| 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(const 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 |
1.9.1 
