Dynalign_object Class Reference

#include <Dynalign_object.h>

Inheritance diagram for Dynalign_object:

List of all members.

Public Member Functions

Dynalign_object ()

Dynalign_object (const char sequence1[], const char sequence2[], const bool IsRNA=true)

Dynalign_object (const char filename1[], const int type1, const char filename2[], const int type2, const bool IsRNA=true)

Constructor.

Dynalign_object (const char filename[])

Constructor.

Dynalign_object (const char *filename, const short maxtrace, const short bpwin, const short awin, const short percent)

int Dynalign (const short int maxtrace=20, const short int bpwin=5, const short int awin=1, const short int percent=20, const short int imaxseparation=-99, const float gap=0.4, const bool singleinsert=true, const char savefile[]=NULL, const bool optimalonly=false, const short int singlefold_subopt_percent=30, const bool local=false, const short int numProcessors=1, const int maxpairs=-1)

Predict the lowest free energy structure common to two sequences and suboptimal solutions with the Dynalign algorithm.

void WriteAlignment (const char filename[])

Write the alignment to disk.

int ForceAlignment (const int i, const int k)

Force an alignment during a Dynalign calculation).

int GetForcedAlignment (const int i, const int seq)

Get an alignment constraint.

int ReadAlignmentConstraints (const char filename[])

Read alignment constraints from disk.

int Templatefromct (const char ctfilename[])

Read a ct file to determine what pairs will be allowed for sequence 1 in a subsequent dynalign calculation.

int Templatefromdsv (const char dsvfilename[], const float maxdsvchange)

double GetBestPairEnergy (const int sequence, const int i, const int j)

Report the best energy for pair i-j from sequence number sequence (1 or 2).

double GetLowestEnergy ()

Report the lowest total free energy change from a Dynalign calculation.

char * GetErrorMessage (const int error)

Return error messages based on code from GetErrorCode and other error codes.

void SetProgress (TProgressDialog &Progress)

void StopProgress ()

~Dynalign_object ()

Private Member Functions

void CommonConstructor ()

void AllocateForceAlign ()

void storetemplatefilename (const char *name)

Private Attributes

short ** align

short ** forcealign

bool dsv_templated

bool ct_templated

char * templatefilename

float MAXDSV

int modificationflag

dynalignarray * w

dynalignarray * vmod

varray * v

wendarray * w5

wendarray * w3

short * lowend

short * highend

datatable * data

short gap

short lowest

int Maxtrace

bool savefileread

double *** array

Detailed Description

Dynalign_object Class.

The Dynalign_object class provides an entry point for the Dynalign algorithm. The class is inherited from the TwoRNA class, which itself contains two instances to the class RNA.

Constructor & Destructor Documentation

Dynalign_object::Dynalign_object ( )

Constructor This is a default constructor that calls the TwoRNA default constructor.

Dynalign_object::Dynalign_object	(	const char	sequence1[],
		const char	sequence2[],
		const bool	IsRNA = `true`
	)

This constuctor is available to reach the TwoRNA constructors, from which this class is inherited. This constructor uses two cstrings to provide sequences. IsRNA is true for RNA folding and flase for DNA. Constructor This constuctor is available to reach the TwoRNA constructors, from which this class is inherited. This constructor uses two cstrings to provide sequences. IsRNA is true for RNA folding and false for DNA. Input sequences should contain A,C,G,T,U,a,c,g,t,u,x,X. Capitalization makes no difference. T=t=u=U. If IsRNA is true, the backbone is RNA, so U is assumed. If IsRNA is false, the backbone is DNA, so T is assumed. x=X= nucleotide that neither stacks nor pairs. For now, any unknown nuc is considered 'X'. Both sequences are passed to underlying RNA classes for each sequence.

Parameters:

	sequence1	is a NULL terminated c string for sequence 1.
	sequence2	is a NULL terminated c string for sequence 2.
	IsRNA	is a bool that indicates whether these sequences are RNA or DNA. true=RNA. false=DNA. Default is true. Both sequences must have the same backbone.

Dynalign_object::Dynalign_object	(	const char	filename1[],
		const int	type1,
		const char	filename2[],
		const int	type2,
		const bool	IsRNA = `true`
	)

Constructor.

This constuctor is available to reach the TwoRNA constructors, from which this class is inherited. This constructor uses two ctsirngs as filenames, accompanied by integers to set the file type. IsRNA is true for RNA folding and false for DNA. The existing files, specified by filenames, can either be a ct file, a sequence, or an RNAstructure save file. Therefore, the user provides a flag for the file type: type = 1 => .ct file, type = 2 => .seq file, type = 3 => partition function save (.pfs) file, type = 4 => folding save file (.sav). The file opening is performed by the constructors for the RNA classes that underlie each sequence. This constructor generates internal error codes that can be accessed by GetErrorCode() after the constructor is called. 0 = no error. The errorcode can be resolved to a c string using GetErrorMessage. Note that the contructor needs to be explicitly told, via IsRNA, what the backbone is because files do not store this information. Note also that save files explicitly store the thermodynamic parameters, therefore changing the backbone type as compaared to the original calculation will not change structure predictions.

Parameters:

	filename1	is a null terminated c string and refers to sequence 1.
	filename2	is a null terminated c string and refers to sequence 2.
	type1	is an integer that indicates the file type for sequence 1.
	type2	is an integer that indicates the file type for sequence 2.
	IsRNA	is a bool that indicates whether these sequences are RNA or DNA. true=RNA. false=DNA. Default is true. Only one backbone is allowed for both sequences.

Dynalign_object::Dynalign_object ( const char filename[] )

Constructor.

This constructor allows the user to read a dynalign save file (.dsv) to get base pairing information. This constructor generates internal error codes that can be accessed by GetErrorCode() after the constructor is called. 0 = no error. The errorcode can be resolved to a c string using GetErrorMessage.

Parameters:

filename[]

is a cstring that indicates the filename of a .dsv file.

Dynalign_object::Dynalign_object	(	const char *	filename,
		const short	maxtrace,
		const short	bpwin,
		const short	awin,
		const short	percent
	)

Constructor This constructor is used to perform Dynaligh refolding. This does not allow any changes in constraints, but does allow the creation of different set of suboptimal structures. This constructor generates internal error codes that can be accessed by GetErrorCode() after the constructor is called. 0 = no error. The errorcode can be resolved to a c string using GetErrorMessage.

Parameters:

	filename	is the name of a Dynalign save file name (.dsv).
	maxtrace	is the maximum number of common structures to be determined. The recommended default is 20.
	bpwin	the the base pair window parameter, where 0 allows the structures to have similar pairs and larger windows make the structures more diverse. The recommended default is 5.
	awin	is the alignment window parameter, where 0 allows the alignments to be similar and larger values make the alignments more diverse. The recommended default is 1.
	percent	is the maximum percent difference in total folding free energy change above the lowest for suboptimal common structures. The recommended default is 20.

Dynalign_object::~Dynalign_object ( )

Member Function Documentation

void Dynalign_object::AllocateForceAlign ( ) [private]

void Dynalign_object::CommonConstructor ( ) [private]

int Dynalign_object::Dynalign	(	const short int	maxtrace = `20`,
		const short int	bpwin = `5`,
		const short int	awin = `1`,
		const short int	percent = `20`,
		const short int	imaxseparation = `-99`,
		const float	gap = `0.4`,
		const bool	singleinsert = `true`,
		const char	savefile[] = `NULL`,
		const bool	optimalonly = `false`,
		const short int	singlefold_subopt_percent = `30`,
		const bool	local = `false`,
		const short int	numProcessors = `1`,
		const int	maxpairs = `-1`
	)

Predict the lowest free energy structure common to two sequences and suboptimal solutions with the Dynalign algorithm.

In case of error, the function returns a non-zero that can be parsed by GetErrorMessage() or GetErrorMessageString().

Parameters:

	maxtrace	is the maximum number of common structures to be determined. The defaults is 20.
	bpwin	the the base pair window parameter, where 0 allows the structures to have similar pairs and larger windows make the structures more diverse. The default is 5.
	awin	is the alignment window parameter, where 0 allows the alignments to be similar and larger values make the alignments more diverse. The default is 1.
	percent	is the maximum percent difference in total folding free energy change above the lowest for suboptimal common structures. The defaults is 20.
	imaxseparation	is the maximum separation between aligned nucleotides. Values >= 0 are the traditional parameter, those below zero trigger the HMM alignment method, which is now prefered.
	gap	is the cost of adding gap nucleotides in the alignment in kcal/mol.
	singleinsert	is whether single basepair inserts are allowed in one sequence vs the other.
	savefile	is c-string with the name of a dynalign savefile (*.dsv) to be created.
	optimalonly	can be used to turn on a calculation of only the energy (when true) and not the structures.
	singlefold_subopt_percent	is the maximum % difference of folding energy above the lowest free energy structure for pairs in single sequence folding that will be allowed in the dynalign calculation.
	local	is whether Dynalign is being run in local (true) or global mode (false).
	numProcessors	is the number of processors to use for the calculation. This requires a compilation for SMP.
	maxpairs	is under development for multiple sequence folding. Use -1 (default) for now.

Returns:: An int that indicates an error code (0 = no error, non-zero = error occurred).

int Dynalign_object::ForceAlignment	(	const int	i,
		const int	k
	)

Force an alignment during a Dynalign calculation).

Nucleotide i from sequence 1 will be aligned to nucleotide k in sequence 2 in subsequent Dynalign calculation. The function returns 0 with no error and a non-zero otherwise that can be parsed by GetErrorMessage() or GetErrorMessageString().

Parameters:

	i	is the index of nucleotide from sequence 1.
	k	is the index of nucleotide from sequence 2.

Returns:: An integer that indicates an error code (0 = no error, 100 = nucleotide i out of range, 101 = nucleotide k out of range).

double Dynalign_object::GetBestPairEnergy	(	const int	sequence,
		const int	i,
		const int	j
	)

Report the best energy for pair i-j from sequence number sequence (1 or 2).

This function reports the lowest ffolding free energy for any pairs between i-j in sequence number sequence (1 or 2). This requires a search over all possible pairs in the second sequence. NOTE: This function ONLY works after reading a Dynalign save file (.dsv) using the constructor. This is because the Dynalign energies are not normally stored after calling Dynalign. This function generates internal error codes that can be accessed by GetErrorCode() after the constructor is called. 0 = no error, 107 = Data not available, 108 = nucleotide out of range. The errorcode can be resolved to a c string using GetErrorMessage.

Parameters:

	sequence	is an integer indicating the sequence # (must be 1 or 2).
	i	is the 5' nucleotide in a pair.
	j	is the 3' nucleotide in a pair.

Returns:: A double that gives an energy in kcal/mol.

char * Dynalign_object::GetErrorMessage ( const int error )

Return error messages based on code from GetErrorCode and other error codes.

0 = no error 100-999 = Error associated with Dynalign, to be handled here. >=1000 = Errors for underlying sequence, get message from TwoRNA base class. Current errors handled here are: 100 "Nucleotide from sequence 1 is out of range.\n"; 101 "Nucleotide from sequence 2 is out of range.\n"; 102 "Alignment constraint file not found.\n"; 103 "Error reading alignment constraint file.\n"; 104 "CT file not found.\n"; 105 "A template has already been specified; only one is allowed.\n"; 106 "DSV file not found.\n"; 107 "Data not available to calculate energy.\n" 108 "Nucleotide out of range.\n"; 109 "Value of maxpairs is too large to be achievable.\n" 110 "Error reading thermodynamic parameters."

Parameters:

error

is the integer error code provided by GetErrorCode() or by a call to a function that returns an error.

Returns:: A pointer to a c string that provides an error message or from other functions that return integer error codes.

Reimplemented from TwoRNA.

int Dynalign_object::GetForcedAlignment	(	const int	i,
		const int	seq
	)

Get an alignment constraint.

Parameters:

	i	is the nucleotide number.
	seq	is the sequence (1 or 2) from which i is derived.

Returns:: An integer that indicates the nucleotide to which i is forced to be aligned, where 0 indicates no alignment.

double Dynalign_object::GetLowestEnergy ( )

Report the lowest total free energy change from a Dynalign calculation.

NOTE: This function ONLY works after reading a Dynalign save file (.dsv) using the constructor. This is because the Dynalign energies are not normally stored after calling Dynalign. This function generates internal error codes that can be accessed by GetErrorCode() after the constructor is called. 0 = no error, 107 = Data not available, 108 = nucleotide out of range. The errorcode can be resolved to a c string using GetErrorMessage.

Returns:: a double that gives an energy in kcal/mol.

int Dynalign_object::ReadAlignmentConstraints ( const char filename[] )

Read alignment constraints from disk.

The file format is: i1 k1 i2 k2 -1 -1 Where each line gives a aligned pair (i from sequence 1 and k from sequence 2). The file terminates with -1 -1 to indicate the file end. The function returns 0 with no error and a non-zero otherwise that can be parsed by GetErrorMessage() or GetErrorMessageString().

Parameters:

filename

is a c string that is the file name to be read.

Returns:: An integer that indicates an error code (0 = no error, 102 = file not found, 103 = error reading constraint file).

void Dynalign_object::SetProgress ( TProgressDialog & Progress )

Provide a TProgressDialog for following calculation progress. A TProgressDialog class has a public function void update(int percent) that indicates the progress of a long calculation.

Parameters:

Progress

is a TProgressDialog class.

void Dynalign_object::StopProgress ( )

Provide a means to stop using a TProgressDialog. StopProgress tells the RNA class to no longer follow progress. This should be called if the TProgressDialog is deleted, so that this class does not make reference to it.

void Dynalign_object::storetemplatefilename ( const char * name ) [private]

int Dynalign_object::Templatefromct ( const char ctfilename[] )

Read a ct file to determine what pairs will be allowed for sequence 1 in a subsequent dynalign calculation.

