InspectInfile Class Reference [File IO]

Inspect input file adapter. More...

#include <OpenMS/FORMAT/InspectInfile.h>

List of all members.

Public Member Functions
	InspectInfile ()
	default constructor
	InspectInfile (const InspectInfile &inspect_infile)
	copy constructor
virtual	~InspectInfile ()
	destructor
InspectInfile &	operator= (const InspectInfile &inspect_infile)
	assignment operator
bool	operator== (const InspectInfile &inspect_infile) const
	equality operator
void	store (const String &filename)
void	handlePTMs (const String &modification_line, const String &modifications_filename, const bool monoisotopic)
const String &	getSpectra () const
	Specifies a spectrum file to search.
void	setSpectra (const String &spectra)
const String &	getDb () const
	Specifies the name of a database (.trie file) to search.
void	setDb (const String &db)
const String &	getEnzyme () const
	Specifies the name of a enzyme. "Trypsin", "None", and "Chymotrypsin" are the available values.
void	setEnzyme (const String &enzyme)
Int	getModificationsPerPeptide () const
	Number of PTMs permitted in a single peptide.
void	setModificationsPerPeptide (Int modifications_per_peptide)
UInt	getBlind () const
	run Inspect in a blind mode
void	setBlind (UInt blind)
Real	getMaxPTMsize () const
	the maximum modification size (in Da) to consider in a blind search
void	setMaxPTMsize (Real maxptmsize)
Real	getPrecursorMassTolerance () const
	Specifies the parent mass tolerance, in Daltons.
void	setPrecursorMassTolerance (Real precursor_mass_tolerance)
Real	getPeakMassTolerance () const
	How far b and y peaks can be shifted from their expected masses.
void	setPeakMassTolerance (Real peak_mass_tolerance)
UInt	getMulticharge () const
	If set to true, attempt to guess the precursor charge and mass, and consider multiple charge states if feasible.
void	setMulticharge (UInt multicharge)
const String &	getInstrument () const
	If set to QTOF, uses a QTOF-derived fragmentation model, and does not attempt to correct the parent mass.
void	setInstrument (const String &instrument)
Int	getTagCount () const
	Number of tags to generate.
void	setTagCount (Int TagCount)
const Map< String, std::vector < String > > &	getModifications () const
	return the modifications (the modification names map to the affected residues, the mass change and the type)
Private Attributes
String	spectra_
	Specifies a spectrum file to search.
String	db_
	Specifies the name of a database (.trie file) to search. The .trie file contains one or more protein sequences delimited by asterisks, with no whitespace or other data.
String	enzyme_
	Specifies the name of a enzyme. "Trypsin", "None", and "Chymotrypsin" are the available values.
Int	modifications_per_peptide_
	allowed number of modifications per peptide
UInt	blind_
Real	maxptmsize_
	0 - false, 1 - true, 2 - not set
Real	precursor_mass_tolerance_
	Specifies the parent mass tolerance, in Daltons. A candidate's flanking mass can differ from the tag's flanking mass by no more than ths amount. <0 is not set.
Real	peak_mass_tolerance_
	How far b and y peaks can be shifted from their expected masses. Default is 0.5. Higher values produce a more sensitive but much slower search. <0 is not set.
UInt	multicharge_
String	instrument_
	0 - false, 1 - true, 2 - not set
Int	tag_count_
	Number of tags to generate. <0 is not set.
Map< String, std::vector < String > >	PTMname_residues_mass_type_
	the modification names map to the affected residues, the mass change and the type

---

Detailed Description

Inspect input file adapter.

Creates a file that can be used for Inspect search from a peak list.

---

Constructor & Destructor Documentation

InspectInfile

(

)

default constructor

InspectInfile

(

const InspectInfile &

inspect_infile

)

copy constructor

virtual ~InspectInfile

(

)

[virtual]

destructor

---

Member Function Documentation

UInt getBlind

(

)

const

run Inspect in a blind mode

If true, use the MS-Alignment algorithm to perform a blind search (allowing arbitrary modification masses). Running a blind search with one mod per peptide is slower than the normal (tag-based) search; running time is approximately 1 second per spectra per megabyte of database. Running a blind search with two mods is significantly slower. We recommend performing "blind" searches against a small database, containing proteins output by an earlier search.

const String& getDb

(

)

const

Specifies the name of a database (.trie file) to search.

The .trie file contains one or more protein sequences delimited by asterisks, with no whitespace or other data. Use PrepDB.py (see above) to prepare a .trie file. Most .trie files have a corresponding .index file giving the names of the proteins. You can specify at most one database.

const String& getEnzyme

(

)

const

Specifies the name of a enzyme. "Trypsin", "None", and "Chymotrypsin" are the available values.

const String& getInstrument

(

)

const

If set to QTOF, uses a QTOF-derived fragmentation model, and does not attempt to correct the parent mass.

Real getMaxPTMsize

(

)

const

the maximum modification size (in Da) to consider in a blind search

Defaults to 200. Larger values require more time to search.

const Map<String, std::vector<String> >& getModifications

(

)

const

return the modifications (the modification names map to the affected residues, the mass change and the type)

Int getModificationsPerPeptide

(

)

const

Number of PTMs permitted in a single peptide.

UInt getMulticharge

(

)

const

If set to true, attempt to guess the precursor charge and mass, and consider multiple charge states if feasible.

Real getPeakMassTolerance

(

)

const

How far b and y peaks can be shifted from their expected masses.

Default is 0.5. Higher values produce a more sensitive but much slower search.

Real getPrecursorMassTolerance

(

)

const

Specifies the parent mass tolerance, in Daltons.

A candidate's flanking mass can differ from the tag's flanking mass by no more than this amount.

const String& getSpectra

(

)

const

Specifies a spectrum file to search.

You can specify the name of a directory to search every file in that directory (non-recursively). Supported spectra file formats are .mzXML, .mzData, .ms2, dta, and .pkl. Multiple spectra in one .dta file are not supported.

Int getTagCount

(

)

const

Number of tags to generate.

void handlePTMs	(	const String &	modification_line,
		const String &	modifications_filename,
		const bool	monoisotopic
	)

retrieves the name, mass change, affected residues, type and position for all modifications from a string

Parameters:

	modification_line
	modifications_filename
	monoisotopic	if true, masses are considered to be monoisotopic

Exceptions:

	FileNotReadable	if the modifications_filename could not be read
	FileNotFound	if modifications_filename could not be found
	ParseError	if modifications_filename could not be parsed

InspectInfile& operator=

(

const InspectInfile &

inspect_infile

)

assignment operator

bool operator==

(

const InspectInfile &

inspect_infile

)

const

equality operator

void setBlind

(

UInt

blind

)

void setDb

(

const String &

db

)

void setEnzyme

(

const String &

enzyme

)

void setInstrument

(

const String &

instrument

)

void setMaxPTMsize

(

Real

maxptmsize

)

void setModificationsPerPeptide

(

Int

modifications_per_peptide

)

void setMulticharge

(

UInt

multicharge

)

void setPeakMassTolerance

(

Real

peak_mass_tolerance

)

void setPrecursorMassTolerance

(

Real

precursor_mass_tolerance

)

void setSpectra

(

const String &

spectra

)

void setTagCount

(

Int

TagCount

)

void store

(

const String &

filename

)

stores the experiment data in an Inspect input file that can be used as input for Inspect shell execution

Parameters:

filename

set the given filename

Exceptions:

UnableToCreateFile

is thrown if the file could not be created

---

Member Data Documentation

UInt blind_ [private]

If true, use the MS-Alignment algorithm to perform a blind search (allowing arbitrary modification masses). Running a blind search with one mod per peptide is slower than the normal (tag-based) search; running time is approximately 1 second per spectra per megabyte of database. Running a blind search with two mods is significantly slower. We recommend performing "blind" searches against a small database, containing proteins output by an earlier search. (The "Summary.py" script can be used to generate a second-pass database from initial search results)

String db_ [private]

Specifies the name of a database (.trie file) to search. The .trie file contains one or more protein sequences delimited by asterisks, with no whitespace or other data.

String enzyme_ [private]

Specifies the name of a enzyme. "Trypsin", "None", and "Chymotrypsin" are the available values.

String instrument_ [private]

0 - false, 1 - true, 2 - not set

If set to QTOF, uses a QTOF-derived fragmentation model, and does not attempt to correct the parent mass.

Real maxptmsize_ [private]

0 - false, 1 - true, 2 - not set

For blind search, specifies the maximum modification size (in Da) to consider. Defaults to 200. Larger values require more time to search. <0 is not set

Int modifications_per_peptide_ [private]

allowed number of modifications per peptide

UInt multicharge_ [private]

If set to true, attempt to guess the precursor charge and mass, and consider multiple charge states if feasible.

Real peak_mass_tolerance_ [private]

How far b and y peaks can be shifted from their expected masses. Default is 0.5. Higher values produce a more sensitive but much slower search. <0 is not set.

Real precursor_mass_tolerance_ [private]

Specifies the parent mass tolerance, in Daltons. A candidate's flanking mass can differ from the tag's flanking mass by no more than ths amount. <0 is not set.

Map<String, std::vector<String> > PTMname_residues_mass_type_ [private]

the modification names map to the affected residues, the mass change and the type

String spectra_ [private]

Specifies a spectrum file to search.

Int tag_count_ [private]

Number of tags to generate. <0 is not set.