Abstract class that defines the interface to handle archiving objects into sqlite3 database. More...

#include <Archivable.h>

Inheritance diagram for SubcloneSeeker::Archivable:

Public Member Functions
	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 ()=0

virtual std::string	createTableStatementStr ()=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	id

Detailed Description

Abstract class that defines the interface to handle archiving objects into sqlite3 database.

This abstract class defines the required behaviors when handling object archiving to and from a sqlite3 database, which will be used by the project to store computation results. As of now four methods are required for any class that wishes to support archiving:

return a string describing the name of the table
create the table in a given database
store an object into the table
retrieve an object from the table with an identifier

The unarchiving procedure uses an integer id to determine which database record is to be used for unarchiving. This would require that an SERIAL column exists in the table.

Constructor & Destructor Documentation

SubcloneSeeker::Archivable::Archivable ( )

inline

Minimal constructor to reset all member variables

Member Function Documentation

sqlite3_int64 Archivable::archiveObjectToDB ( sqlite3 * database )

Archive the object into the database

Parameters

database An open sqlite3 database connection handle

Returns: The id of the newly inserted object, if successful; or -1 if error occurred

virtual int SubcloneSeeker::Archivable::bindObjectToStatement ( sqlite3_stmt * statement )

protectedpure virtual

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

Implemented in SubcloneSeeker::Subclone, SubcloneSeeker::EventCluster, SubcloneSeeker::SegmentalMutation, and SubcloneSeeker::SNP.

virtual std::string SubcloneSeeker::Archivable::createObjectStatementStr ( )

protectedpure virtual

return the unbound statement for record creation

Returns: unbound statement for record creation

Implemented in SubcloneSeeker::Subclone, SubcloneSeeker::EventCluster, SubcloneSeeker::SegmentalMutation, and SubcloneSeeker::SNP.

bool Archivable::createTableInDB ( sqlite3 * database )

Create the storage table in the database

Parameters

database An open sqlite3 database connection handle

Returns: Whether the operation is successful or not

virtual std::string SubcloneSeeker::Archivable::createTableStatementStr ( )

protectedpure virtual

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 ","

Implemented in SubcloneSeeker::Subclone, SubcloneSeeker::EventCluster, and SubcloneSeeker::SomaticEvent.

sqlite3_int64 SubcloneSeeker::Archivable::getId ( )

inline

get access function of id

Returns: the database identifier of the object

virtual std::string SubcloneSeeker::Archivable::getTableName ( )

protectedpure virtual

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

Returns: Table name

Implemented in SubcloneSeeker::LOH, SubcloneSeeker::CNV, SubcloneSeeker::Subclone, SubcloneSeeker::EventCluster, and SubcloneSeeker::SNP.

virtual std::string SubcloneSeeker::Archivable::selectObjectColumnListStr ( )

protectedpure virtual

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

Implemented in SubcloneSeeker::Subclone, SubcloneSeeker::EventCluster, SubcloneSeeker::SegmentalMutation, and SubcloneSeeker::SNP.

void SubcloneSeeker::Archivable::setId ( sqlite3_int64 nid )

inline

Set the database id

Parameters

nid	the new database id

bool Archivable::unarchiveObjectFromDB	(	sqlite3 *	database,
		sqlite3_int64	id
	)

Unarchive an object from the database

Parameters

database	An open sqlite3 database connection handle
id	The identifier with which the correct record is to be found

Returns: Whether the operation is successful or not

virtual void SubcloneSeeker::Archivable::updateObjectFromStatement ( sqlite3_stmt * statement )

protectedpure virtual

Populate archivable properties from a prepared statement during unarchiving

Parameters

statement A prepared statement contains the retrieved row

Implemented in SubcloneSeeker::Subclone, SubcloneSeeker::EventCluster, SubcloneSeeker::SegmentalMutation, and SubcloneSeeker::SNP.

virtual std::string SubcloneSeeker::Archivable::updateObjectStatementStr ( )

protectedpure virtual

return the unbound statement for record update

Returns: unbound statement for record update

Implemented in SubcloneSeeker::Subclone, SubcloneSeeker::EventCluster, SubcloneSeeker::SegmentalMutation, and SubcloneSeeker::SNP.

std::vector< sqlite3_int64 > Archivable::vecAllObjectsID ( sqlite3 * database )

Return a std::vector of all ids of records of the current object's class

Returns: A vector of sqlite3_int64, describing all records with the same class

Member Data Documentation

sqlite3_int64 SubcloneSeeker::Archivable::id

protected

the database identifier for a specific record

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

src/Archivable.h
src/Archivable.cc

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation