#include <Dynalign_object.h>

Inheritance diagram for Dynalign_object:

Public Member Functions
	Dynalign_object ()

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

	Dynalign_object (const char filename1[], const RNAInputType type1, const char filename2[], const RNAInputType type2, const bool IsRNA=true)
	Constructor. More...

	Dynalign_object (const char filename1[], const RNAInputType type1, const char filename2[], const RNAInputType type2, const Thermodynamics *thermo1)

	Dynalign_object (const char filename[])
	Constructor. More...

	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. More...

void	WriteAlignment (const char filename[])
	Write the alignment to disk. More...

int	ForceAlignment (const int i, const int k)
	Force an alignment during a Dynalign calculation). More...

int	GetForcedAlignment (const int i, const int seq)
	Get an alignment constraint. More...

int	ReadAlignmentConstraints (const char filename[])
	Read alignment constraints from disk. More...

int	Templatefromct (const char ctfilename[])
	Read a ct file to determine what pairs will be allowed for sequence 1 in a subsequent dynalign calculation. More...

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). More...

double	GetLowestEnergy ()
	Report the lowest total free energy change from a Dynalign calculation. More...

const char *	GetErrorMessage (const int error)
	Return error messages based on code from GetErrorCode and other error codes. More...

void	SetProgress (ProgressHandler &Progress)

void	StopProgress ()

	~Dynalign_object ()

Public Member Functions inherited from TwoRNA
	TwoRNA (const char sequence1[], const char sequence2[], bool IsRNA=true)
	Constructor - user provides a sequences as c strings. More...

	TwoRNA (const char filename1[], const RNAInputType type1, const char filename2[], const RNAInputType type2, bool IsRNA=true)
	Constructor - user provides a filenames for existing files as a c string. More...

	TwoRNA (const char filename1[], const RNAInputType type1, const char filename2[], const RNAInputType type2, const Thermodynamics *copyThermo)

	TwoRNA ()

int	SetTemperature (double temperature)
	Set the temperature at which the calculation will be performed in K. More...

double	GetTemperature () const
	Get the current folding temperature in K. More...

int	GetErrorCode () const
	Return an error code, where a return of zero is no error. More...

const char *	GetErrorMessage (const int error)
	Return error messages based on code from GetErrorCode and other error codes. More...

const string	GetErrorDetails () const

void	SetErrorDetails (const string &details)

std::string	GetErrorMessageString (const int error)
	Return error messages based on code from GetErrorCode and other error codes. More...

void	ResetError ()
	Reset the underlying RNA objects internal error code, after an error is handled. More...

RNA *	GetRNA1 ()
	return A pointer to the underlying structure class for sequence 1. More...

RNA *	GetRNA2 ()
	return A pointer to the underlying structure class for sequence 2. More...

	~TwoRNA ()
	Destructor. More...

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

Additional Inherited Members
Public Attributes inherited from TwoRNA
char	compoundmessage [COMPOUNDMESSAGELENGTH]
	Provide facility for storing and accessing error messages. More...

Protected Attributes inherited from TwoRNA
int	ErrorCodeTwo

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 RNAInputType	type1,
		const char	filename2[],
		const RNAInputType	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	filename1[],
		const RNAInputType	type1,
		const char	filename2[],
		const RNAInputType	type2,
		const Thermodynamics *	thermo1
	)

Constructor Constructor that copies thermodynamic parameter tables from an existing Thermodynamics (or RNA etc) instance. 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.

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.
thermo1	is a pointer to the Thermodynamics object to copy. The internal datatables object is stored by reference, so subsequence changes made to it WILL affect this object.

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.

const 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.

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 ( ProgressHandler & 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:

RNA_class/Dynalign_object.h
RNA_class/Dynalign_object.cpp

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation