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)


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.


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)


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

Generated on Mon Apr 23 16:48:03 2012 for RNAstructure Classes by  doxygen 1.5.7.1