treemerge_p.cc File Reference

#include "treemerge_p.h"
#include <assert.h>
#include <cmath>
#include <algorithm>
#include <iostream>
#include "SomaticEvent.h"
#include "SegmentalMutation.h"
#include "EventCluster.h"
#include "Subclone.h"

Classes
class	TreeMergeTraverseSecondary
	Traverse the secondary tree, and try to place every node it encounters onto the primary tree, which was given as a constructor parameter. More...

Macros
#define	MIN_CLONE_FRAC   0.05
#define	OUTPUT_SEV(sev)

Functions
SomaticEventPtr_vec	nodeEventsList (Subclone *node)
SomaticEventPtr_vec	SomaticEventDifference (const SomaticEventPtr_vec &master, const SomaticEventPtr_vec &unwanted)
bool	eventSetContains (const SomaticEventPtr_vec &v_container, const SomaticEventPtr_vec &v_containee)
bool	resultSetComparator (const SomaticEventPtr_vec &v1, const SomaticEventPtr_vec &v2)
SomaticEventPtr_vec	checkPlacement (Subclone *pnode, SomaticEventPtr_vec somaticEvents, bool *placeableOnSubtree, int *cp)
bool	TreeMerge (Subclone *p, Subclone *q)

Detailed Description

The implementation file for the implementation part of 'treemerge'

Author

Yi Qiao

Macro Definition Documentation

#define MIN_CLONE_FRAC   0.05

The minimal fraction a subclone has to have to be considered in the merging process

#define OUTPUT_SEV

(

sev

)

Value:

for(size_t output_sev_i=0; output_sev_i<(sev).size(); output_sev_i++) {     \
        std::cout<<dynamic_cast<CNV*>((sev)[output_sev_i])->range.chrom<<", ";  \
    }                                                                           \
    std::cout<<std::endl;

Print a SomaticEventPtr_vec that contains CNVs, for debugging propose

Function Documentation

SomaticEventPtr_vec checkPlacement	(	Subclone *	pnode,
		SomaticEventPtr_vec	somaticEvents,
		bool *	placeableOnSubtree,
		int *	cp = NULL
	)

Check if a node with certain somatic events can be placed on a subtree of a different subclonal structure.

Parameters

pnode	The root of a subtree of the subclonal structure, to which the new node is being placed on.
somaticEvents	The somatic events found in the new node, containing all its parents' ones.
placeableOnSubtree	An output boolean variable indicating whether the placement is successful or not.
cp	The number of children nodes that are able to contain the floating node. Used for debugging purpose.

Returns

A vector containing events not found on the subtree to the point the node is placed.

bool eventSetContains	(	const SomaticEventPtr_vec &	v_container,
		const SomaticEventPtr_vec &	v_containee
	)

Check if a somatic event vector contains all the events found in another vector.

Parameters

v_container	The container vector
v_containee	The containee vector

Returns

True if the container vector contains all the events found in the containee vector, false otherwise

SomaticEventPtr_vec nodeEventsList

(

Subclone *

node

)

Generate a list of events from a given subclone node. In the subclone data structure, events of a parent is not duplicated in the children nodes. This function will, from a given subclone node, trace back to the root of the tree, and returning all the events it encounters.

Parameters

node	The subclone node to generate event list from.

Returns

A vector of all the events explicitly or implicitly contained by the given node.

bool resultSetComparator	(	const SomaticEventPtr_vec &	v1,
		const SomaticEventPtr_vec &	v2
	)

Compare SomaticEvent vectors by size.

Parameters

v1	The first SomaticEventPtr vector
v2	The second SomaticEventPtr vector

Returns

True if v1 has less events than v2, false otherwise

SomaticEventPtr_vec SomaticEventDifference	(	const SomaticEventPtr_vec &	master,
		const SomaticEventPtr_vec &	unwanted
	)

Calculate the difference between two vectors of somatic events

Parameters

master	The somatic event vector that contains the wanted events
unwanted	The somatic event vector that contains the unwanted events

Returns

A somatic event vector that contains all the events in 'master' that are not found in 'unwanted'

bool TreeMerge	(	Subclone *	p,
		Subclone *	q
	)

Check if two subclonal trees are compatible.

Parameters

p	The first subclone tree
q	The second subclone tree

Returns

True if the two trees are compatible, false otherwise