OSWData Class Reference

Holds all or partial information from an OSW file. More...

#include <OpenMS/DATASTRUCTURES/OSWData.h>

Collaboration diagram for OSWData:

Public Member Functions
void	addTransition (const OSWTransition &tr)
	Adds a transition; do this before adding Proteins. More...
void	addTransition (OSWTransition &&tr)
void	addProtein (OSWProtein &&prot)
const std::vector< OSWProtein > &	getProteins () const
void	setProtein (const Size index, OSWProtein &&protein)
Size	transitionCount () const
	get the total number of transitions (chromatograms) More...
const OSWTransition &	getTransition (const UInt32 id) const
	obtain a certain transition meta information with id (this matches the ID of a chromatogram in an sqMass file). More...
const std::map< UInt32, OSWTransition > &	getTransitions () const
	get all transitions mapped by their ID (UInt32) More...
void	setSqlSourceFile (const String &filename)
const String &	getSqlSourceFile () const
void	setRunID (const UInt64 run_id)
UInt64	getRunID () const
void	clear ()
	forget all data More...
void	clearProteins ()
	only forget protein data More...
void	buildNativeIDResolver (const MSExperiment &chrom_traces)
	Create an internal mapping from the nativeIDs of all chromatograms (extracted by OpenSwathWorkflow (e.g. as sqMass file)) to their index (.getChromatograms[index]) More...
UInt	fromNativeID (int transition_id) const

Protected Member Functions
void	checkTransitions_ (const OSWProtein &prot) const

Private Attributes
std::map< UInt32, OSWTransition >	transitions_
std::vector< OSWProtein >	proteins_
String	source_file_
	remember from which sql OSW file this data is loaded (to lazy load more data) More...
UInt64	run_id_
	the ID of this run from the SQL RUN table More...
std::map< UInt32, UInt32 >	transID_to_index_
	map a Transition.ID (==native_id) to a chromatogram index in the sqMass experiment which contains the raw data More...

Detailed Description

Holds all or partial information from an OSW file.

First, fill in all transitions and only then add proteins (which reference transitions via their transition-ids deep down). References will be checked and enforced (exception otherwise – see addProtein()).

Member Function Documentation

addProtein()

void addProtein

(

OSWProtein &&

prot

)

Adds a protein, which has all its subcomponents already populated All transition references internally are checked to make sure they are valid. You can add stub proteins, by omitting their peptide references.

Exceptions

Exception::Precondition()

if transition IDs within protein are unknown

addTransition() [1/2]

void addTransition ( const OSWTransition &  tr )

inline

Adds a transition; do this before adding Proteins.

References OSWTransition::getID().

addTransition() [2/2]

void addTransition ( OSWTransition &&  tr )

inline

buildNativeIDResolver()

void buildNativeIDResolver

(

const MSExperiment &

chrom_traces

)

Create an internal mapping from the nativeIDs of all chromatograms (extracted by OpenSwathWorkflow (e.g. as sqMass file)) to their index (.getChromatograms[index])

The mapping is stored internally and can be used to translate transition.ids (which are native_ids) to a chromatogram index of the external sqMass file.

The mapping can be queried using fromNativeID(int transition.id).

Make sure that the other OSW data is loaded (at least via OSWFile::readMinimal()) before building this mapping here.

Parameters

chrom_traces

The external sqMass file, which we build the mapping on

Exceptions

Exception::MissingInformation	if any nativeID is not known internally
Exception::Precondition	if the run_ids do not match

checkTransitions_()

void checkTransitions_ ( const OSWProtein &  prot ) const

protected

All transition references are checked against transitions_ to make sure they are valid.

Exceptions

Exception::Precondition()

if transition IDs within protein are unknown

clear()

void clear

(

)

forget all data

clearProteins()

void clearProteins

(

)

only forget protein data

fromNativeID()

UInt fromNativeID

(

int

transition_id

)

const

resolve a transition.id (=nativeID) to a simple chromatogram index (.getChromatograms[index]) of the corresponding sqMass file Requires prior call to buildNativeIDResolver(), throws Exception::InvalidValue otherwise (or when nativeID is not known)

getProteins()

const std::vector<OSWProtein>& getProteins ( ) const

inline

constant accessor to proteins. There is no mutable access to prevent accidental violation of invariants (i.e. no matching transitions)

getRunID()

UInt64 getRunID ( ) const

inline

getSqlSourceFile()

const String& getSqlSourceFile ( ) const

inline

getTransition()

const OSWTransition& getTransition ( const UInt32  id ) const

inline

obtain a certain transition meta information with id (this matches the ID of a chromatogram in an sqMass file).

getTransitions()

const std::map<UInt32, OSWTransition>& getTransitions ( ) const

inline

get all transitions mapped by their ID (UInt32)

setProtein()

void setProtein ( const Size  index, OSWProtein &&  protein  )

inline

Replace existing protein at position index Note: this is NOT the protein ID, but the index into the internal protein vector. See getProteins()

Parameters

index	A valid index into the getProteins() vector
protein	The protein to replace the existing one

Exceptions

Exception::Precondition()

if transition IDs within protein are unknown

setRunID()

void setRunID ( const UInt64  run_id )

inline

setSqlSourceFile()

void setSqlSourceFile ( const String &  filename )

inline

transitionCount()

Size transitionCount ( ) const

inline

get the total number of transitions (chromatograms)

Member Data Documentation

proteins_

std::vector<OSWProtein> proteins_

private

run_id_

UInt64 run_id_

private

the ID of this run from the SQL RUN table

source_file_

String source_file_

private

remember from which sql OSW file this data is loaded (to lazy load more data)

transID_to_index_

std::map<UInt32, UInt32> transID_to_index_

private

map a Transition.ID (==native_id) to a chromatogram index in the sqMass experiment which contains the raw data

transitions_

std::map<UInt32, OSWTransition> transitions_

private