SubcloneSeeker::SomaticEvent Class Reference

Abstract data structure class that represents any type of somatic mutation. More...

#include <SomaticEvent.h>

Inheritance diagram for SubcloneSeeker::SomaticEvent:

Public Member Functions
	SomaticEvent ()
void	setClusterID (sqlite3_int64 clusterID)
virtual bool	isEqualTo (SomaticEvent *anotherEvent, unsigned long resolution=10000L)
sqlite3_int64	clusterID ()
virtual DBObjectID_vec	allObjectsOfCluster (sqlite3 *database, sqlite3_int64 clusterID)
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)

Public Attributes
double	frequency

Protected Member Functions
virtual std::string	createTableStatementStr ()
Protected Member Functions inherited from SubcloneSeeker::Archivable
virtual std::string	getTableName ()=0
virtual std::string	createObjectStatementStr ()=0
virtual std::string	updateObjectStatementStr ()=0
virtual std::string	selectObjectColumnListStr ()=0
virtual int	bindObjectToStatement (sqlite3_stmt *statement)=0
virtual void	updateObjectFromStatement (sqlite3_stmt *statement)=0

Protected Attributes
sqlite3_int64	ofClusterID
Protected Attributes inherited from SubcloneSeeker::Archivable
sqlite3_int64	id

Detailed Description

Abstract data structure class that represents any type of somatic mutation.

The most important aspect of the mutations represented by this class is that it has an cell frequency associated, which describes in what fraction of the cells does this specific event exist

Constructor & Destructor Documentation

SubcloneSeeker::SomaticEvent::SomaticEvent ( )

inline

minimal constructor to reset member variables

Member Function Documentation

DBObjectID_vec SomaticEvent::allObjectsOfCluster ( sqlite3 *  database, sqlite3_int64  clusterID  )

virtual

Return all objects with the given cluster id as their parent

Returns

a vector of objectIDs (whose type depends on concrete class)

sqlite3_int64 SubcloneSeeker::SomaticEvent::clusterID ( )

inline

Retrieve cluster id this event belongs to

Returns

the cluster id

std::string SomaticEvent::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.

virtual bool SubcloneSeeker::SomaticEvent::isEqualTo ( SomaticEvent *  anotherEvent, unsigned long  resolution = 10000L  )

inlinevirtual

Check equality

Parameters

anotherEvent	The other SomaticEvent object to compare to
resolution	The boundry resolution with respect to chromosome location

Returns

whether two SomaticEvent objects are representing the same event

Reimplemented in SubcloneSeeker::CNV.

void SubcloneSeeker::SomaticEvent::setClusterID ( sqlite3_int64  clusterID )

inline

Set the cluster's database id to which this event belongs

Parameters

clusterID

The cluster's database record id

Member Data Documentation

double SubcloneSeeker::SomaticEvent::frequency

Cell frequency

sqlite3_int64 SubcloneSeeker::SomaticEvent::ofClusterID

protected

to which cluster in database does this event belongs

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

• src/SomaticEvent.h
• src/SomaticEvent.cc