Bundle Class Reference

The Bundle class keeps track of a group of targets that have shared ambiguous (multi-mapped) reads. More...

#include <bundles.h>

List of all members.

Public Member Functions
	Bundle (Target *targ)
	Bundle Constructor.
const Bundle *	get_rep () const
	A private method for returning the root of the merge tree that this bundle is a node in.
void	incr_counts (size_t incr_amt=1)
	A member function that increases the total bundle observed fragment counts by a given amount.
void	incr_mass (double incr_amt)
	A member function that increases the total bundle mass (logged) by a given amount.
void	reset_mass ()
	A member function that resets the Bundle mass to (log) 0.
size_t	size () const
	An accessor for the number of Targets in the bundle.
const std::vector< Target * > *	targets () const
	An accessor for a pointer to the vector of pointers to Targets in the bundle.
size_t	counts () const
	An accessor for the the total number of observed fragments mapped to targets in the bundle.
double	mass () const
	An accessor for the the total mass of observed fragments mapped to targets in the bundle (logged), including the initial pseudo-mass.
Friends
class	BundleTable

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Detailed Description

The Bundle class keeps track of a group of targets that have shared ambiguous (multi-mapped) reads.

Author:

Adam Roberts

Date:

2011 Artistic License 2.0

Definition at line 76 of file bundles.h.

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Constructor & Destructor Documentation

Bundle::Bundle

(

Target *

targ

)

Bundle Constructor.

Parameters:

targ	a pointer to the initial Target object in the bundle.

Definition at line 34 of file bundles.cpp.

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Member Function Documentation

size_t Bundle::counts

(

)

const

An accessor for the the total number of observed fragments mapped to targets in the bundle.

Returns:

The total number of fragments mapped to targets in the bundle.

Definition at line 72 of file bundles.cpp.

const Bundle* Bundle::get_rep

(

)

const

A private method for returning the root of the merge tree that this bundle is a node in.

Returns:

A pointer to the bundle at the root of the merge tree for this bundle.

void Bundle::incr_counts

(

size_t

incr_amt = 1

)

A member function that increases the total bundle observed fragment counts by a given amount.

Parameters:

incr_amt

the amount to increase the counts by.

Definition at line 49 of file bundles.cpp.

void Bundle::incr_mass

(

double

incr_amt

)

A member function that increases the total bundle mass (logged) by a given amount.

Parameters:

incr_amt

the amount to increase the mass by (logged).

Definition at line 58 of file bundles.cpp.

double Bundle::mass

(

)

const

An accessor for the the total mass of observed fragments mapped to targets in the bundle (logged), including the initial pseudo-mass.

Returns:

The total mass of fragments mapped to targets in the bundle.

Definition at line 80 of file bundles.cpp.

void Bundle::reset_mass

(

)

A member function that resets the Bundle mass to (log) 0.

Call is not passed on to _merged_into.

Definition at line 67 of file bundles.cpp.

size_t Bundle::size

(

)

const

An accessor for the number of Targets in the bundle.

Returns:

The number of Targets in the bundle.

Definition at line 41 of file bundles.cpp.

const std::vector<Target*>* Bundle::targets

(

)

const [inline]

An accessor for a pointer to the vector of pointers to Targets in the bundle.

The returned value does not outlive this.

Returns:

Pointer to the vector pointing to bundle Targets.

Definition at line 143 of file bundles.h.

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The documentation for this class was generated from the following files:

• src/bundles.h
• src/bundles.cpp