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BigString Class Reference

#include <OpenMS/DATASTRUCTURES/BigString.h>

List of all members.


Detailed Description

concatenates Proteins given as FASTAEntry to one big string separated by a unique character (by default $)

Concatenates the strings given as FASTAEntry separating them with a unique character and storing the headers of FASTAEntry as well as the position of separator characters. So a substring can be accessed easily and the corresponding header can be found fast by using bineary search.

Public Types

typedef std::pair< String, StringFASTAEntry

Public Member Functions

 BigString ()
 constructor
 BigString (const BigString &bs)
 copy constructor
virtual ~BigString ()
 desctructor
void add (FASTAEntry const &new_entry)
 add new string to bigString
void setSeparator (const char sep)
 setter for separator character by default $
char getSeparator ()
 getter for separator character
unsigned int size ()
 returns the number of strings
unsigned int length ()
 length of bigString
void getPeptide (FASTAEntry &entry, unsigned int start, unsigned int length) throw (Exception::InvalidValue)
 getPeptide from start position with given length this includes FASTAHeader
const StringgetBigString () const
 returns bigString

Protected Member Functions

unsigned int getIndex_ (unsigned int index, unsigned int start, unsigned int end)
 private function to implement binary search
unsigned int getIndex_ (unsigned int index)
 retrieves index of inserted protein by bigStringPosition

Protected Attributes

String big_string_
 concatenated String
char separator_
 separator sign
unsigned int count_
 number of Strings added to big_string
unsigned int len_
 length of the big_string
std::vector< unsigned int > sep_indices_
 indices of separators
std::vector< StringFASTA_header_
 vector with headers of FASTAEntry


Member Typedef Documentation

typedef std::pair<String,String> FASTAEntry


Constructor & Destructor Documentation

BigString (  ) 

constructor

BigString ( const BigString bs  ) 

copy constructor

virtual ~BigString (  )  [virtual]

desctructor


Member Function Documentation

void add ( FASTAEntry const &  new_entry  ) 

add new string to bigString

Parameters:
new_entry FASTAEntry to be added to big_string

void setSeparator ( const char  sep  ) 

setter for separator character by default $

Parameters:
sep separator character

char getSeparator (  ) 

getter for separator character

Returns:
separator character

unsigned int size (  ) 

returns the number of strings

Returns:
int with number of strings

unsigned int length (  ) 

length of bigString

Returns:
int with length of the created bigString

void getPeptide ( FASTAEntry entry,
unsigned int  start,
unsigned int  length 
) throw (Exception::InvalidValue)

getPeptide from start position with given length this includes FASTAHeader

Parameters:
start start index
length length of desired substring
Returns:
FASTAEntry describing the protein
Exceptions:
InvalidValue if a peptide is part of two different fasta entrys

const String& getBigString (  )  const

returns bigString

Returns:
const reference to bigString

unsigned int getIndex_ ( unsigned int  index,
unsigned int  start,
unsigned int  end 
) [protected]

private function to implement binary search

Parameters:
index 
start start index
end end inxed
Returns:
int with index

unsigned int getIndex_ ( unsigned int  index  )  [protected]

retrieves index of inserted protein by bigStringPosition

Parameters:
index 
Returns:
int with index


Member Data Documentation

String big_string_ [protected]

concatenated String

char separator_ [protected]

separator sign

unsigned int count_ [protected]

number of Strings added to big_string

unsigned int len_ [protected]

length of the big_string

std::vector<unsigned int> sep_indices_ [protected]

indices of separators

std::vector<String> FASTA_header_ [protected]

vector with headers of FASTAEntry


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:43 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1