SubcloneSeeker::SNP Class Reference

Single Nucleotide Polymorphism. More...

#include <SNP.h>

Inheritance diagram for SubcloneSeeker::SNP:

Public Attributes
GenomicLocation	location
Public Attributes inherited from SubcloneSeeker::SomaticEvent
double	frequency

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

Additional Inherited Members
Public Member Functions inherited from SubcloneSeeker::SomaticEvent
	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)
Protected Attributes inherited from SubcloneSeeker::SomaticEvent
sqlite3_int64	ofClusterID
Protected Attributes inherited from SubcloneSeeker::Archivable
sqlite3_int64	id

Detailed Description

Single Nucleotide Polymorphism.

A SNP is a point mutation at a specific location on the genome that the DNA nucleotide is different from a more common alternative

Member Function Documentation

int SNP::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 SNP::createObjectStatementStr ( )

protectedvirtual

return the unbound statement for record creation

Returns

unbound statement for record creation

Implements SubcloneSeeker::Archivable.

std::string SNP::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 SNP::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 SNP::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 SNP::updateObjectStatementStr ( )

protectedvirtual

return the unbound statement for record update

Returns

unbound statement for record update

Implements SubcloneSeeker::Archivable.

Member Data Documentation

GenomicLocation SubcloneSeeker::SNP::location

At which location did the SNP occurred

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

• src/SNP.h
• src/SNP.cc