SequestInfile Member List

This is the complete list of members for SequestInfile, including all inherited members.

addEnzymeInfo(std::vector< String > &enzyme_info)	SequestInfile
database_	SequestInfile	protected
enzyme_info_	SequestInfile	protected
enzyme_number_	SequestInfile	protected
getDatabase() const	SequestInfile
getEnzymeInfo_() const	SequestInfile	protected
getEnzymeInfoAsString() const	SequestInfile
getEnzymeName() const	SequestInfile
getEnzymeNumber() const	SequestInfile
getIonCutoffPercentage() const	SequestInfile
getIonSeriesWeights() const	SequestInfile
getMassTypeFragment() const	SequestInfile
getMassTypeParent() const	SequestInfile
getMatchPeakAllowedError() const	SequestInfile
getMatchPeakCount() const	SequestInfile
getMatchPeakTolerance() const	SequestInfile
getMaxAAPerModPerPeptide() const	SequestInfile
getMaxInternalCleavageSites() const	SequestInfile
getMaxModsPerPeptide() const	SequestInfile
getModifications() const	SequestInfile
getNeutralLossesForIons() const	SequestInfile
getNormalizeXcorr() const	SequestInfile
getNucleotideReadingFrame() const	SequestInfile
getOutputLines() const	SequestInfile
getPartialSequence() const	SequestInfile
getPeakMassTolerance() const	SequestInfile
getPeptideMassUnit() const	SequestInfile
getPrecursorMassTolerance() const	SequestInfile
getPrintDuplicateReferences() const	SequestInfile
getProteinMassFilter() const	SequestInfile
getRemovePrecursorNearPeaks() const	SequestInfile
getResiduesInUpperCase() const	SequestInfile
getSequenceHeaderFilter() const	SequestInfile
getShowFragmentIons() const	SequestInfile
handlePTMs(const String &modification_line, const String &modifications_filename, const bool monoisotopic)	SequestInfile
ion_cutoff_percentage_	SequestInfile	protected
ion_series_weights_	SequestInfile	protected
mass_type_fragment_	SequestInfile	protected
mass_type_parent_	SequestInfile	protected
match_peak_allowed_error_	SequestInfile	protected
match_peak_count_	SequestInfile	protected
match_peak_tolerance_	SequestInfile	protected
max_AA_per_mod_per_peptide_	SequestInfile	protected
max_internal_cleavage_sites_	SequestInfile	protected
max_mods_per_peptide_	SequestInfile	protected
neutral_losses_for_ions_	SequestInfile	protected
normalize_xcorr_	SequestInfile	protected
nucleotide_reading_frame_	SequestInfile	protected
operator=(const SequestInfile &sequest_infile)	SequestInfile
operator==(const SequestInfile &sequest_infile) const	SequestInfile
output_lines_	SequestInfile	protected
partial_sequence_	SequestInfile	protected
peak_mass_tolerance_	SequestInfile	protected
peptide_mass_unit_	SequestInfile	protected
precursor_mass_tolerance_	SequestInfile	protected
print_duplicate_references_	SequestInfile	protected
protein_mass_filter_	SequestInfile	protected
PTMname_residues_mass_type_	SequestInfile	protected
remove_precursor_near_peaks_	SequestInfile	protected
residues_in_upper_case_	SequestInfile	protected
sequence_header_filter_	SequestInfile	protected
SequestInfile()	SequestInfile
SequestInfile(const SequestInfile &sequest_infile)	SequestInfile
setDatabase(const String &database)	SequestInfile
setEnzyme(String enzyme_name)	SequestInfile
setIonCutoffPercentage(float ion_cutoff_percentage)	SequestInfile
setIonSeriesWeights(const String &ion_series_weights)	SequestInfile
setMassTypeFragment(bool mass_type_fragment)	SequestInfile
setMassTypeParent(bool mass_type_parent)	SequestInfile
setMatchPeakAllowedError(Size match_peak_allowed_error)	SequestInfile
setMatchPeakCount(Size match_peak_count)	SequestInfile
setMatchPeakTolerance(float match_peak_tolerance)	SequestInfile
setMaxAAPerModPerPeptide(Size max_aa_per_mod_per_peptide)	SequestInfile
setMaxInternalCleavageSites(Size max_internal_cleavage_sites)	SequestInfile
setMaxModsPerPeptide(Size max_mods_per_peptide)	SequestInfile
setNeutralLossesForIons(const String &neutral_losses_for_ions)	SequestInfile
setNormalizeXcorr(bool normalize_xcorr)	SequestInfile
setNucleotideReadingFrame(Size nucleotide_reading_frame)	SequestInfile
setOutputLines(Size output_lines)	SequestInfile
setPartialSequence(const String &partial_sequence)	SequestInfile
setPeakMassTolerance(float peak_mass_tolerance)	SequestInfile
setPeptideMassUnit(Size peptide_mass_unit)	SequestInfile
setPrecursorMassTolerance(float precursor_mass_tolerance)	SequestInfile
setPrintDuplicateReferences(bool print_duplicate_references)	SequestInfile
setProteinMassFilter(const String &protein_mass_filter)	SequestInfile
setRemovePrecursorNearPeaks(bool remove_precursor_near_peaks)	SequestInfile
setResiduesInUpperCase(bool residues_in_upper_case)	SequestInfile
setSequenceHeaderFilter(const String &sequence_header_filter)	SequestInfile
setShowFragmentIons(bool show_fragments)	SequestInfile
setStandardEnzymeInfo_()	SequestInfile	protected
show_fragment_ions_	SequestInfile	protected
snd_database_	SequestInfile	protected
store(const String &filename)	SequestInfile
~SequestInfile()	SequestInfile	virtual