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

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

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

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

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