TwoRNA Class Reference

TwoRNA Class. More...

#include <TwoRNA.h>

Inheritance diagram for TwoRNA:

Public Member Functions
	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...

Public Attributes
char	compoundmessage [COMPOUNDMESSAGELENGTH]
	Provide facility for storing and accessing error messages. More...

Protected Attributes
int	ErrorCodeTwo

Private Attributes
RNA *	rna1
RNA *	rna2
string	lastErrorDetails

Detailed Description

TwoRNA Class.

The TwoRNA class provides an entry point for all the two sequence prediction routines of RNAstructure. This contains two instances of the RNA class to provide the functionality of RNA.

Constructor & Destructor Documentation

TwoRNA() [1/4]

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

Constructor - user provides a sequences as c strings.

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.

TwoRNA() [2/4]

TwoRNA::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.

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.

TwoRNA() [3/4]

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

TwoRNA 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.
copyThermo	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.

TwoRNA() [4/4]

TwoRNA::TwoRNA

(

)

Constructor Default constructor that requires no parameters.

~TwoRNA()

TwoRNA::~TwoRNA

(

)

Destructor.

The destructor cleans up all memory allocation.

Member Function Documentation

GetErrorCode()

int TwoRNA::GetErrorCode

(

)

const

Return an error code, where a return of zero is no error.

This function returns and error flag that is generated during construction by RNA(const char &filename, const int type, const bool IsRNA=true) or from CalculateFreeEnergy(). An error of zero is always no error. Other codes are errors and a c-string can be fetched for the error with GetErrorMessage().

Returns

An integer that provides the error code.

GetErrorDetails()

const string TwoRNA::GetErrorDetails

(

)

const

GetErrorMessage()

const char * TwoRNA::GetErrorMessage

(

const int

error

)

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

0 = no error 1000 = Error associated with sequence 1 or with a procedure, function will get message from sequence 1 (the inherited RNA class). 2000 = Error associated with sequence 2, function will get message from sequence 2 (the RNA2 class). 3000 = Errors with each sequence, function will get messages from each.

Parameters

error

is the integer error code provided by GetErrorCode().

Returns

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

GetErrorMessageString()

std::string TwoRNA::GetErrorMessageString

(

const int

error

)

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

Although RNA generally uses c strings, this member function returns a string that is suitable for interfacing with JAVA, etc. See the error list in the GetErrorMessage() entry.

Parameters

error

is the integer error code provided by GetErrorCode() or from other functions that return integer error codes.

Returns

A string that provides an error message.

GetRNA1()

RNA * TwoRNA::GetRNA1

(

)

return A pointer to the underlying structure class for sequence 1.

Access the underlying RNA class. This is provided for use with two sequence methods. Generally, there is no need for end users to use this function.

Returns

A pointer to the underlying RNA class for sequence 1.

GetRNA2()

RNA * TwoRNA::GetRNA2

(

)

return A pointer to the underlying structure class for sequence 2.

Access the underlying RNA class. This is provided for use with two sequence methods. Generally, there is no need for end users to use this function.

Returns

A pointer to the underlying RNA class for sequence 2.

GetTemperature()

double TwoRNA::GetTemperature

(

)

const

Get the current folding temperature in K.

Returns

A double that indicates the folding temperature in K.

ResetError()

void TwoRNA::ResetError

(

)

Reset the underlying RNA objects internal error code, after an error is handled.

SetErrorDetails()

void TwoRNA::SetErrorDetails

(

const string &

details

)

SetTemperature()

int TwoRNA::SetTemperature

(

double

temperature

)

Set the temperature at which the calculation will be performed in K.

This function allows the user to specify folding temperatures other than 310.15 K (37 degrees C). This changes folding free energy changes that would be returned for existing structures and would alter the set of structures predicted. When this function is called, the thermodynamic parameter files are immediately read from disk. These include both enthalpy parameters (.dh files) and free energy changes at 310.15 (.dat files). The files must either be at a location indicated by the $DATAPATH environment variable or in pwd. Changing the temperature only alters subsequent calculations. For example, if a structure prediction method has been called, the set of predicted structures are not changed at the time of a call to SetTemperature. Likewise, SetTemperature must be called before calling a structure prediction method if a temperature other than the 310.15 K default is desired. The function returns an error code where 0 is no error and non-zero errors can be parsed by by GetErrorMessage() or GetErrorMessageString() in an inheriting class.

Member Data Documentation

compoundmessage

char TwoRNA::compoundmessage[COMPOUNDMESSAGELENGTH]

Provide facility for storing and accessing error messages.

ErrorCodeTwo

int TwoRNA::ErrorCodeTwo

protected

lastErrorDetails

string TwoRNA::lastErrorDetails

private

rna1

RNA* TwoRNA::rna1

private

rna2

RNA * TwoRNA::rna2

private

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

• RNA_class/TwoRNA.h
• RNA_class/TwoRNA.cpp