| OpenMS 2.5.0

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