The class that represents a subclone in a subclonal structure tree. More...

#include <Subclone.h>

Inheritance diagram for SubcloneSeeker::Subclone:

Public Member Functions
	Subclone ()

void	setParentId (sqlite3_int64 pid)

double	fraction () const

void	setFraction (double fraction)

double	treeFraction () const

void	setTreeFraction (double fraction)

std::vector< EventCluster * > &	vecEventCluster ()

void	addEventCluster (EventCluster *cluster)

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

virtual	~TreeNode ()

TreeNodeVec_t &	getVecChildren ()

TreeNode *	getParent ()

void	addChild (TreeNode *child)

void	removeChild (TreeNode *child)

bool	isLeaf () const

bool	isRoot () const

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)

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
double	_fraction

double	_treeFraction

std::vector< EventCluster * >	_eventClusters

sqlite3_int64	parentId

Protected Attributes inherited from SubcloneSeeker::TreeNode
TreeNodeVec_t	children

TreeNode *	parent

Protected Attributes inherited from SubcloneSeeker::Archivable
sqlite3_int64	id

Additional Inherited Members
Static Public Member Functions inherited from SubcloneSeeker::TreeNode
static void	PreOrderTraverse (TreeNode *root, TreeTraverseDelegate &traverseDelegate)

static void	PostOrderTraverse (TreeNode *root, TreeTraverseDelegate &traverseDelegate)

Detailed Description

The class that represents a subclone in a subclonal structure tree.

This class implements both the TreeNode and Archivable interfaces, so that it can be a node in a tree structure, and at the same time be archived into a sqlite3 database. This is the fundamental building block of subclonal deconvoution solutions.

Constructor & Destructor Documentation

SubcloneSeeker::Subclone::Subclone ( )

inline

Minimal constructor to reset all member variables

Member Function Documentation

void Subclone::addEventCluster ( EventCluster * cluster )

Add a given EventCluster into the subclone

Parameters

cluster The EventCluster to be added to the subclone

int Subclone::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.

std::string Subclone::createObjectStatementStr ( )

protectedvirtual

return the unbound statement for record creation

Returns: unbound statement for record creation

Implements SubcloneSeeker::Archivable.

std::string Subclone::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.

double SubcloneSeeker::Subclone::fraction ( ) const

inline

return the fraction

Returns: percentage of this subclone

std::string Subclone::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::string Subclone::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::Subclone::setFraction ( double fraction )

inline

update the fraction

Parameters

fraction The new fraction value

void SubcloneSeeker::Subclone::setParentId ( sqlite3_int64 pid )

inline

set parent id

Parameters

pid	The new parent id

void SubcloneSeeker::Subclone::setTreeFraction ( double fraction )

inline

update the tree fraction

Parameters

fraction The new tree fraction value

double SubcloneSeeker::Subclone::treeFraction ( ) const

inline

return the tree fraction

Returns: percentage of the subtree rooted by this subclone

void Subclone::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 Subclone::updateObjectStatementStr ( )

protectedvirtual

return the unbound statement for record update

Returns: unbound statement for record update

Implements SubcloneSeeker::Archivable.

std::vector<EventCluster *>& SubcloneSeeker::Subclone::vecEventCluster ( )

inline

retreve a vector of all EventClusters this subclone has

Returns: member EventCluster vector

Member Data Documentation

std::vector<EventCluster *> SubcloneSeeker::Subclone::_eventClusters

protected

the event clusters this subclone contains

double SubcloneSeeker::Subclone::_fraction

protected

The percentage of this subclone

double SubcloneSeeker::Subclone::_treeFraction

protected

The total fraction taken by the subtree rooted by this object

sqlite3_int64 SubcloneSeeker::Subclone::parentId

protected

The database id of the parent node, 0 represents a root

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

src/Subclone.h
src/Subclone.cc

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation