| OpenMS 2.5.0

Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
SequestInfile Class Reference
Format » File IO

Sequest input file adapter. More...

`#include <OpenMS/FORMAT/SequestInfile.h>`

## Public Member Functions

| SequestInfile ()
| default constructor More...
| SequestInfile (const SequestInfile &sequest_infile)
| copy constructor More...
virtual | ~SequestInfile ()
| destructor More...
SequestInfile & | operator= (const SequestInfile &sequest_infile)
| assignment operator More...
bool | operator== (const SequestInfile &sequest_infile) const
| equality operator More...
void | store (const String &filename)
const String | getEnzymeInfoAsString () const
| returns the enzyme list as a string More...
const String & | getDatabase () const
| returns the used database More...
void | setDatabase (const String &database)
| sets the used database More...
const String & | getNeutralLossesForIons () const
| returns whether neutral losses are considered for the a-, b- and y-ions More...
void | setNeutralLossesForIons (const String &neutral_losses_for_ions)
| sets whether neutral losses are considered for the a-, b- and y-ions More...
const String & | getIonSeriesWeights () const
| returns the weights for the a-, b-, c-, d-, v-, w-, x-, y- and z-ion series More...
void | setIonSeriesWeights (const String &ion_series_weights)
| sets the weights for the a-, b-, c-, d-, v-, w-, x-, y- and z-ion series More...
const String & | getPartialSequence () const
| returns the partial sequences (space delimited) that have to occur in the theoretical spectra More...
void | setPartialSequence (const String &partial_sequence)
| sets the partial sequences (space delimited) that have to occur in the theoretical spectra More...
const String & | getSequenceHeaderFilter () const
| returns the sequences (space delimited) that have to occur, or be absent (preceded by a tilde) in the header of a protein to be considered More...
void | setSequenceHeaderFilter (const String &sequence_header_filter)
| sets the sequences (space delimited) that have to occur, or be absent (preceded by a tilde) in the header of a protein to be considered More...
const String & | getProteinMassFilter () const
| returns the protein mass filter (either min and max mass, or mass and tolerance value in percent) More...
void | setProteinMassFilter (const String &protein_mass_filter)
| sets the protein mass filter (either min and max mass, or mass and tolerance value in percent) More...
float | getPeakMassTolerance () const
| returns the peak mass tolerance More...
void | setPeakMassTolerance (float peak_mass_tolerance)
| sets the peak mass tolerance More...
float | getPrecursorMassTolerance () const
| returns the precursor mass tolerance More...
void | setPrecursorMassTolerance (float precursor_mass_tolerance)
| sets the precursor mass tolerance More...
float | getMatchPeakTolerance () const
| returns the match peak tolerance More...
void | setMatchPeakTolerance (float match_peak_tolerance)
| sets the match peak tolerance More...
float | getIonCutoffPercentage () const
| returns the the cutoff of the ratio matching theoretical peaks/theoretical peaks More...
void | setIonCutoffPercentage (float ion_cutoff_percentage)
| sets the ion cutoff of the ratio matching theoretical peaks/theoretical peaks More...
Size | getPeptideMassUnit () const
| returns the peptide mass unit More...
void | setPeptideMassUnit (Size peptide_mass_unit)
| sets the peptide mass unit More...
Size | getOutputLines () const
| return the number of peptides to be displayed More...
void | setOutputLines (Size output_lines)
| sets the number of peptides to be displayed More...
Size | getEnzymeNumber () const
| returns the enzyme used for cleavage (by means of the number from a list of enzymes) More...
String | getEnzymeName () const
| returns the enzyme used for cleavage More...
Size | setEnzyme (String enzyme_name)
| sets the enzyme used for cleavage (by means of the number from a list of enzymes) More...
Size | getMaxAAPerModPerPeptide () const
| returns the maximum number of amino acids containing the same modification in a peptide More...
void | setMaxAAPerModPerPeptide (Size max_aa_per_mod_per_peptide)
| sets the maximum number of amino acids containing the same modification in a peptide More...
Size | getMaxModsPerPeptide () const
| returns the maximum number of modifications that are allowed in a peptide More...
void | setMaxModsPerPeptide (Size max_mods_per_peptide)
| set the maximum number of modifications that are allowed in a peptide More...
Size | getNucleotideReadingFrame () const
| returns the nucleotide reading frame More...
void | setNucleotideReadingFrame (Size nucleotide_reading_frame)
Size | getMaxInternalCleavageSites () const
| returns the maximum number of internal cleavage sites More...
void | setMaxInternalCleavageSites (Size max_internal_cleavage_sites)
| sets the maximum number of internal cleavage sites More...
Size | getMatchPeakCount () const
| returns the number of top abundant peaks to match with theoretical ones More...
void | setMatchPeakCount (Size match_peak_count)
| sets the number of top abundant peaks to with theoretical ones More...
Size | getMatchPeakAllowedError () const
| returns the number of top abundant peaks that are allowed not to match with a theoretical peak More...
void | setMatchPeakAllowedError (Size match_peak_allowed_error)
| sets the number of top abundant peaks that are allowed not to match with a theoretical peak More...
bool | getShowFragmentIons () const
| returns whether fragment ions shall be displayed More...
void | setShowFragmentIons (bool show_fragments)
| sets whether fragment ions shall be displayed More...
bool | getPrintDuplicateReferences () const
| returns whether all proteins containing a found peptide should be displayed More...
void | setPrintDuplicateReferences (bool print_duplicate_references)
| sets whether all proteins containing a found peptide should be displayed More...
bool | getRemovePrecursorNearPeaks () const
| return whether peaks near (15 amu) the precursor peak are removed More...
void | setRemovePrecursorNearPeaks (bool remove_precursor_near_peaks)
| sets whether peaks near (15 amu) the precursor peak are removed More...
bool | getMassTypeParent () const
| return the mass type of the parent (0 - monoisotopic, 1 - average mass) More...
void | setMassTypeParent (bool mass_type_parent)
| sets the mass type of the parent (0 - monoisotopic, 1 - average mass) More...
bool | getMassTypeFragment () const
| return the mass type of the fragments (0 - monoisotopic, 1 - average mass) More...
void | setMassTypeFragment (bool mass_type_fragment)
| sets the mass type of the fragments (0 - monoisotopic, 1 - average mass) More...
bool | getNormalizeXcorr () const
| returns whether normalized xcorr values are displayed More...
void | setNormalizeXcorr (bool normalize_xcorr)
| sets whether normalized xcorr values are displayed More...
bool | getResiduesInUpperCase () const
| returns whether residues are in upper case More...
void | setResiduesInUpperCase (bool residues_in_upper_case)
| sets whether residues are in upper case More...
void | addEnzymeInfo (std::vector< String > &enzyme_info)
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...
void | handlePTMs (const String &modification_line, const String &modifications_filename, const bool monoisotopic)

## Protected Member Functions

const std::map< String, std::vector< String > > & | getEnzymeInfo_ () const
| returns the enzyme list More...
void | setStandardEnzymeInfo_ ()
| returns some standard enzymes (used to initialize the enzyme list) More...

## Protected Attributes

std::map< String, std::vector< String > > | enzyme_info_
| an endline-delimited list of enzymes; each with cutting direction 0 (N to C) /1; cuts after (list of aa); doesn't cut before (list of aa); the attributes are tab-delimited More...
String | database_
| database used More...
String | snd_database_
| second database used More...
String | neutral_losses_for_ions_
| whether neutral losses are considered for the a-; b- and y-ions (e.g. 011 for b- and y-ions) More...
String | ion_series_weights_
| weights for the a-; b-; c-; d-; v-; w-; x-; y- and z-ion series; space delimited More...
String | partial_sequence_
| space-delimited list of sequence parts that have to occur in the theoretical spectra More...
String | sequence_header_filter_
| space-delimited list of sequences that have to occur or be absent (preceded by a tilde) in a protein header; to be considered More...
String | protein_mass_filter_
float | precursor_mass_tolerance_
| tolerance for matching a theoretical to an experimental peptide More...
float | peak_mass_tolerance_
| tolerance for matching a theoretical to an experimental peak More...
float | match_peak_tolerance_
| minimum distance between two experimental peaks More...
float | ion_cutoff_percentage_
| cutoff of the ratio matching theoretical peaks/theoretical peaks More...
Size | peptide_mass_unit_
| peptide mass unit (0 = amu; 1 = mmu; 2 = ppm) More...
Size | output_lines_
| number of peptides to be displayed More...
Size | enzyme_number_
| number of the enzyme used for cleavage More...
Size | max_AA_per_mod_per_peptide_
| maximum number of amino acids containing the same modification in a peptide More...
Size | max_mods_per_peptide_
| maximum number of modifications per peptide More...
Size | nucleotide_reading_frame_
Size | max_internal_cleavage_sites_
| maximum number of internal cleavage sites More...
Size | match_peak_count_
| number of the top abundant peaks to match with theoretical one More...
Size | match_peak_allowed_error_
| number of peaks that may lack this test More...
bool | show_fragment_ions_
| whether to display fragment ions More...
bool | print_duplicate_references_
| whether all proteins containing a found peptide should be displayed More...
bool | remove_precursor_near_peaks_
| whether peaks near (15 amu) the precursor peak are removed More...
bool | mass_type_parent_
| mass type of the parent peak (0 - monoisotopic; 1 - average) More...
bool | mass_type_fragment_
| mass type of fragment peaks (0 - monoisotopic; 1 - average) More...
bool | normalize_xcorr_
| whether to display normalized xcorr values More...
bool | residues_in_upper_case_
| whether residues are in upper case 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...

## Detailed Description

Sequest input file adapter.

Creates a sequest.params file for Sequest search from a peak list.

## Constructor & Destructor Documentation

## ◆ SequestInfile() [1/2]

SequestInfile | ( |  | ) |

default constructor

## ◆ SequestInfile() [2/2]

SequestInfile | ( | const SequestInfile & | sequest_infile | ) |

copy constructor

## ◆ ~SequestInfile()

virtual ~SequestInfile | ( |  | ) |

virtual

destructor

## Member Function Documentation

## ◆ addEnzymeInfo()

void addEnzymeInfo | ( | std::vector< String > & | enzyme_info | ) |

adds an enzyme to the list and sets is as used the vector consists of four strings: name, cut direction: 0 (N to C) / 1, cuts after (list of aa), doesn't cut before (list of aa)

## ◆ getDatabase()

const String& getDatabase | ( |  | ) | const

returns the used database

## ◆ getEnzymeInfo_()

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

protected

returns the enzyme list

## ◆ getEnzymeInfoAsString()

const String getEnzymeInfoAsString | ( |  | ) | const

returns the enzyme list as a string

## ◆ getEnzymeName()

String getEnzymeName | ( |  | ) | const

returns the enzyme used for cleavage

## ◆ getEnzymeNumber()

Size getEnzymeNumber | ( |  | ) | const

returns the enzyme used for cleavage (by means of the number from a list of enzymes)

## ◆ getIonCutoffPercentage()

float getIonCutoffPercentage | ( |  | ) | const

returns the the cutoff of the ratio matching theoretical peaks/theoretical peaks

## ◆ getIonSeriesWeights()

const String& getIonSeriesWeights | ( |  | ) | const

returns the weights for the a-, b-, c-, d-, v-, w-, x-, y- and z-ion series

## ◆ getMassTypeFragment()

bool getMassTypeFragment | ( |  | ) | const

return the mass type of the fragments (0 - monoisotopic, 1 - average mass)

## ◆ getMassTypeParent()

bool getMassTypeParent | ( |  | ) | const

return the mass type of the parent (0 - monoisotopic, 1 - average mass)

## ◆ getMatchPeakAllowedError()

Size getMatchPeakAllowedError | ( |  | ) | const

returns the number of top abundant peaks that are allowed not to match with a theoretical peak

## ◆ getMatchPeakCount()

Size getMatchPeakCount | ( |  | ) | const

returns the number of top abundant peaks to match with theoretical ones

## ◆ getMatchPeakTolerance()

float getMatchPeakTolerance | ( |  | ) | const

returns the match peak tolerance

## ◆ getMaxAAPerModPerPeptide()

Size getMaxAAPerModPerPeptide | ( |  | ) | const

returns the maximum number of amino acids containing the same modification in a peptide

## ◆ getMaxInternalCleavageSites()

Size getMaxInternalCleavageSites | ( |  | ) | const

returns the maximum number of internal cleavage sites

## ◆ getMaxModsPerPeptide()

Size getMaxModsPerPeptide | ( |  | ) | const

returns the maximum number of modifications that are allowed in a peptide

## ◆ getModifications()

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)

## ◆ getNeutralLossesForIons()

const String& getNeutralLossesForIons | ( |  | ) | const

returns whether neutral losses are considered for the a-, b- and y-ions

## ◆ getNormalizeXcorr()

bool getNormalizeXcorr | ( |  | ) | const

returns whether normalized xcorr values are displayed

## ◆ getNucleotideReadingFrame()

Size getNucleotideReadingFrame | ( |  | ) | const

returns the nucleotide reading frame

## ◆ getOutputLines()

Size getOutputLines | ( |  | ) | const

return the number of peptides to be displayed

## ◆ getPartialSequence()

const String& getPartialSequence | ( |  | ) | const

returns the partial sequences (space delimited) that have to occur in the theoretical spectra

## ◆ getPeakMassTolerance()

float getPeakMassTolerance | ( |  | ) | const

returns the peak mass tolerance

## ◆ getPeptideMassUnit()

Size getPeptideMassUnit | ( |  | ) | const

returns the peptide mass unit

## ◆ getPrecursorMassTolerance()

float getPrecursorMassTolerance | ( |  | ) | const

returns the precursor mass tolerance

## ◆ getPrintDuplicateReferences()

bool getPrintDuplicateReferences | ( |  | ) | const

returns whether all proteins containing a found peptide should be displayed

## ◆ getProteinMassFilter()

const String& getProteinMassFilter | ( |  | ) | const

returns the protein mass filter (either min and max mass, or mass and tolerance value in percent)

## ◆ getRemovePrecursorNearPeaks()

bool getRemovePrecursorNearPeaks | ( |  | ) | const

return whether peaks near (15 amu) the precursor peak are removed

## ◆ getResiduesInUpperCase()

bool getResiduesInUpperCase | ( |  | ) | const

returns whether residues are in upper case

## ◆ getSequenceHeaderFilter()

const String& getSequenceHeaderFilter | ( |  | ) | const

returns the sequences (space delimited) that have to occur, or be absent (preceded by a tilde) in the header of a protein to be considered

## ◆ getShowFragmentIons()

bool getShowFragmentIons | ( |  | ) | const

returns whether fragment ions shall be displayed

## ◆ handlePTMs()

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 |

Exceptions

  Exception::FileNotFound | is thrown if the given file is not found
  Exception::FileNotReadable | is thrown if the given file could not be read
  Exception::ParseError | is thrown if the given file could not be parsed

## ◆ operator=()

SequestInfile& operator= | ( | const SequestInfile & | sequest_infile | ) |

assignment operator

## ◆ operator==()

bool operator== | ( | const SequestInfile & | sequest_infile | ) | const

equality operator

## ◆ setDatabase()

void setDatabase | ( | const String & | database | ) |

sets the used database

## ◆ setEnzyme()

Size setEnzyme | ( | String | enzyme_name | ) |

sets the enzyme used for cleavage (by means of the number from a list of enzymes)

## ◆ setIonCutoffPercentage()

void setIonCutoffPercentage | ( | float | ion_cutoff_percentage | ) |

sets the ion cutoff of the ratio matching theoretical peaks/theoretical peaks

## ◆ setIonSeriesWeights()

void setIonSeriesWeights | ( | const String & | ion_series_weights | ) |

sets the weights for the a-, b-, c-, d-, v-, w-, x-, y- and z-ion series

## ◆ setMassTypeFragment()

void setMassTypeFragment | ( | bool | mass_type_fragment | ) |

sets the mass type of the fragments (0 - monoisotopic, 1 - average mass)

## ◆ setMassTypeParent()

void setMassTypeParent | ( | bool | mass_type_parent | ) |

sets the mass type of the parent (0 - monoisotopic, 1 - average mass)

## ◆ setMatchPeakAllowedError()

void setMatchPeakAllowedError | ( | Size | match_peak_allowed_error | ) |

sets the number of top abundant peaks that are allowed not to match with a theoretical peak

## ◆ setMatchPeakCount()

void setMatchPeakCount | ( | Size | match_peak_count | ) |

sets the number of top abundant peaks to with theoretical ones

## ◆ setMatchPeakTolerance()

void setMatchPeakTolerance | ( | float | match_peak_tolerance | ) |

sets the match peak tolerance

## ◆ setMaxAAPerModPerPeptide()

void setMaxAAPerModPerPeptide | ( | Size | max_aa_per_mod_per_peptide | ) |

sets the maximum number of amino acids containing the same modification in a peptide

## ◆ setMaxInternalCleavageSites()

void setMaxInternalCleavageSites | ( | Size | max_internal_cleavage_sites | ) |

sets the maximum number of internal cleavage sites

## ◆ setMaxModsPerPeptide()

void setMaxModsPerPeptide | ( | Size | max_mods_per_peptide | ) |

set the maximum number of modifications that are allowed in a peptide

## ◆ setNeutralLossesForIons()

void setNeutralLossesForIons | ( | const String & | neutral_losses_for_ions | ) |

sets whether neutral losses are considered for the a-, b- and y-ions

## ◆ setNormalizeXcorr()

void setNormalizeXcorr | ( | bool | normalize_xcorr | ) |

sets whether normalized xcorr values are displayed

## ◆ setNucleotideReadingFrame()

void setNucleotideReadingFrame | ( | Size | nucleotide_reading_frame | ) |

sets the nucleotide reading frame: 0 The FASTA file contains amino acid codes. No translation is needed. This is the best and fastest case. 1 The DNA sequence is scanned left to right (forward direction). The amino acid code starts with the first DNA code. 2 The DNA sequence is scanned left to right (forward direction). The amino acid code starts with the second DNA code. 3 The DNA sequence is scanned left to right (forward direction). The amino acid code starts with the third DNA code. 4 The DNA sequence is scanned right to left (backward direction for the complementary strand). The amino acid code starts with the first DNA code. 5 The DNA sequence is scanned right to left (backward direction for the complementary strand). The amino acid code starts with the second DNA code. 6 The DNA sequence is scanned right to left (backward direction for the complementary strand). The amino acid code starts with the third DNA code. 7 Use each of the DNA translations of the codes 1, 2, 3. 8 Use each of the DNA translations of the codes 4, 5, 6. 9 Use each of the DNA translations of the codes 1, 2, 3, 4, 5, 6.

## ◆ setOutputLines()

void setOutputLines | ( | Size | output_lines | ) |

sets the number of peptides to be displayed

## ◆ setPartialSequence()

void setPartialSequence | ( | const String & | partial_sequence | ) |

sets the partial sequences (space delimited) that have to occur in the theoretical spectra

## ◆ setPeakMassTolerance()

void setPeakMassTolerance | ( | float | peak_mass_tolerance | ) |

sets the peak mass tolerance

## ◆ setPeptideMassUnit()

void setPeptideMassUnit | ( | Size | peptide_mass_unit | ) |

sets the peptide mass unit

## ◆ setPrecursorMassTolerance()

void setPrecursorMassTolerance | ( | float | precursor_mass_tolerance | ) |

sets the precursor mass tolerance

## ◆ setPrintDuplicateReferences()

void setPrintDuplicateReferences | ( | bool | print_duplicate_references | ) |

sets whether all proteins containing a found peptide should be displayed

## ◆ setProteinMassFilter()

void setProteinMassFilter | ( | const String & | protein_mass_filter | ) |

sets the protein mass filter (either min and max mass, or mass and tolerance value in percent)

## ◆ setRemovePrecursorNearPeaks()

void setRemovePrecursorNearPeaks | ( | bool | remove_precursor_near_peaks | ) |

sets whether peaks near (15 amu) the precursor peak are removed

## ◆ setResiduesInUpperCase()

void setResiduesInUpperCase | ( | bool | residues_in_upper_case | ) |

sets whether residues are in upper case

## ◆ setSequenceHeaderFilter()

void setSequenceHeaderFilter | ( | const String & | sequence_header_filter | ) |

sets the sequences (space delimited) that have to occur, or be absent (preceded by a tilde) in the header of a protein to be considered

## ◆ setShowFragmentIons()

void setShowFragmentIons | ( | bool | show_fragments | ) |

sets whether fragment ions shall be displayed

## ◆ setStandardEnzymeInfo_()

void setStandardEnzymeInfo_ | ( |  | ) |

protected

returns some standard enzymes (used to initialize the enzyme list)

## ◆ store()

void store | ( | const String & | filename | ) |

stores the experiment data in a Sequest input file that can be used as input for Sequest shell execution

Parameters

  filename | the name of the file in which the infile is stored into

Exceptions

  Exception::UnableToCreateFile | is thrown if the file could not be created

## Member Data Documentation

## ◆ database_

String database_

protected

database used

## ◆ enzyme_info_

std::map<String, std::vector<String> > enzyme_info_

protected

an endline-delimited list of enzymes; each with cutting direction 0 (N to C) /1; cuts after (list of aa); doesn't cut before (list of aa); the attributes are tab-delimited

## ◆ enzyme_number_

Size enzyme_number_

protected

number of the enzyme used for cleavage

## ◆ ion_cutoff_percentage_

float ion_cutoff_percentage_

protected

cutoff of the ratio matching theoretical peaks/theoretical peaks

## ◆ ion_series_weights_

String ion_series_weights_

protected

weights for the a-; b-; c-; d-; v-; w-; x-; y- and z-ion series; space delimited

## ◆ mass_type_fragment_

bool mass_type_fragment_

protected

mass type of fragment peaks (0 - monoisotopic; 1 - average)

## ◆ mass_type_parent_

bool mass_type_parent_

protected

mass type of the parent peak (0 - monoisotopic; 1 - average)

## ◆ match_peak_allowed_error_

Size match_peak_allowed_error_

protected

number of peaks that may lack this test

## ◆ match_peak_count_

Size match_peak_count_

protected

number of the top abundant peaks to match with theoretical one

## ◆ match_peak_tolerance_

float match_peak_tolerance_

protected

minimum distance between two experimental peaks

## ◆ max_AA_per_mod_per_peptide_

Size max_AA_per_mod_per_peptide_

protected

maximum number of amino acids containing the same modification in a peptide

## ◆ max_internal_cleavage_sites_

Size max_internal_cleavage_sites_

protected

maximum number of internal cleavage sites

0 The FASTA file contains amino acid codes. No translation is needed. This is the best and fastest case. 1 The DNA sequence is scanned left to right (forward direction). The amino acid code starts with the first DNA code. 2 The DNA sequence is scanned left to right (forward direction). The amino acid code starts with the second DNA code. 3 The DNA sequence is scanned left to right (forward direction). The amino acid code starts with the third DNA code. 4 The DNA sequence is scanned right to left (backward direction for the complementary strand). The amino acid code starts with the first DNA code. 5 The DNA sequence is scanned right to left (backward direction for the complementary strand). The amino acid code starts with the second DNA code. 6 The DNA sequence is scanned right to left (backward direction for the complementary strand). The amino acid code starts with the third DNA code. 7 Use each of the DNA translations of the codes 1; 2; 3. 8 Use each of the DNA translations of the codes 4; 5; 6. 9 Use each of the DNA translations of the codes 1; 2; 3; 4; 5; 6.

## ◆ max_mods_per_peptide_

Size max_mods_per_peptide_

protected

maximum number of modifications per peptide

## ◆ neutral_losses_for_ions_

String neutral_losses_for_ions_

protected

whether neutral losses are considered for the a-; b- and y-ions (e.g. 011 for b- and y-ions)

## ◆ normalize_xcorr_

bool normalize_xcorr_

protected

whether to display normalized xcorr values

## ◆ nucleotide_reading_frame_

Size nucleotide_reading_frame_

protected

nucleotide reading frame:

## ◆ output_lines_

Size output_lines_

protected

number of peptides to be displayed

## ◆ partial_sequence_

String partial_sequence_

protected

space-delimited list of sequence parts that have to occur in the theoretical spectra

## ◆ peak_mass_tolerance_

float peak_mass_tolerance_

protected

tolerance for matching a theoretical to an experimental peak

## ◆ peptide_mass_unit_

Size peptide_mass_unit_

protected

peptide mass unit (0 = amu; 1 = mmu; 2 = ppm)

## ◆ precursor_mass_tolerance_

float precursor_mass_tolerance_

protected

tolerance for matching a theoretical to an experimental peptide

## ◆ print_duplicate_references_

bool print_duplicate_references_

protected

whether all proteins containing a found peptide should be displayed

## ◆ protein_mass_filter_

String protein_mass_filter_

protected

## ◆ PTMname_residues_mass_type_

std::map<String, std::vector<String> > PTMname_residues_mass_type_

protected

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

## ◆ remove_precursor_near_peaks_

bool remove_precursor_near_peaks_

protected

whether peaks near (15 amu) the precursor peak are removed

## ◆ residues_in_upper_case_

bool residues_in_upper_case_

protected

whether residues are in upper case

## ◆ sequence_header_filter_

String sequence_header_filter_

protected

space-delimited list of sequences that have to occur or be absent (preceded by a tilde) in a protein header; to be considered

## ◆ show_fragment_ions_

bool show_fragment_ions_

protected

whether to display fragment ions

## ◆ snd_database_

String snd_database_

protected

second database used