gene.c File Reference

Class Gene. More...

#include "gene.h"
#include "misc.h"
#include "binary.h"
#include <string.h>
#include <stdlib.h>

Functions
Gene *	Gene_new (tipId_t tipId)
	Constructor for Gene. More...
void	Gene_tabulate (Gene *self, BranchTab *bt, int doSing)
	Tabulate branch lengths by tipId. More...
Gene *	Gene_join (Gene *lchild, Gene *rchild)
	Create a parental Gene by coalescing two children. More...
void	Gene_free (Gene *gene)
	Destroy a Gene.

Detailed Description

Class Gene.

Defines the objects that are linked together to form a gene genealogy.

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

Gene_join()

Gene * Gene_join	(	Gene *	lchild,
		Gene *	rchild
	)

Create a parental Gene by coalescing two children.

The tipId of the parental gene is generated by "or"ing those of the two children. The parental gene has pointers to the children, and the children have pointers to the parent.

Returns

pointer to parental gene.

References Gene_new().

Gene_new()

Gene * Gene_new

(

tipId_t

tipId

)

Constructor for Gene.

Parameters

[in]

tipId

the identifier of this gene

Referenced by Gene_join(), and PopNode_newSample().

Gene_tabulate()

void Gene_tabulate	(	Gene *	self,
		BranchTab *	bt,
		int	doSing
	)

Tabulate branch lengths by tipId.

Ignore root (which has null parent) because mutations there don't contribute to genetic variation.

If doSing==0, then also ignore nodes with only one descendant. These are recognizable because their tipIds are powers of 2.

Tabulate everything else.

References BranchTab_add(), and Gene_tabulate().

Referenced by Gene_tabulate().