib.h>
#include <inttypes.h>
#include <jwsc/base/error.h>
#include <jwsc/vector/vector.h>

Go to the source code of this file.

Enumerations
enum	Haplo_ancestor_type { HAPLO_ANCESTOR_NONE = 0, HAPLO_ANCESTOR_DIRECT, HAPLO_ANCESTOR_INDIRECT }
	Type of ancestry relating two haplo groups. More...
Functions
Error *	read_haplo_groups (const char *fname)
	Reads the haplo groups from a file.
Error *	lookup_haplo_group_index_from_label (uint32_t *index_out, const char *label)
	Looks up the index for a haplo group based on its label.
Error *	lookup_haplo_group_label_from_index (const char **label_out, uint32_t index)
	Looks up a haplo group label from its index.
Error *	lookup_haplo_group_ancestor_index_from_haplo_group_index (uint32_t *index_out, uint32_t index)
	Looks up the index of the immediate ancestor for the haplogroup specified by the index.
uint32_t	get_num_haplo_groups ()
	Returns the number of haplo groups represented.
uint8_t	is_ancestor (uint32_t index_1, uint32_t index_2)
	Returns whether a haplo group label is an ancestor of another.
Haplo_ancestor_type	find_ancestor_index_of_pair (uint32_t *index_out, uint32_t index_1, uint32_t index_2)
	Finds the lowest common ancestor between two haplo group labels.
Haplo_ancestor_type	find_ancestor_index_of_set (uint32_t *index_out, const Vector_u32 *indices)
	Finds the lowest common ancestor between a set of haplo group labels.

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Detailed Description

Provides a mapping between haplo groups and their sequential ordering.

Author:

Joseph Schlecht

License:

Creative Commons BY-NC-SA 3.0

Definition in file haplo_groups.h.

---

Enumeration Type Documentation

enum Haplo_ancestor_type

Type of ancestry relating two haplo groups.

Enumerator:

HAPLO_ANCESTOR_NONE
HAPLO_ANCESTOR_DIRECT
HAPLO_ANCESTOR_INDIRECT

Definition at line 60 of file haplo_groups.h.

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Function Documentation

Error* read_haplo_groups

(

const char *

fname

)

Reads the haplo groups from a file.

The file is expected to be a valid xml document according to haplo.dtd.

Parameters:

fname

File to read the haplo groups from.

Returns:

On success, NULL is returned; otherwise an Error is returned.

Definition at line 324 of file haplo_groups.c.

Error* lookup_haplo_group_index_from_label	(	uint32_t *	index_out,
		const char *	label
	)

Looks up the index for a haplo group based on its label.

Parameters:

index_out	Result parameter.
label	Haplo group label to look-up the sequential index for.

Returns:

On success, NULL is returned; otherwise an Error is returned.

Definition at line 384 of file haplo_groups.c.

Error* lookup_haplo_group_label_from_index	(	const char **	label_out,
		uint32_t	index
	)

Looks up a haplo group label from its index.

Parameters:

label_out	Result parameter.
index	Index representing one of the haplo groups.

Returns:

On success, NULL is returned; otherwise an Error is returned.

Definition at line 414 of file haplo_groups.c.

Error* lookup_haplo_group_ancestor_index_from_haplo_group_index	(	uint32_t *	index_out,
		uint32_t	index
	)

Looks up the index of the immediate ancestor for the haplogroup specified by the index.

Definition at line 440 of file haplo_groups.c.

uint32_t get_num_haplo_groups

(

)

Returns the number of haplo groups represented.

Returns:

The number of haplo groups represented.

Definition at line 484 of file haplo_groups.c.

uint8_t is_ancestor	(	uint32_t	index_1,
		uint32_t	index_2
	)

Returns whether a haplo group label is an ancestor of another.

Parameters:

index_1	Index whose ancestors are to be searched.
index_2	Index to test if it is an ancestor of index_1.

Returns:

If index_2 is an ancestor of index_1, 1 is returned; otherwise 0.

Definition at line 594 of file haplo_groups.c.

Haplo_ancestor_type find_ancestor_index_of_pair	(	uint32_t *	index_out,
		uint32_t	index_1,
		uint32_t	index_2
	)

Finds the lowest common ancestor between two haplo group labels.

Parameters:

index_out	Result parameter.
index_1	Index of haplo label to find the common ancestor of.
index_2	Index of haplo label to find the common ancestor of.

Returns:

A value of Haplo_ancestor_type.

Definition at line 608 of file haplo_groups.c.

Haplo_ancestor_type find_ancestor_index_of_set	(	uint32_t *	index_out,
		const Vector_u32 *	indices
	)

Finds the lowest common ancestor between a set of haplo group labels.

Parameters:

index_out	Result parameter.
indices	Set of indices to find the common ancestor of.

Returns:

A value of Haplo_ancestor_type.

Definition at line 639 of file haplo_groups.c.