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SequestInfile Member List

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

aas_single_letter_SequestInfile [protected, static]
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(Real ion_cutoff_percentage)SequestInfile
setIonSeriesWeights(const String &ion_series_weights)SequestInfile
setMassTypeFragment(bool mass_type_fragment)SequestInfile
setMassTypeParent(bool mass_type_parent)SequestInfile
setMatchPeakAllowedError(UInt match_peak_allowed_error)SequestInfile
setMatchPeakCount(UInt match_peak_count)SequestInfile
setMatchPeakTolerance(Real match_peak_tolerance)SequestInfile
setMaxAAPerModPerPeptide(UInt max_aa_per_mod_per_peptide)SequestInfile
setMaxInternalCleavageSites(UInt max_internal_cleavage_sites)SequestInfile
setMaxModsPerPeptide(UInt max_mods_per_peptide)SequestInfile
setNeutralLossesForIons(const String &neutral_losses_for_ions)SequestInfile
setNormalizeXcorr(bool normalize_xcorr)SequestInfile
setNucleotideReadingFrame(UInt nucleotide_reading_frame)SequestInfile
setOutputLines(UInt output_lines)SequestInfile
setPartialSequence(const String &partial_sequence)SequestInfile
setPeakMassTolerance(Real peak_mass_tolerance)SequestInfile
setPeptideMassUnit(UInt peptide_mass_unit)SequestInfile
setPrecursorMassTolerance(Real 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]


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