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Library Class Reference

#include <Library.h>

List of all members.

Public Methods
	Library (void)
virtual	~Library ()
void	initialize (void)
void	addFragment (const Fragment &p_fragment, int p_position=Library::LAST_POSITION)
void	deleteFragmentByIndex (const int p_position)
void	pruneBasedOnOccurence (float p_fraction_to_keep)
void	pruneZeroOccurence (void)
void	pruneWithGoodnessFraction (const float p_threshold_fraction)
void	pruneNWorstFragment (const int p_number)
void	resetFragmentList (void)
void	buildSubLibrary (const int p_nbr_division, const int p_index, Library *p_library) const
void	shuffle (void)
double	calculateSumScoreUpTo (float p_fraction)
const std::string &	getLibraryName (void) const
void	setLibraryName (const std::string &p_Name)
Fragment *	getFragmentByIndex (const int p_index) const
const std::vector< Fragment * > &	getFragmentList (void) const
const std::vector< Fragment * > &	getRejectedFragmentList (void) const
int	getNumberOfFragment (void) const
int	getNumberOfRejectedFragment (void) const
int	getNumberOfInitialFragment (void) const
void	setIsKeptConstant (const bool p_is_kept_constant)
bool	getIsKeptConstant (void) const
int	getPotentialGoodnessCount (void) const
void	setPotentialGoodnessCount (int p_potential)

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Detailed Description

This class is a dimension in a combinatorial library. It contains a list of Fragment object part of this library of reagents.

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Constructor & Destructor Documentation

Library::Library (  void    )  [inline]

Default constructor.

virtual Library::~Library (    )  [virtual]

Default destructor

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Member Function Documentation

void Library::addFragment (  const Fragment &    p_fragment, int    p_position = Library::LAST_POSITION )

Add a fragment to the Library. Parameters: p_fragment  Is the Fragment object to add to the list. p_position  Is the position where the Fragment is inserted/added. If this argument is omitted, the Fragment is added at the end of the Fragment list.

void Library::buildSubLibrary (  const int    p_nbr_division, const int    p_index, Library *    p_library )  const

Subdivide the main Fragment list in equally sized smaller libraries, build one of these and return it. Parameters: p_nbr_division  Number of division considered. p_index  Index of the subdivision to build. The values should be between 0 and p_nbr_division. p_library  A valid pointer on a Library where the sublibrary will be stored.

double Library::calculateSumScoreUpTo (  float    p_fraction )

Sum up the occurence count of the Fragment from first to last. The Fragment list is not sorted before. Parameters: p_fraction  Fraction of Fragment in main list to consider. A value of 0.3 means that the first 30% of Fragments will be considered in the list.

void Library::deleteFragmentByIndex (  const int    p_position )

Remove the Fragment in the list at the specified position. Parameters: p_position  Index of the Fragment to be removed from the Fragment list. This must be [0, fragment list size[ .

Fragment* Library::getFragmentByIndex (  const int    p_index )  const [inline]

Return a pointer on a Fragment at a specified position. Parameters: p_index  Position of the Fragment to be returned [0,nbr_fragment_in_list[.

const std::vector<Fragment*>& Library::getFragmentList (  void    )  const [inline]

Return the main list of Fragment.

bool Library::getIsKeptConstant (  void    )  const [inline]

Returns 'true' if the Library is kept constant (not responding to removal methods). Return 'false' otherwise.

const std::string& Library::getLibraryName (  void    )  const [inline]

Getter of the Library's name.

int Library::getNumberOfFragment (  void    )  const [inline]

Return the number of Fragment in main list (kept, not rejected).

int Library::getNumberOfInitialFragment (  void    )  const [inline]

Return the number of Fragment initially read (size of main list and rejected list added).

int Library::getNumberOfRejectedFragment (  void    )  const [inline]

Return the number of Fragment in rejected list.

int Library::getPotentialGoodnessCount (  void    )  const [inline]

Return the maximum occurence count that this library can possibly get. This has to be initially set with the method setPotentialGoodnessCount().

const std::vector<Fragment*>& Library::getRejectedFragmentList (  void    )  const [inline]

Return the rejected list of Fragments.

void Library::initialize (  void    )

Remove all the links to the fragments associated to this Library. Reset other properties as well.

void Library::pruneBasedOnOccurence (  float    p_fraction_to_keep )

Move the Fragments with the lowest occurence counter into the rejected list. The list of fragment do not contain these moved fragments anymore. The Fragment list is first sorted. Parameters: p_fraction_to_keep  This argument specifies the fraction of the Fragment in the list to be kept. The fraction to move into the rejected list is 1.0 - p_fraction_to_keep.

void Library::pruneNWorstFragment (  const int    p_number )

Remove the last fragments in the sorted list (based on occurence count, highest count first). The removed Fragments are moved into the rejected list. Parameters: p_number  The number of Fragments to remove.

void Library::pruneWithGoodnessFraction (  const float    p_threshold_fraction )

Remove some Fragment from the main list, add them in the rejected list. Set to zero the occurence count in all remaining fragment. The Fragment list is first sorted. Parameters: p_threshold_fraction  This identifies which Fragment to eliminate. All Fragments with an occurence count less than p_threshold_fraction * potential_maximum_occurence_count are moved to the rejected list. The occurence count of all remaining Fragment is set zero.

void Library::pruneZeroOccurence (  void    )

Move all the Fragments with a zero occurence counter to the rejected list.

void Library::resetFragmentList (  void    )

Empty the rejected fragment list and put back these fragments into the main Fragment list.

void Library::setIsKeptConstant (  const bool    p_is_kept_constant )  [inline]

Set this Library as constant or not. Parameters: p_is_kept_constant  If this is 'true' the library will not be pruned by removal methods. Otherwise, the removal methods will be effective (default if this method has not been called with the value 'true' before).

void Library::setLibraryName (  const std::string &    p_Name )  [inline]

Setter of the Library's name.

void Library::setPotentialGoodnessCount (  int    p_potential )  [inline]

Set the maximum occurence count that this Library can possibly get.

void Library::shuffle (  void    )

Shuffle the fragments: randomly change the fragment positions.

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

• Library.h

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