This results in all pairs but those in the ct being disallowed.

Parameters:

ctfilename

is the name of the ct file to be read to provide the template.

Returns:: An integer that indicates an error code (0=no error, 104=file not found, 105=template is already specified)

int Dynalign_object::Templatefromdsv	(	const char	dsvfilename[],
		const float	maxdsvchange
	)

This reads a dsv file and only allows pairs with folding free energy change between the lowest and lowest + maxdsvchange in a subsequent dynalign calculation.

Parameters:

	dsvfilename	is the name of the ct file to be read to provide the template.
	maxdsvchange	in a float that gives a percent difference in free energy above the lowest free energy change.

Returns:: An integer that indicates an error code (0=no error, 106=file not found, 105=template is already specified)

void Dynalign_object::WriteAlignment ( const char filename[] )

Write the alignment to disk.

This function should be called after loading a dynalign save file or after a dynalign calculation has been performed. This function generates no error flag. Nothing can go wrong...

Parameters:

filename

is the file to which the alignment should be written.

Member Data Documentation

short** Dynalign_object::align [private]

double*** Dynalign_object::array [private]

bool Dynalign_object::ct_templated [private]

datatable* Dynalign_object::data [private]

bool Dynalign_object::dsv_templated [private]

short** Dynalign_object::forcealign [private]

short Dynalign_object::gap [private]

short * Dynalign_object::highend [private]

short* Dynalign_object::lowend [private]

short Dynalign_object::lowest [private]

float Dynalign_object::MAXDSV [private]

int Dynalign_object::Maxtrace [private]

int Dynalign_object::modificationflag [private]

bool Dynalign_object::savefileread [private]

char* Dynalign_object::templatefilename [private]

varray* Dynalign_object::v [private]

dynalignarray * Dynalign_object::vmod [private]

dynalignarray* Dynalign_object::w [private]

wendarray * Dynalign_object::w3 [private]

wendarray* Dynalign_object::w5 [private]

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

I:/RNAstructure/RNA_class/Dynalign_object.h
I:/RNAstructure/RNA_class/Dynalign_object.cpp


Public Member Functions
	Dynalign_object ()
	Dynalign_object (const char sequence1[], const char sequence2[], const bool IsRNA=true)
	Dynalign_object (const char filename1[], const int type1, const char filename2[], const int type2, const bool IsRNA=true)
	Constructor.
	Dynalign_object (const char filename[])
	Constructor.
	Dynalign_object (const char *filename, const short maxtrace, const short bpwin, const short awin, const short percent)
int	Dynalign (const short int maxtrace=20, const short int bpwin=5, const short int awin=1, const short int percent=20, const short int imaxseparation=-99, const float gap=0.4, const bool singleinsert=true, const char savefile[]=NULL, const bool optimalonly=false, const short int singlefold_subopt_percent=30, const bool local=false, const short int numProcessors=1, const int maxpairs=-1)
	Predict the lowest free energy structure common to two sequences and suboptimal solutions with the Dynalign algorithm.
void	WriteAlignment (const char filename[])
	Write the alignment to disk.
int	ForceAlignment (const int i, const int k)
	Force an alignment during a Dynalign calculation).
int	GetForcedAlignment (const int i, const int seq)
	Get an alignment constraint.
int	ReadAlignmentConstraints (const char filename[])
	Read alignment constraints from disk.
int	Templatefromct (const char ctfilename[])
	Read a ct file to determine what pairs will be allowed for sequence 1 in a subsequent dynalign calculation.
int	Templatefromdsv (const char dsvfilename[], const float maxdsvchange)
double	GetBestPairEnergy (const int sequence, const int i, const int j)
	Report the best energy for pair i-j from sequence number sequence (1 or 2).
double	GetLowestEnergy ()
	Report the lowest total free energy change from a Dynalign calculation.
char *	GetErrorMessage (const int error)
	Return error messages based on code from GetErrorCode and other error codes.
void	SetProgress (TProgressDialog &Progress)
void	StopProgress ()
	~Dynalign_object ()
Private Member Functions
void	CommonConstructor ()
void	AllocateForceAlign ()
void	storetemplatefilename (const char *name)
Private Attributes
short **	align
short **	forcealign
bool	dsv_templated
bool	ct_templated
char *	templatefilename
float	MAXDSV
int	modificationflag
dynalignarray *	w
dynalignarray *	vmod
varray *	v
wendarray *	w5
wendarray *	w3
short *	lowend
short *	highend
datatable *	data
short	gap
short	lowest
int	Maxtrace
bool	savefileread
double ***	array