An index of sample labels. More...

#include "error.h"
#include "lblndx.h"
#include "misc.h"
#include "strdblqueue.h"
#include <stdio.h>
#include <string.h>
#include <assert.h>

Functions
int	comparePtrs (const void void_x, const void void_y)
	Compare pointers to pointers to two tipId_t values. More...

tipId_t	LblNdx_getTipId_1 (const LblNdx self, const char lbl)

static int	make_map (size_t n, int map[n], tipId_t collapse)

static void	make_rm_map (size_t n, int map[n], tipId_t remove)

void	LblNdx_init (LblNdx *self)
	Set everything to zero.

void	LblNdx_addSamples (LblNdx self, unsigned nsamples, const char lbl)
	Add samples for a single population. More...

const char *	LblNdx_lbl (const LblNdx *self, unsigned i)
	Return the label associated with index i.

unsigned	LblNdx_size (const LblNdx *self)
	Return number of samples, which equals number of labels.

void	LblNdx_sanityCheck (const LblNdx self, const char file, int line)

int	LblNdx_equals (const LblNdx lhs, const LblNdx rhs)
	Return 1 if the two arguments are equal; 0 otherwise.

tipId_t	LblNdx_getTipId (const LblNdx self, const char lbl)
	Reverse lookup. More...

void	LblNdx_print (const LblNdx self, FILE fp)
	Print a LblNdx.

char *	patLbl (size_t n, char buff[n], tipId_t tid, const LblNdx *lblndx)
	Generate a label for site pattern tid. More...

int	compare_tipId (const void void_x, const void void_y)
	Compare pointers to two tipId_t values. More...

void	orderpat (int n, unsigned ord[n], tipId_t pat[n])
	On entry, pat is an array of n tipId_t values. More...

int	LblNdx_collapse (LblNdx self, tipId_t collapse, const char lbl)
	Reduce dimension of LblNdx object by collapsing several entries into a single entry. More...

int	LblNdx_rmPops (LblNdx *self, tipId_t remove)

int	LblNdx_from_StrDblQueue (LblNdx lndx, StrDblQueue queue)
	Initialize a pre-allocated LblNdx from a StrDblQueue. More...

Detailed Description

An index of sample labels.

Author: Alan R. Rogers

Copyright: Copyright (c) 2016, Alan R. Rogers roger.nosp@m.s@an.nosp@m.thro..nosp@m.utah.nosp@m..edu. This file is released under the Internet Systems Consortium License, which can be found in file "LICENSE".

Function Documentation

◆ compare_tipId()

int compare_tipId	(	const void *	void_x,
		const void *	void_y
	)

Compare pointers to two tipId_t values.

Parameters

void_x,void_y pointers to tipId_t values

Returns: <0, 0, or >0 depending on whether the first arg is <, ==, or > the second.

References num1bits().

◆ comparePtrs()

int comparePtrs	(	const void *	void_x,
		const void *	void_y
	)

Compare pointers to pointers to two tipId_t values.

Parameters

void_x,void_y pointers to pointers to tipId_t values

Returns: <0, 0, or >0 depending on whether the first arg is <, ==, or > the second.

References num1bits().

◆ LblNdx_addSamples()

void LblNdx_addSamples	(	LblNdx *	self,
		unsigned	nsamples,
		const char *	lbl
	)

Add samples for a single population.

Should be called once for each sampled population.

Referenced by LblNdx_from_StrDblQueue(), and parseSegment().

◆ LblNdx_collapse()

int LblNdx_collapse	(	LblNdx *	self,
		tipId_t	collapse,
		const char *	lbl
	)

Reduce dimension of LblNdx object by collapsing several entries into a single entry.

The "on" bits of "collapse" indicate the entries to be collapsed. they are collapsed into the entry indicated by the bit in the lowest position. "lbl" is the label assigned to this entry. The dimension of the rewritten LblNdx object is reduced by one less than the number of "on" bits in "collapse". The function returns 0 on success, EDOM if the number of "on" bits in "collapse" exceeds self->n, and BUFFER_OVERFLOW if any of the write operations would overflow.

◆ LblNdx_from_StrDblQueue()

int LblNdx_from_StrDblQueue	(	LblNdx *	lndx,
		StrDblQueue *	queue
	)

Initialize a pre-allocated LblNdx from a StrDblQueue.

On input, each entry of the StrDblQueue refers to a single site pattern. The string in each entry should be of form "a:b:c", where the colons separate fields, and each field is the label of a sample. On return, lndx contains all these labels, indexed in their order of appearance with the queue.

References LblNdx_addSamples(), and LblNdx_getTipId().

◆ LblNdx_getTipId()

tipId_t LblNdx_getTipId	(	const LblNdx *	self,
		const char *	lbl
	)

Reverse lookup.

Return tipId_t value corresponding to label, which may be composite. The parts of a composite label are delimited by the ':' character. If label (or any of its parts) is not present in LblNdx, return 0.

Referenced by BranchTab_from_StrDblQueue(), and LblNdx_from_StrDblQueue().

◆ orderpat()

void orderpat	(	int	n,
		unsigned	ord[n],
		tipId_t	pat[n]
	)

On entry, pat is an array of n tipId_t values.

On return, ord[0] is the index of the first value, ord[1] is that of the 2nd, and so on.

◆ patLbl()

char * patLbl	(	size_t	n,
		char	buff[n],
		tipId_t	tid,
		const LblNdx *	lblndx
	)

Generate a label for site pattern tid.

Label goes into buff. Function returns a pointer to buff;

Functions