#include <OpenMS/FORMAT/SequestInfile.h>

Collaboration diagram for SequestInfile:

Public Member Functions
	SequestInfile ()
	default constructor

	SequestInfile (const SequestInfile &sequest_infile)
	copy constructor

virtual	~SequestInfile ()
	destructor

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

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

void	store (const std::string &filename)

const std::string	getEnzymeInfoAsString () const
	returns the enzyme list as a string

const std::string &	getDatabase () const
	returns the used database

void	setDatabase (const std::string &database)
	sets the used database

const std::string &	getNeutralLossesForIons () const
	returns whether neutral losses are considered for the a-, b- and y-ions

void	setNeutralLossesForIons (const std::string &neutral_losses_for_ions)
	sets whether neutral losses are considered for the a-, b- and y-ions

const std::string &	getIonSeriesWeights () const
	returns the weights for the a-, b-, c-, d-, v-, w-, x-, y- and z-ion series

void	setIonSeriesWeights (const std::string &ion_series_weights)
	sets the weights for the a-, b-, c-, d-, v-, w-, x-, y- and z-ion series

const std::string &	getPartialSequence () const
	returns the partial sequences (space delimited) that have to occur in the theoretical spectra

void	setPartialSequence (const std::string &partial_sequence)
	sets the partial sequences (space delimited) that have to occur in the theoretical spectra

const std::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

void	setSequenceHeaderFilter (const std::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

const std::string &	getProteinMassFilter () const
	returns the protein mass filter (either min and max mass, or mass and tolerance value in percent)

void	setProteinMassFilter (const std::string &protein_mass_filter)
	sets the protein mass filter (either min and max mass, or mass and tolerance value in percent)

float	getPeakMassTolerance () const
	returns the peak mass tolerance

void	setPeakMassTolerance (float peak_mass_tolerance)
	sets the peak mass tolerance

float	getPrecursorMassTolerance () const
	returns the precursor mass tolerance

void	setPrecursorMassTolerance (float precursor_mass_tolerance)
	sets the precursor mass tolerance

float	getMatchPeakTolerance () const
	returns the match peak tolerance

void	setMatchPeakTolerance (float match_peak_tolerance)
	sets the match peak tolerance

float	getIonCutoffPercentage () const
	returns the the cutoff of the ratio matching theoretical peaks/theoretical peaks

void	setIonCutoffPercentage (float ion_cutoff_percentage)
	sets the ion cutoff of the ratio matching theoretical peaks/theoretical peaks

Size	getPeptideMassUnit () const
	returns the peptide mass unit

void	setPeptideMassUnit (Size peptide_mass_unit)
	sets the peptide mass unit

Size	getOutputLines () const
	return the number of peptides to be displayed

void	setOutputLines (Size output_lines)
	sets the number of peptides to be displayed

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

std::string	getEnzymeName () const
	returns the enzyme used for cleavage

Size	setEnzyme (const std::string &enzyme_name)
	sets the enzyme used for cleavage (by means of the number from a list of enzymes)

Size	getMaxAAPerModPerPeptide () const
	returns the maximum number of amino acids containing the same modification in a peptide

void	setMaxAAPerModPerPeptide (Size max_aa_per_mod_per_peptide)
	sets the maximum number of amino acids containing the same modification in a peptide

Size	getMaxModsPerPeptide () const
	returns the maximum number of modifications that are allowed in a peptide

void	setMaxModsPerPeptide (Size max_mods_per_peptide)
	set the maximum number of modifications that are allowed in a peptide

Size	getNucleotideReadingFrame () const
	returns the nucleotide reading frame

void	setNucleotideReadingFrame (Size nucleotide_reading_frame)

Size	getMaxInternalCleavageSites () const
	returns the maximum number of internal cleavage sites

void	setMaxInternalCleavageSites (Size max_internal_cleavage_sites)
	sets the maximum number of internal cleavage sites

Size	getMatchPeakCount () const
	returns the number of top abundant peaks to match with theoretical ones

void	setMatchPeakCount (Size match_peak_count)
	sets the number of top abundant peaks to with theoretical ones

Size	getMatchPeakAllowedError () const
	returns the number of top abundant peaks that are allowed not to match with a theoretical peak

void	setMatchPeakAllowedError (Size match_peak_allowed_error)
	sets the number of top abundant peaks that are allowed not to match with a theoretical peak

bool	getShowFragmentIons () const
	returns whether fragment ions shall be displayed

void	setShowFragmentIons (bool show_fragments)
	sets whether fragment ions shall be displayed

bool	getPrintDuplicateReferences () const
	returns whether all proteins containing a found peptide should be displayed

void	setPrintDuplicateReferences (bool print_duplicate_references)
	sets whether all proteins containing a found peptide should be displayed

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

void	setRemovePrecursorNearPeaks (bool remove_precursor_near_peaks)
	sets whether peaks near (15 amu) the precursor peak are removed

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

void	setMassTypeParent (bool mass_type_parent)
	sets the mass type of the parent (0 - monoisotopic, 1 - average mass)

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

void	setMassTypeFragment (bool mass_type_fragment)
	sets the mass type of the fragments (0 - monoisotopic, 1 - average mass)

bool	getNormalizeXcorr () const
	returns whether normalized xcorr values are displayed

void	setNormalizeXcorr (bool normalize_xcorr)
	sets whether normalized xcorr values are displayed

bool	getResiduesInUpperCase () const
	returns whether residues are in upper case

void	setResiduesInUpperCase (bool residues_in_upper_case)
	sets whether residues are in upper case

void	addEnzymeInfo (std::vector< std::string > &enzyme_info)

const std::map< std::string, std::vector< std::string > > &	getModifications () const
	return the modifications (the modification names map to the affected residues, the mass change and the type)

void	handlePTMs (const std::string &modification_line, const std::string &modifications_filename, const bool monoisotopic)

Protected Member Functions
const std::map< std::string, std::vector< std::string > > &	getEnzymeInfo_ () const
	returns the enzyme list

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

Protected Attributes
std::map< std::string, std::vector< std::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

std::string	database_
	database used

std::string	snd_database_
	second database used

std::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)

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

std::string	partial_sequence_
	space-delimited list of sequence parts that have to occur in the theoretical spectra

std::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

std::string	protein_mass_filter_

float	precursor_mass_tolerance_
	tolerance for matching a theoretical to an experimental peptide

float	peak_mass_tolerance_
	tolerance for matching a theoretical to an experimental peak

float	match_peak_tolerance_
	minimum distance between two experimental peaks

float	ion_cutoff_percentage_
	cutoff of the ratio matching theoretical peaks/theoretical peaks

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

Size	output_lines_
	number of peptides to be displayed

Size	enzyme_number_
	number of the enzyme used for cleavage

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

Size	max_mods_per_peptide_
	maximum number of modifications per peptide

Size	nucleotide_reading_frame_

Size	max_internal_cleavage_sites_
	maximum number of internal cleavage sites

Size	match_peak_count_
	number of the top abundant peaks to match with theoretical one

Size	match_peak_allowed_error_
	number of peaks that may lack this test

bool	show_fragment_ions_
	whether to display fragment ions

bool	print_duplicate_references_
	whether all proteins containing a found peptide should be displayed

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

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

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

bool	normalize_xcorr_
	whether to display normalized xcorr values

bool	residues_in_upper_case_
	whether residues are in upper case

std::map< std::string, std::vector< std::string > >	PTMname_residues_mass_type_
	the modification names map to the affected residues, the mass change and the type

Detailed Description

@brief 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< std::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 std::string & getDatabase ( ) const

returns the used database

◆ getEnzymeInfo_()

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

protected

returns the enzyme list

◆ getEnzymeInfoAsString()

const std::string getEnzymeInfoAsString ( ) const

returns the enzyme list as a string

◆ getEnzymeName()

std::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 std::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< std::string, std::vector< std::string > > & getModifications ( ) const

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

◆ getNeutralLossesForIons()

const std::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 std::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 std::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 std::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 std::string &	modification_line,
		const std::string &	modifications_filename,
		const bool	monoisotopic
	)

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

@param[in] modification_line
@param[in] modifications_filename
@param[in] monoisotopic

@throw Exception::FileNotFound is thrown if the given file is not found
@throw Exception::FileNotReadable is thrown if the given file could not be read
@throw 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 std::string & database )

sets the used database

◆ setEnzyme()

Size setEnzyme ( const std::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 std::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 std::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 std::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 std::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 std::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 std::string & filename )

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

Parameters

[out] 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_

std::string database_

protected

database used

◆ enzyme_info_

std::map<std::string, std::vector<std::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_

std::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_

std::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_

std::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_

std::string protein_mass_filter_

protected

◆ PTMname_residues_mass_type_

std::map<std::string, std::vector<std::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_

std::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_

std::string snd_database_

protected

second database used

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SequestInfile() [1/2]

◆ SequestInfile() [2/2]

◆ ~SequestInfile()

Member Function Documentation

◆ addEnzymeInfo()

◆ getDatabase()

◆ getEnzymeInfo_()

◆ getEnzymeInfoAsString()

◆ getEnzymeName()

◆ getEnzymeNumber()

◆ getIonCutoffPercentage()

◆ getIonSeriesWeights()

◆ getMassTypeFragment()

◆ getMassTypeParent()

◆ getMatchPeakAllowedError()

◆ getMatchPeakCount()

◆ getMatchPeakTolerance()

◆ getMaxAAPerModPerPeptide()

◆ getMaxInternalCleavageSites()

◆ getMaxModsPerPeptide()

◆ getModifications()

◆ getNeutralLossesForIons()

◆ getNormalizeXcorr()

◆ getNucleotideReadingFrame()

◆ getOutputLines()

◆ getPartialSequence()

◆ getPeakMassTolerance()

◆ getPeptideMassUnit()

◆ getPrecursorMassTolerance()

◆ getPrintDuplicateReferences()

◆ getProteinMassFilter()

◆ getRemovePrecursorNearPeaks()

◆ getResiduesInUpperCase()

◆ getSequenceHeaderFilter()

◆ getShowFragmentIons()

◆ handlePTMs()

◆ operator=()

◆ operator==()

◆ setDatabase()

◆ setEnzyme()

◆ setIonCutoffPercentage()

◆ setIonSeriesWeights()

◆ setMassTypeFragment()

◆ setMassTypeParent()

◆ setMatchPeakAllowedError()

◆ setMatchPeakCount()

◆ setMatchPeakTolerance()

◆ setMaxAAPerModPerPeptide()

◆ setMaxInternalCleavageSites()

◆ setMaxModsPerPeptide()

◆ setNeutralLossesForIons()

◆ setNormalizeXcorr()

◆ setNucleotideReadingFrame()

◆ setOutputLines()

◆ setPartialSequence()

◆ setPeakMassTolerance()

◆ setPeptideMassUnit()

◆ setPrecursorMassTolerance()

◆ setPrintDuplicateReferences()

◆ setProteinMassFilter()

◆ setRemovePrecursorNearPeaks()

◆ setResiduesInUpperCase()

◆ setSequenceHeaderFilter()

◆ setShowFragmentIons()

◆ setStandardEnzymeInfo_()

◆ store()

Member Data Documentation

◆ database_

◆ enzyme_info_

◆ enzyme_number_

◆ ion_cutoff_percentage_

◆ ion_series_weights_

◆ mass_type_fragment_

◆ mass_type_parent_

◆ match_peak_allowed_error_