CleanFile< GENOME_TYPE > Class Template Reference

#include <cleanfile.h>

List of all members.

Public Member Functions
void	getCleanRes (string fileRes)
	CleanFile (string &filename)
	~CleanFile ()
void	intersection (const CleanFile< GENOME_TYPE > &clean, vector< SEQ< GENOME_TYPE > > &res1, vector< SEQ< GENOME_TYPE > > &res2, string fileRes) const
void	MakeLegal ()
Private Types
typedef std::set< SEQ< GENOME_TYPE > >::iterator	itr
Private Member Functions
void	copy_title (FILE *file, FILE *legal_file) const
void	legalize_it (FILE *file)
int	check_it (string buff)
bool	isspace (char c)
bool	isdigit (char c)
int	skipspaces (string ar)
int	checkO (string Or)
int	checkS (string Start)
int	checkE (string End)
int	checkK (string KO)
GENOME_TYPE	string2GENOMEType (string str)
const char	get_or (string Orientation)
void	copy_it (string buff, FILE *LG) const
void	Tokenize (const string &str, vector< string > &tokens, const string &delimiters)
Private Attributes
string	fileN
set< SEQ< GENOME_TYPE > > *	segments

template<class GENOME_TYPE>
class CleanFile< GENOME_TYPE >

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Member Typedef Documentation

template<class GENOME_TYPE> typedef std::set< SEQ<GENOME_TYPE> >::iterator CleanFile< GENOME_TYPE >::itr [private]

An auxiliary declaration of a set iterator.

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Constructor & Destructor Documentation

template<class GENOME_TYPE> CleanFile< GENOME_TYPE >::CleanFile (  string &  filename  )

Main constructor. Parameters: filename,:  The file *.anchor.

template<class GENOME_TYPE> CleanFile< GENOME_TYPE >::~CleanFile (   )

Destructor.

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Member Function Documentation

template<class GENOME_TYPE> int CleanFile< GENOME_TYPE >::check_it (  string  buff  )  [private]

Given one entry from the file *.anchor, the method checks its regularity. Parameters: buff,:  The entry itself. Returns: 0 if legal, 1 otherwise.

template<class GENOME_TYPE> int CleanFile< GENOME_TYPE >::checkE (  string  End  )  [private]

Checks if End is a legal number. Parameters: End,:  string Returns: 0 if legal, 1 otherwise.

template<class GENOME_TYPE> int CleanFile< GENOME_TYPE >::checkK (  string  KO  )  [private]

Checks if the KO is legal. Parameters: KO,:  string Returns: 0 if legal, 1 otherwise.

template<class GENOME_TYPE> int CleanFile< GENOME_TYPE >::checkO (  string  Or  )  [private]

Checks if Or is a legal orientation value. Parameters: Or,:  string Returns: 0 if legal, 1 otherwise.

template<class GENOME_TYPE> int CleanFile< GENOME_TYPE >::checkS (  string  Start  )  [private]

Checks if Start is a legal number. Parameters: Start,:  string Returns: 0 if legal, 1 otherwise.

template<class GENOME_TYPE> void CleanFile< GENOME_TYPE >::copy_it (  string  buff, FILE *  LG )  const [private]

Copies buff to file LG. Parameters: buff,:  string. LG,:  FILE*.

template<class GENOME_TYPE> void CleanFile< GENOME_TYPE >::copy_title (  FILE *  file, FILE *  legal_file )  const [private]

Copies the title of the original file (*.anchor) to the "legal" file (*.anchor.clean). Parameters: file,:  FILE* of the *.anchor. legal_file,:  FILE* of the *.anchor.clean.

template<class GENOME_TYPE> const char CleanFile< GENOME_TYPE >::get_or (  string  Orientation  )  [private]

Extracts the orientation out of the string Orientation. Parameters: Orientation,:  string. Returns: + or - according to the extracted value.

template<class GENOME_TYPE> void CleanFile< GENOME_TYPE >::getCleanRes (  string  fileRes  )

Copies the result of the CleanFile phase into the file fileRes. Parameters: fileRes,:  The name of the file where the result will be saved in (*.anchor.clean in our case).

template<class GENOME_TYPE> void CleanFile< GENOME_TYPE >::intersection (  const CleanFile< GENOME_TYPE > &  clean, vector< SEQ< GENOME_TYPE > > &  res1, vector< SEQ< GENOME_TYPE > > &  res2, string  fileRes )  const

Copies the intersection result between two CleanFile objects into the file fileRes and returns two vector of the intersected entries, one of each CleanFile object. Parameters: clean,:  A CleanFile object which will be tested with intersection with the calling object. res1,:  A vector< SEQ<GENOME_TYPE> > reference where the entries of the calling object (which are a part of the intersection) will be saved in. res2,:  A vector< SEQ<GENOME_TYPE> > reference where the entries of the "clean" object (which are a part of the intersection) will be saved in. fileRes,:  The name of the file where the intersection result will be saved in.

template<class GENOME_TYPE> bool CleanFile< GENOME_TYPE >::isdigit (  char  c  )  [private]

Checks if the given character is a digit. Parameters: c,:  char Returns: bool: true if c is a digit, false otherwise

template<class GENOME_TYPE> bool CleanFile< GENOME_TYPE >::isspace (  char  c  )  [private]

Checks if the given character is a space. Parameters: c,:  char Returns: bool: true if c is space, false otherwise

template<class GENOME_TYPE> void CleanFile< GENOME_TYPE >::legalize_it (  FILE *  file  )  [private]

The main method of this class which legalizes the *.anchor file. Parameters: file,:  FILE* of the *.anchor file.

template<class GENOME_TYPE> void CleanFile< GENOME_TYPE >::MakeLegal (   )

The main method of the CleanFile class is MakeLegal which actually invokes the legalizing process.

template<class GENOME_TYPE> int CleanFile< GENOME_TYPE >::skipspaces (  string  ar  )  [private]

Skips leading spaces of the given string. Parameters: ar,:  string Returns: int: The first index of the cell that differs from space

template<class GENOME_TYPE> GENOME_TYPE CleanFile< GENOME_TYPE >::string2GENOMEType (  string  str  )  [private]

Converts a string into an unsigned GENOME_TYPE number. Parameters: str,:  string Returns: The unsigned GENOME_TYPE number.

template<class GENOME_TYPE> void CleanFile< GENOME_TYPE >::Tokenize (  const string &  str, vector< string > &  tokens, const string &  delimiters )  [private]

Splits str into tokens according to the given delimiters. Parameters: str,:  string. tokens,:  vector<string> reference to the place where the result will be saved in. delimiters,:  string

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Member Data Documentation

template<class GENOME_TYPE> string CleanFile< GENOME_TYPE >::fileN [private]

fileN variable holds the name of the file (*.anchor) containing the KO's.

template<class GENOME_TYPE> set< SEQ<GENOME_TYPE> >* CleanFile< GENOME_TYPE >::segments [private]

A set of all legal entries (SEQ<GENOME_TYPE> objects) of the given file.

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

• C:/cygwin/doc/cleanfile.h

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