OpenMS
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Inspect input file adapter. More...
#include <OpenMS/FORMAT/InspectInfile.h>
Public Member Functions | |
InspectInfile () | |
default constructor More... | |
InspectInfile (const InspectInfile &inspect_infile) | |
copy constructor More... | |
virtual | ~InspectInfile () |
destructor More... | |
InspectInfile & | operator= (const InspectInfile &inspect_infile) |
assignment operator More... | |
bool | operator== (const InspectInfile &inspect_infile) const |
equality operator More... | |
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. More... | |
void | setSpectra (const String &spectra) |
const String & | getDb () const |
Specifies the name of a database (.trie file) to search. More... | |
void | setDb (const String &db) |
const String & | getEnzyme () const |
Specifies the name of a enzyme. "Trypsin", "None", and "Chymotrypsin" are the available values. More... | |
void | setEnzyme (const String &enzyme) |
Int | getModificationsPerPeptide () const |
Number of PTMs permitted in a single peptide. More... | |
void | setModificationsPerPeptide (Int modifications_per_peptide) |
UInt | getBlind () const |
run Inspect in a blind mode More... | |
void | setBlind (UInt blind) |
float | getMaxPTMsize () const |
the maximum modification size (in Da) to consider in a blind search More... | |
void | setMaxPTMsize (float maxptmsize) |
float | getPrecursorMassTolerance () const |
Specifies the parent mass tolerance, in Daltons. More... | |
void | setPrecursorMassTolerance (float precursor_mass_tolerance) |
float | getPeakMassTolerance () const |
How far b and y peaks can be shifted from their expected masses. More... | |
void | setPeakMassTolerance (float 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. More... | |
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. More... | |
void | setInstrument (const String &instrument) |
Int | getTagCount () const |
Number of tags to generate. More... | |
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) More... | |
Private Attributes | |
String | spectra_ |
Specifies a spectrum file to search. More... | |
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. More... | |
String | enzyme_ |
Specifies the name of a enzyme. "Trypsin", "None", and "Chymotrypsin" are the available values. More... | |
Int | modifications_per_peptide_ |
allowed number of modifications per peptide More... | |
UInt | blind_ |
float | maxptmsize_ |
0 - false, 1 - true, 2 - not set More... | |
float | 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 this amount. <0 is not set. More... | |
float | 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. More... | |
UInt | multicharge_ |
String | instrument_ |
0 - false, 1 - true, 2 - not set More... | |
Int | tag_count_ |
Number of tags to generate. <0 is not set. More... | |
std::map< String, std::vector< String > > | PTMname_residues_mass_type_ |
the modification names map to the affected residues, the mass change and the type More... | |
Inspect input file adapter.
Creates a file that can be used for Inspect search from a peak list.
InspectInfile | ( | ) |
default constructor
InspectInfile | ( | const InspectInfile & | inspect_infile | ) |
copy constructor
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virtual |
destructor
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.
float getMaxPTMsize | ( | ) | const |
the maximum modification size (in Da) to consider in a blind search
Defaults to 200. Larger values require more time to search.
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.
float 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.
float 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
modification_line | |
modifications_filename | |
monoisotopic | if true, masses are considered to be monoisotopic |
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 | ( | float | maxptmsize | ) |
void setModificationsPerPeptide | ( | Int | modifications_per_peptide | ) |
void setMulticharge | ( | UInt | multicharge | ) |
void setPeakMassTolerance | ( | float | peak_mass_tolerance | ) |
void setPrecursorMassTolerance | ( | float | 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
filename | set the given filename |
UnableToCreateFile | is thrown if the file could not be created |
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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)
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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.
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private |
Specifies the name of a enzyme. "Trypsin", "None", and "Chymotrypsin" are the available values.
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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.
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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
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private |
allowed number of modifications per peptide
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private |
If set to true, attempt to guess the precursor charge and mass, and consider multiple charge states if feasible.
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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.
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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 this amount. <0 is not set.
the modification names map to the affected residues, the mass change and the type
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private |
Specifies a spectrum file to search.
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private |
Number of tags to generate. <0 is not set.