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>

List of all members.

Public Types
typedef std::pair< String, String >	FASTAEntry
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
Size	size ()
	returns the number of strings
Size	length ()
	length of bigString
void	getPeptide (FASTAEntry &entry, Size start, Size length)
	getPeptide from start position with given length this includes FASTAHeader
const String &	getBigString () const
	returns bigString
Protected Member Functions
Size	getIndex_ (Size index, Size start, Size end)
	private function to implement binary search
Size	getIndex_ (Size index)
	retrieves index of inserted protein by bigStringPosition
Protected Attributes
String	big_string_
	concatenated String
char	separator_
	separator sign
Size	count_
	number of Strings added to big_string
Size	len_
	length of the big_string
std::vector< Size >	sep_indices_
	indices of separators
std::vector< String >	FASTA_header_
	vector with headers of FASTAEntry

---

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.

---

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

const String& getBigString

(

)

const

returns bigString

Returns:

const reference to bigString

Size getIndex_	(	Size	index,
		Size	start,
		Size	end
	)			[protected]

private function to implement binary search

Parameters:

	index
	start	start index
	end	end inxed

Returns:

int with index

Size getIndex_

(

Size

index

)

[protected]

retrieves index of inserted protein by bigStringPosition

Parameters:

index

Returns:

int with index

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

char getSeparator

(

)

getter for separator character

Returns:

separator character

Size length

(

)

length of bigString

Returns:

int with length of the created bigString

void setSeparator

(

const char

sep

)

setter for separator character by default $

Parameters:

sep

separator character

Size size

(

)

returns the number of strings

Returns:

int with number of strings

---

Member Data Documentation

String big_string_ [protected]

concatenated String

Size count_ [protected]

number of Strings added to big_string

std::vector<String> FASTA_header_ [protected]

vector with headers of FASTAEntry

Size len_ [protected]

length of the big_string

std::vector<Size> sep_indices_ [protected]

indices of separators

char separator_ [protected]

separator sign