#include <TwoRNA.h>
Inherited by Dynalign_object.
Public Member Functions | |
| TwoRNA (const char sequence1[], const char sequence2[], bool IsRNA=true) | |
| Constructor - user provides a sequences as c strings. | |
| TwoRNA (const char filename1[], const int type1, const char filename2[], const int type2, bool IsRNA=true) | |
| Constructor - user provides a filenames for existing files as a c string. | |
| TwoRNA () | |
| int | GetErrorCode () |
| Return an error code, where a return of zero is no error. | |
| char * | GetErrorMessage (const int error) |
| Return error messages based on code from GetErrorCode and other error codes. | |
| std::string | GetErrorMessageString (const int error) |
| Return error messages based on code from GetErrorCode and other error codes. | |
| RNA * | GetRNA1 () |
| return A pointer to the underlying structure class for sequence 1. | |
| RNA * | GetRNA2 () |
| return A pointer to the underlying structure class for sequence 2. | |
| ~TwoRNA () | |
| Destructor. | |
Public Attributes | |
| char | compoundmessage [COMPOUNDMESSAGELENGTH] |
| Provide facility for storing and accessing error messages. | |
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.
| 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.
| 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::TwoRNA | ( | const char | filename1[], | |
| const int | type1, | |||
| const char | filename2[], | |||
| const int | 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.
| 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::TwoRNA | ( | ) |
Constructor Default constructor that requires no parameters.
Constructor Default constructor that requires no parameters.
| TwoRNA::~TwoRNA | ( | ) |
Destructor.
The destructor cleans up all memory allocation.
| int TwoRNA::GetErrorCode | ( | ) |
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().
| 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.
| error | is the integer error code provided by GetErrorCode(). |
Reimplemented in Dynalign_object.
| 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.
| error | is the integer error code provided by GetErrorCode() or from other functions that return integer error codes. |
| RNA * TwoRNA::GetRNA1 | ( | ) |
| RNA * TwoRNA::GetRNA2 | ( | ) |
1.5.7.1