RNAstructure Classes  Version 6.1
Dynalign_object Class Reference

Dynalign_object Class. More...

#include <Dynalign_object.h>

Inheritance diagram for Dynalign_object:
TwoRNA

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...
 
RNAGetRNA1 ()
 return A pointer to the underlying structure class for sequence 1. More...
 
RNAGetRNA2 ()
 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
sequence1is a NULL terminated c string for sequence 1.
sequence2is a NULL terminated c string for sequence 2.
IsRNAis 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
filename1is a null terminated c string and refers to sequence 1.
filename2is a null terminated c string and refers to sequence 2.
type1is an integer that indicates the file type for sequence 1.
type2is an integer that indicates the file type for sequence 2.
IsRNAis 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
filename1is a null terminated c string and refers to sequence 1.
filename2is a null terminated c string and refers to sequence 2.
type1is an integer that indicates the file type for sequence 1.
type2is an integer that indicates the file type for sequence 2.
thermo1is 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
filenameis the name of a Dynalign save file name (.dsv).
maxtraceis the maximum number of common structures to be determined. The recommended default is 20.
bpwinthe 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.
awinis 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.
percentis 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
maxtraceis the maximum number of common structures to be determined. The defaults is 20.
bpwinthe 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.
awinis the alignment window parameter, where 0 allows the alignments to be similar and larger values make the alignments more diverse. The default is 1.
percentis the maximum percent difference in total folding free energy change above the lowest for suboptimal common structures. The defaults is 20.
imaxseparationis the maximum separation between aligned nucleotides. Values >= 0 are the traditional parameter, those below zero trigger the HMM alignment method, which is now prefered.
gapis the cost of adding gap nucleotides in the alignment in kcal/mol.
singleinsertis whether single basepair inserts are allowed in one sequence vs the other.
savefileis c-string with the name of a dynalign savefile (*.dsv) to be created.
optimalonlycan be used to turn on a calculation of only the energy (when true) and not the structures.
singlefold_subopt_percentis 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.
localis whether Dynalign is being run in local (true) or global mode (false).
numProcessorsis the number of processors to use for the calculation. This requires a compilation for SMP.
maxpairsis 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
iis the index of nucleotide from sequence 1.
kis 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
sequenceis an integer indicating the sequence # (must be 1 or 2).
iis the 5' nucleotide in a pair.
jis 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
erroris 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
iis the nucleotide number.
seqis 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
filenameis 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
Progressis 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
ctfilenameis 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
dsvfilenameis the name of the ct file to be read to provide the template.
maxdsvchangein 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
filenameis 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: