RibonucleotideDB Class Reference

Database of ribonucleotides (modified and unmodified) More...

#include <OpenMS/CHEMISTRY/RibonucleotideDB.h>

Collaboration diagram for RibonucleotideDB:

Public Types
using	ConstRibonucleotidePtr = const Ribonucleotide *
typedef std::vector< std::unique_ptr< Ribonucleotide > >::const_iterator	ConstIterator
	const iterator type definition More...

Public Member Functions
	~RibonucleotideDB ()=default
	destructor More...
	RibonucleotideDB (const RibonucleotideDB &other)=delete
	copy constructor not available More...
RibonucleotideDB &	operator= (const RibonucleotideDB &other)=delete
	assignment operator not available More...
ConstIterator	begin () const
	Const iterator to beginning of database. More...
ConstIterator	end () const
	Const iterator to end of database. More...
ConstRibonucleotidePtr	getRibonucleotide (const std::string &code)
	Get a ribonucleotide by its code (short name) More...
ConstRibonucleotidePtr	getRibonucleotidePrefix (const std::string &seq)
	Get the ribonucleotide with the longest code that matches a prefix of seq. More...
std::pair< ConstRibonucleotidePtr, ConstRibonucleotidePtr >	getRibonucleotideAlternatives (const std::string &code)
	Get the alternatives for an ambiguous modification code. More...

Static Public Member Functions
static RibonucleotideDB *	getInstance ()
	replacement for constructor (singleton pattern) More...

Protected Member Functions
	RibonucleotideDB ()
	default constructor More...
void	readFromFile_ (const std::string &path)
	read (modified) nucleotides from input file More...
void	readFromJSON_ (const std::string &path)
	read from a newer version of Modomics that uses a JSON file More...
const std::unique_ptr< Ribonucleotide >	parseRow_ (const std::string &row, Size line_count)
	create a (modified) nucleotide from an input row More...

Protected Attributes
std::vector< std::unique_ptr< Ribonucleotide > >	ribonucleotides_
	list of known (modified) nucleotides More...
std::unordered_map< std::string, Size >	code_map_
	mapping of codes (short names) to indexes into ribonucleotides_ More...
std::map< std::string, std::pair< ConstRibonucleotidePtr, ConstRibonucleotidePtr > >	ambiguity_map_
	mapping of ambiguity codes to the alternatives they represent More...
Size	max_code_length_

Detailed Description

Database of ribonucleotides (modified and unmodified)

The information in this class comes primarily from the Modomics database (http://modomics.genesilico.pl/modifications/) and is read from a tab-separated text file in data/CHEMISTRY/Modomics.tsv. In addition, OpenMS-specific (as well as potentially user-supplied) modification definitions are read from the file data/CHEMISTRY/Custom_RNA_modifications.tsv.

Member Typedef Documentation

ConstIterator

typedef std::vector<std::unique_ptr<Ribonucleotide> >::const_iterator ConstIterator

const iterator type definition

ConstRibonucleotidePtr

using ConstRibonucleotidePtr = const Ribonucleotide *

Constructor & Destructor Documentation

~RibonucleotideDB()

~RibonucleotideDB ( )

default

destructor

RibonucleotideDB() [1/2]

RibonucleotideDB ( const RibonucleotideDB &  other )

delete

copy constructor not available

RibonucleotideDB() [2/2]

RibonucleotideDB ( )

protected

default constructor

Member Function Documentation

begin()

ConstIterator begin ( ) const

inline

Const iterator to beginning of database.

end()

ConstIterator end ( ) const

inline

Const iterator to end of database.

getInstance()

static RibonucleotideDB* getInstance ( )

static

replacement for constructor (singleton pattern)

Referenced by NucleicAcidSearchEngine::getModifications_(), NucleicAcidSearchEngine::registerOptionsAndFlags_(), and NucleicAcidSearchEngine::resolveAmbiguousMods_().

getRibonucleotide()

ConstRibonucleotidePtr getRibonucleotide

(

const std::string &

code

)

Get a ribonucleotide by its code (short name)

Exceptions

Exception::ElementNotFound

if nothing was found

getRibonucleotideAlternatives()

std::pair<ConstRibonucleotidePtr, ConstRibonucleotidePtr> getRibonucleotideAlternatives

(

const std::string &

code

)

Get the alternatives for an ambiguous modification code.

Exceptions

Exception::ElementNotFound

if nothing was found

getRibonucleotidePrefix()

ConstRibonucleotidePtr getRibonucleotidePrefix

(

const std::string &

seq

)

Get the ribonucleotide with the longest code that matches a prefix of seq.

Exceptions

Exception::ElementNotFound

if nothing was found

operator=()

RibonucleotideDB& operator= ( const RibonucleotideDB &  other )

delete

assignment operator not available

parseRow_()

const std::unique_ptr<Ribonucleotide> parseRow_ ( const std::string &  row, Size  line_count  )

protected

create a (modified) nucleotide from an input row

readFromFile_()

void readFromFile_ ( const std::string &  path )

protected

read (modified) nucleotides from input file

readFromJSON_()

void readFromJSON_ ( const std::string &  path )

protected

read from a newer version of Modomics that uses a JSON file

Member Data Documentation

ambiguity_map_

std::map<std::string, std::pair<ConstRibonucleotidePtr, ConstRibonucleotidePtr> > ambiguity_map_

protected

mapping of ambiguity codes to the alternatives they represent

code_map_

std::unordered_map<std::string, Size> code_map_

protected

mapping of codes (short names) to indexes into ribonucleotides_

max_code_length_

Size max_code_length_

protected

ribonucleotides_

std::vector<std::unique_ptr<Ribonucleotide> > ribonucleotides_

protected

list of known (modified) nucleotides