#include <OpenMS/FORMAT/InspectInfile.h>
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 | |
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. | |
void | setSpectra (const std::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) |
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 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) | |
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 |
InspectInfile | ( | ) |
default constructor
InspectInfile | ( | const InspectInfile & | inspect_infile | ) |
copy constructor
virtual ~InspectInfile | ( | ) | [virtual] |
destructor
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 | ) |
return the modifications (the modification names map to the affected residues, the mass change and the type)
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.
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
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
Generated Tue Apr 1 15:36:44 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |