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) |
| Real | getMaxPTMsize () const |
| the maximum modification size (in Da) to consider in a blind search More... | |
| void | setMaxPTMsize (Real maxptmsize) |
| Real | getPrecursorMassTolerance () const |
| Specifies the parent mass tolerance, in Daltons. More... | |
| void | setPrecursorMassTolerance (Real precursor_mass_tolerance) |
| Real | getPeakMassTolerance () const |
| How far b and y peaks can be shifted from their expected masses. More... | |
| 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. 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 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_ |
| Real | maxptmsize_ |
| 0 - false, 1 - true, 2 - not set More... | |
| 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. More... | |
| 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. 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... | |
| 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
|
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.
| 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.
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
| 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 | ( | 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
| 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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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.
|
private |
Specifies the name of a enzyme. "Trypsin", "None", and "Chymotrypsin" are the available values.
|
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.
|
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.
|
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.
|
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.
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.
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:30 using doxygen 1.8.5 |