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InspectInfile Class Reference
[File IO]

#include <OpenMS/FORMAT/InspectInfile.h>

List of all members.


Detailed Description

Inspect input file adapter.

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

Public Member Functions

 InspectInfile ()
 default constructor
 InspectInfile (const InspectInfile &inspect_infile)
 copy constructor
virtual ~InspectInfile ()
 destructor
InspectInfileoperator= (const InspectInfile &inspect_infile)
 assignment operator
bool operator== (const InspectInfile &inspect_infile) const
 equality operator
void store (const String &filename) throw (Exception::UnableToCreateFile)
 stores the experiment data in an Inspect input file that can be used as input for Inspect shell execution
void handlePTMs (const String &modification_line, const String &modifications_filename, const bool monoisotopic) throw (Exception::FileNotReadable, Exception::FileNotFound, Exception::ParseError)
 retrieves the name, mass change, affected residues, type and position for all modifications from a string
const std::string & getSpectra () const
 Specifies a spectrum file to search.
void setSpectra (const std::string &spectra)
const StringgetDb () const
 Specifies the name of a database (.trie file) to search.
void setDb (const String &db)
const StringgetEnzyme () 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)
const Real getMaxPTMsize () const
 the maximum modification size (in Da) to consider in a blind search
void setMaxPTMsize (Real maxptmsize)
const Real getPrecursorMassTolerance () const
 Specifies the parent mass tolerance, in Daltons.
void setPrecursorMassTolerance (Real precursor_mass_tolerance)
const 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 StringgetInstrument () 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 std::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.
std::map< String, std::vector
< String > > 
PTMname_residues_mass_type_
 the modification names map to the affected residues, the mass change and the type


Constructor & Destructor Documentation

InspectInfile (  ) 

default constructor

InspectInfile ( const InspectInfile inspect_infile  ) 

copy constructor

virtual ~InspectInfile (  )  [virtual]

destructor


Member Function Documentation

InspectInfile& operator= ( const InspectInfile inspect_infile  ) 

assignment operator

bool operator== ( const InspectInfile inspect_infile  )  const

equality operator

void store ( const String filename  )  throw (Exception::UnableToCreateFile)

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

void handlePTMs ( const String modification_line,
const String modifications_filename,
const bool  monoisotopic 
) throw (Exception::FileNotReadable, Exception::FileNotFound, Exception::ParseError)

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

const std::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.

void setSpectra ( const std::string &  spectra  ) 

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.

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

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.

void setBlind ( UInt  blind  ) 

const 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.

void setMaxPTMsize ( Real  maxptmsize  ) 

const 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.

void setPrecursorMassTolerance ( Real  precursor_mass_tolerance  ) 

const 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.

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 std::map< String, std::vector< String > >& getModifications (  )  const

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


Member Data Documentation

String spectra_ [private]

Specifies a spectrum file to search.

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.

Int modifications_per_peptide_ [private]

allowed number of modifications per peptide

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)

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

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.

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.

UInt multicharge_ [private]

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

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.

Int tag_count_ [private]

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

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

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


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:44 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1