A collection class that each instance groups many SomaticEvents which share the same cell frequency. More...

#include <EventCluster.h>

Inheritance diagram for SubcloneSeeker::EventCluster:

Public Member Functions
	EventCluster ()

std::vector< SomaticEvent * >	members () const

double	cellFraction () const

void	setCellFraction (double fraction)

void	addEvent (SomaticEvent *event, bool updateFraction=true)

bool	operator< (const EventCluster &another) const

bool	operator> (const EventCluster &another) const

void	setSubcloneID (sqlite3_int64 cloneID)

sqlite3_int64	subcloneID ()

DBObjectID_vec	allObjectsOfSubclone (sqlite3 *database, sqlite3_int64 subcloneID)

Public Member Functions inherited from SubcloneSeeker::Archivable
	Archivable ()

sqlite3_int64	getId ()

void	setId (sqlite3_int64 nid)

bool	createTableInDB (sqlite3 *database)

sqlite3_int64	archiveObjectToDB (sqlite3 *database)

bool	unarchiveObjectFromDB (sqlite3 *database, sqlite3_int64 id)

DBObjectID_vec	vecAllObjectsID (sqlite3 *database)

Static Public Member Functions
static std::vector < EventCluster * >	clustering (const std::vector< SomaticEvent * > &events, double threshold)

Protected Member Functions
virtual std::string	getTableName ()

virtual std::string	createTableStatementStr ()

virtual std::string	createObjectStatementStr ()

virtual std::string	updateObjectStatementStr ()

virtual std::string	selectObjectColumnListStr ()

virtual int	bindObjectToStatement (sqlite3_stmt *statement)

virtual void	updateObjectFromStatement (sqlite3_stmt *statement)

Protected Attributes
std::vector< SomaticEvent * >	_members

double	_cellFraction

sqlite3_int64	ofSubcloneID

Protected Attributes inherited from SubcloneSeeker::Archivable
sqlite3_int64	id

Detailed Description

A collection class that each instance groups many SomaticEvents which share the same cell frequency.

Clustering is a process to group somatic events with (likely) the same into a single entity, based on the simplifying (but likely to be true) assumption that events with the same cell frequency are likely to co-exist in the same subclone

See also: SomaticEvent

Constructor & Destructor Documentation

SubcloneSeeker::EventCluster::EventCluster ( )

inline

Minimal constructor that resets all member variables

Member Function Documentation

void EventCluster::addEvent	(	SomaticEvent *	event,
		bool	updateFraction = `true`
	)

Add an SomaticEvent object into the member list and update cell fraction

Parameters

event	The event to be added as a member
updateFraction	Should the method automatically update the cell fraction of the cluster

DBObjectID_vec EventCluster::allObjectsOfSubclone	(	sqlite3 *	database,
		sqlite3_int64	subcloneID
	)

Retrieve a vector of cluster IDs whose parent subclone is the given id

Parameters

database	A live database connection
subcloneID	The subclone id who contains the clusters

Returns: a vector of cluster ids contained by the given subclone id

int EventCluster::bindObjectToStatement ( sqlite3_stmt * statement )

protectedvirtual

Bind archivable properties to a prepared, unbound sqlite3 statement

Parameters

statement A prepared, unbound sqlite3 statement instance

Returns: How many parameters are bound to the statement + 1

Implements SubcloneSeeker::Archivable.

double SubcloneSeeker::EventCluster::cellFraction ( ) const

inline

Retrieve the cell fraction

Returns: cell fraction centroid calculated from all members

std::vector< EventCluster * > EventCluster::clustering	(	const std::vector< SomaticEvent * > &	events,
		double	threshold
	)

static

SomaticEvent Clustering Algorithm

Parameters

events	A vector of SomaticEvent to be clustered
threshold	The difference threshold to use when doing the clustering

Returns: A vector of EventCluster containing the resulting clusters

std::string EventCluster::createObjectStatementStr ( )

protectedvirtual

return the unbound statement for record creation

Returns: unbound statement for record creation

Implements SubcloneSeeker::Archivable.

std::string EventCluster::createTableStatementStr ( )

protectedvirtual

return the table definition when creating the table in a sqlite3 database

Imagine a generic SQL create statement: CREATE TABLE <tableName> (id INTEGER NOT NULL PRIMARY KEY AUTOINCREMENT <other-columns>); Notice that the returned string must be prefixed with a comma ",", to separate any custom columns from the id column

Returns: The extra column definitions, prefixed with ","

Implements SubcloneSeeker::Archivable.

std::string EventCluster::getTableName ( )

protectedvirtual

returns the name of the table in which all object of a specific class are stored

Returns: Table name

Implements SubcloneSeeker::Archivable.

std::vector<SomaticEvent *> SubcloneSeeker::EventCluster::members ( ) const

inline

Retrieve the member vector reference

Returns: a reference to the members vector

bool SubcloneSeeker::EventCluster::operator< ( const EventCluster & another ) const

inline

Override the < operator for sorting purpose

Parameters

another the other EventCluster to compare to

Returns: true if this object has a smaller cell frequency than the other object, false if otherwise

bool SubcloneSeeker::EventCluster::operator> ( const EventCluster & another ) const

inline

Override the > operator for sorting purpose

Parameters

another the other EventCluster to compare to

Returns: true if this object has a greater cell frequency than the other object, false if otherwise

std::string EventCluster::selectObjectColumnListStr ( )

protectedvirtual

return the list of columns to be used in select statement for getting data from the database

Imagine the generic SQL select statement: SELECT <col1>, <col2>, ... FROM <tableName> WHERE id=?; The method should return the <col1>,<col2>,... part

Returns: the list of columns as string

Implements SubcloneSeeker::Archivable.

void SubcloneSeeker::EventCluster::setCellFraction ( double fraction )

inline

Set a new cell fraction

Parameters

fraction the new cell fraction

void SubcloneSeeker::EventCluster::setSubcloneID ( sqlite3_int64 cloneID )

inline

Set the subclone ID this cluster belongs to

Parameters

cloneID the database id of the subclone this cluster belongs to

sqlite3_int64 SubcloneSeeker::EventCluster::subcloneID ( )

inline

Retrieve the subclone ID

Returns: the subclone id this cluster belongs to

void EventCluster::updateObjectFromStatement ( sqlite3_stmt * statement )

protectedvirtual

Populate archivable properties from a prepared statement during unarchiving

Parameters

statement A prepared statement contains the retrieved row

Implements SubcloneSeeker::Archivable.

std::string EventCluster::updateObjectStatementStr ( )

protectedvirtual

return the unbound statement for record update

Returns: unbound statement for record update

Implements SubcloneSeeker::Archivable.

Member Data Documentation

double SubcloneSeeker::EventCluster::_cellFraction

protected

the cell fraction all members share

std::vector<SomaticEvent *> SubcloneSeeker::EventCluster::_members

protected

the vector that holds all the cluster's members

sqlite3_int64 SubcloneSeeker::EventCluster::ofSubcloneID

protected

to which subclone does this cluster belongs

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

src/EventCluster.h
src/EventCluster.cc

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation