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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]
Generated Tue Apr 1 15:36:45 2008 -- using doxygen 1.5.4
OpenMS / TOPP 1.1