design Class Reference

#include <design.h>

Inherits RNA.

List of all members.

Public Member Functions
	design (const char filename[], const bool IsRNA=true)
	Constructor. Programmer provides a filename for a ct file.
int	design_sequence (const double pernucdefect, const bool random, const int maxdepth=5)
Private Member Functions
void	decompose (int nucstart, int nucend, int currentdepth, int maxdepth, int numbering, int **tree, int missingstart=0, int missingend=0)
bool	closeenoughtocut (int i, int j, int nucstart, int nucend, int missingstart, int missingend, double CLOSENESS)
void	marktree (int beststart, int bestend, int nucstart, int nucend, int missingstart, int missingend, int numbering, int currentdepth, int **tree)
void	bestdecomposition (int nuctstart, int nucend, int currentstart, int currentend, int *beststart, int *bestend, int missingstart, int missingend)
void	SelectSequence (int **tree, bool random, int depth, const double pernucdefect, long seed=1)
void	FindFragments (int **tree, int level, int start, int stop, int missingstart, int missingstop, vector< int > *stackstart, vector< int > *stackend, vector< int > *stackmissingstart, vector< int > *stackmissingend, vector< int > *stackfragmentdepth)
void	FillSequence (int start, int end, int missingstart, int missingend, bool random, randomnumber *dice)
int	MapNuctoFragment (int j, int start, int missingstart, int missingend)

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Constructor & Destructor Documentation

design::design	(	const char	filename[],
		const bool	IsRNA = true
	)

Constructor. Programmer provides a filename for a ct file.

Read a ct with name filename. This is a template for the structure. The sequence in the ct file will be ignored. If IsRNA is true (default), this is RNA, and it is DNA otherwise.

Parameters:

	Filename	is a null terminated cstring that provides the filename and path.
	isRNA	is a bool that is true for RNA (default value) and false for DNA.

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Member Function Documentation

void design::bestdecomposition	(	int	nuctstart,
		int	nucend,
		int	currentstart,
		int	currentend,
		int *	beststart,
		int *	bestend,
		int	missingstart,
		int	missingend
	)			[private]

bool design::closeenoughtocut	(	int	i,
		int	j,
		int	nucstart,
		int	nucend,
		int	missingstart,
		int	missingend,
		double	CLOSENESS
	)			[private]

void design::decompose	(	int	nucstart,
		int	nucend,
		int	currentdepth,
		int	maxdepth,
		int	numbering,
		int **	tree,
		int	missingstart = 0,
		int	missingend = 0
	)			[private]

int design::design_sequence	(	const double	pernucdefect,
		const bool	random,
		const int	maxdepth = 5
	)

Design the sequence. This function will choose a sequence will low ensemble defect to fold to the structure read in the constructor. The sequence is stored in the underlying RNA class.

Parameters:

	pernucdefect	is the maximum allowed ensemble defect per nucleotide.
	random	determines the method for choosing sequence. If false, use pre-selected sequences, and otherwise (true), randomly choose the sequence.
	maxdepth	is the mximum extent to which the structure will be sub-divided in the binary decomposition. The default is 5.

Returns:

An int error code that can be resolved to a message using RNA::GetErrorMessage. A return of 0 means no errors.

void design::FillSequence	(	int	start,
		int	end,
		int	missingstart,
		int	missingend,
		bool	random,
		randomnumber *	dice
	)			[private]

end else, (j!=missingstart)

void design::FindFragments	(	int **	tree,
		int	level,
		int	start,
		int	stop,
		int	missingstart,
		int	missingstop,
		vector< int > *	stackstart,
		vector< int > *	stackend,
		vector< int > *	stackmissingstart,
		vector< int > *	stackmissingend,
		vector< int > *	stackfragmentdepth
	)			[private]

int design::MapNuctoFragment	(	int	j,
		int	start,
		int	missingstart,
		int	missingend
	)			[private]

void design::marktree	(	int	beststart,
		int	bestend,
		int	nucstart,
		int	nucend,
		int	missingstart,
		int	missingend,
		int	numbering,
		int	currentdepth,
		int **	tree
	)			[private]

void design::SelectSequence	(	int **	tree,
		bool	random,
		int	depth,
		const double	pernucdefect,
		long	seed = 1
	)			[private]

end else, (j!=missingstart)

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

• E:/RNAstructure/RNA_class/design.h
• E:/RNAstructure/RNA_class/design.cpp