BigString Class Reference

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

#include <OpenMS/DATASTRUCTURES/BigString.h>

Public Types
typedef std::pair< String, String >	FASTAEntry

Public Member Functions
	BigString ()
	constructor More...
	BigString (const BigString &bs)
	copy constructor More...
virtual	~BigString ()
	destructor More...
void	add (FASTAEntry const &new_entry)
	add new string to bigString More...
void	setSeparator (const char sep)
	setter for separator character by default $ More...
char	getSeparator ()
	getter for separator character More...
Size	size ()
	returns the number of strings More...
Size	length ()
	length of bigString More...
void	getPeptide (FASTAEntry &entry, Size start, Size length)
	getPeptide from start position with given length this includes FASTAHeader More...
const String &	getBigString () const
	returns bigString More...

Protected Member Functions
Size	getIndex_ (Size index, Size start, Size end)
	private function to implement binary search More...
Size	getIndex_ (Size index)
	retrieves index of inserted protein by bigStringPosition More...

Protected Attributes
String	big_string_
	concatenated String More...
char	separator_
	separator sign More...
Size	count_
	number of Strings added to big_string More...
Size	len_
	length of the big_string More...
std::vector< Size >	sep_indices_
	indices of separators More...
std::vector< String >	FASTA_header_
	vector with headers of FASTAEntry More...

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 binary search.

Member Typedef Documentation

FASTAEntry

typedef std::pair<String, String> FASTAEntry

Constructor & Destructor Documentation

BigString() [1/2]

BigString

(

)

constructor

BigString() [2/2]

BigString

(

const BigString &

bs

)

copy constructor

~BigString()

virtual ~BigString ( )

virtual

destructor

Member Function Documentation

add()

void add

(

FASTAEntry const &

new_entry

)

add new string to bigString

Parameters

new_entry

FASTAEntry to be added to big_string

getBigString()

const String& getBigString

(

)

const

returns bigString

Returns

const reference to bigString

getIndex_() [1/2]

Size getIndex_ ( Size  index, Size  start, Size  end  )

protected

private function to implement binary search

Parameters

index
start	start index
end	end index

Returns

int with index

getIndex_() [2/2]

Size getIndex_ ( Size  index )

protected

retrieves index of inserted protein by bigStringPosition

Parameters

index

Returns

int with index

getPeptide()

void getPeptide	(	FASTAEntry &	entry,
		Size	start,
		Size	length
	)

getPeptide from start position with given length this includes FASTAHeader

Parameters

entry	contains the entry of the given range after calling
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

getSeparator()

char getSeparator

(

)

getter for separator character

Returns

separator character

length()

Size length

(

)

length of bigString

Returns

int with length of the created bigString

setSeparator()

void setSeparator

(

const char

sep

)

setter for separator character by default $

Parameters

sep	separator character

size()

Size size

(

)

returns the number of strings

Returns

int with number of strings

Member Data Documentation

big_string_

String big_string_

protected

concatenated String

count_

Size count_

protected

number of Strings added to big_string

FASTA_header_

std::vector<String> FASTA_header_

protected

vector with headers of FASTAEntry

len_

Size len_

protected

length of the big_string

sep_indices_

std::vector<Size> sep_indices_

protected

indices of separators

separator_

char separator_

protected

separator sign