FMWSCA Class Reference

FMWSCA: Framed, Multi-Word String Compare Analyzer. More...

#include <FMWSCA.h>

Inheritance diagram for FMWSCA:

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Collaboration diagram for FMWSCA:

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List of all members.

Public Member Functions
	~FMWSCA ()
	The destructor.
virtual void	showArguments (std::ostream &os)
	Display valid command line arguments for this analyzer.
virtual bool	parseArguments (int &argc, char **argv)
	Process command line arguments.
virtual std::string	getName () const
	Method to obtain human-readable name for this EST analyzer.
Protected Member Functions
virtual float	getMetric (const std::string &refFrame, const std::string &otherFrame, const int wordSize)
Static Protected Attributes
static bool	caseSensitive = false
	Flag to perform case sensitive comparisons.
Private Member Functions
	FMWSCA (const int refESTidx, const std::string &outputFile)
	The default constructor.
Static Private Attributes
static arg_parser::arg_record	argsList []
	The set of c arguments for this EST analyzer.
Friends
class	ESTAnalyzerFactory

Detailed Description

FMWSCA: Framed, Multi-Word String Compare Analyzer.

This analyzer provides a conventional EST analyzer that compares EST base pair data using a given number of base pairs. The total number of base pairs to be compared is called a Frame. A frame is broken into a sequence of words. The frame size and word size (in terms of number of base pairs) is specified as command line arguments. This analyzer compares the tail (3' end) of a given EST sequence with the beginning (5' end) of all other ESTs in a given file. The file must be in FASTA format.

This class has been implemented by extending the FWAnalyzer base class. The base class hierarchy provides most of the standard functionality involved in reading FASTA files and generating formatted output.

Note:: An instance of this class is typically created via the ESTAnalyzerFactory class.

Definition at line 58 of file FMWSCA.h.

Constructor & Destructor Documentation

FMWSCA::~FMWSCA ( )

The destructor.

The destructor frees up all any dynamic memory allocated by this object for its operations.

Definition at line 54 of file FMWSCA.cpp.

FMWSCA::FMWSCA	(	const int	refESTidx,
		const std::string &	outputFile
	)			`[private]`

The default constructor.

The default constructor for this class. The constructor is made private so that this class cannot be directly instantiated. However, since the ESTAnalyzerFactory is a friend of this class, an object can be instantiated via teh ESTAnalyzerFactory::create() method.

Parameters:

`[in]`	refESTidx	The reference EST index value to be used when performing EST analysis. This parameter should be >= 0. This value is simply passed onto the base class.
`[in]`	outputFile	The name of the output file to which the EST analysis data is to be written. This parameter is ignored if this analyzer is used for clustering. If this parameter is the empty string then output is written to standard output. This value is simply passed onto the base class.

Definition at line 49 of file FMWSCA.cpp.

Member Function Documentation

float FMWSCA::getMetric	(	const std::string &	refFrame,
		const std::string &	otherFrame,
		const int	wordSize
	)			`[protected, virtual]`

Definition at line 75 of file FMWSCA.cpp.

virtual std::string FMWSCA::getName ( ) const [inline, virtual]

Method to obtain human-readable name for this EST analyzer.

This method provides a human-readable string identifying the EST analyzer. This string is typically used for display/debugging purposes (particularly via the PEACE Interactive Console).

Returns:: This method returns the string "FMWSCA" identifiying this analyzer.

Implements ESTAnalyzer.

Definition at line 114 of file FMWSCA.h.

bool FMWSCA::parseArguments	(	int &	argc,
		char **	argv
	)			`[virtual]`

Process command line arguments.

This method is used to process command line arguments specific to this EST analyzer. This method is typically used from the main method just after the EST analyzer has been instantiated. This method consumes all valid command line arguments. If the command line arguments were valid and successfully processed, then this method returns true.

Note:: This method consumes its custom command line arguments first and then call's the base class's parseArguments() method.

Parameters:

`[in,out]`	argc	The number of command line arguments to be processed.
`[in,out]`	argv	The array of command line arguments.

Returns:: This method returns true if the command line arguments were successfully processed. Otherwise this method returns false.

Reimplemented from FWAnalyzer.

Definition at line 67 of file FMWSCA.cpp.

References arg_parser::check_args().

void FMWSCA::showArguments ( std::ostream & os ) [virtual]

Display valid command line arguments for this analyzer.

This method must be used to display all valid command line options that are supported by this analyzer (and its base classes).

Note:: This method calls the base class's showArguments first.

Parameters:

[out] os The output stream to which the valid command line arguments must be written.

Reimplemented from FWAnalyzer.

Definition at line 59 of file FMWSCA.cpp.

Friends And Related Function Documentation

friend class ESTAnalyzerFactory [friend]

Definition at line 59 of file FMWSCA.h.

Member Data Documentation

arg_parser::arg_record FMWSCA::argsList [static, private]

Initial value:

 {
    {"--case", "Make comparisons of BP case sensitive",
     &FMWSCA::caseSensitive, arg_parser::BOOLEAN},
    {NULL, NULL, NULL, arg_parser::BOOLEAN}
}

The set of c arguments for this EST analyzer.

This instance variable contains a static list of arguments that are specific to the FMWSCA EST analyzers.

Definition at line 187 of file FMWSCA.h.

bool FMWSCA::caseSensitive = false [static, protected]

Flag to perform case sensitive comparisons.

This flag indicates if the FMWSCA must perform case sensitive string comparisons. By default this analyzer performs case insensitive comparisons. The default can be changed by the user by sepcifying a suitable command line argument. This member is initialized to false. However, its value may be changed by the parseArguments() method.

Definition at line 126 of file FMWSCA.h.

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

FMWSCA Class Reference

Public Member Functions

Protected Member Functions

Static Protected Attributes

Private Member Functions

Static Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation