SequestInfile.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
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// $Maintainer: Timo Sachsenberg $
// $Authors: Martin Langwisch $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/DATASTRUCTURES/String.h>

#include <map>


namespace OpenMS
{
  class OPENMS_DLLAPI SequestInfile
  {
public:
    SequestInfile();

    SequestInfile(const SequestInfile & sequest_infile);

    virtual ~SequestInfile();

    SequestInfile & operator=(const SequestInfile & sequest_infile);

    bool operator==(const SequestInfile & sequest_infile) const;

    void store(const String & filename);

    const String getEnzymeInfoAsString() const;

    const String & getDatabase() const;
    void setDatabase(const String & database);

    const String & getNeutralLossesForIons() const;
    void setNeutralLossesForIons(const String & neutral_losses_for_ions);

    const String & getIonSeriesWeights() const;
    void setIonSeriesWeights(const String & ion_series_weights);

    const String & getPartialSequence() const;
    void setPartialSequence(const String & partial_sequence);

    const String & getSequenceHeaderFilter() const;
    void setSequenceHeaderFilter(const String & sequence_header_filter);

    const String & getProteinMassFilter() const;
    void setProteinMassFilter(const String & protein_mass_filter);


    float getPeakMassTolerance() const;
    void setPeakMassTolerance(float peak_mass_tolerance);

    float getPrecursorMassTolerance() const;
    void setPrecursorMassTolerance(float precursor_mass_tolerance);

    float getMatchPeakTolerance() const;
    void setMatchPeakTolerance(float match_peak_tolerance);

    float getIonCutoffPercentage() const;
    void setIonCutoffPercentage(float ion_cutoff_percentage);

    Size getPeptideMassUnit() const;
    void setPeptideMassUnit(Size peptide_mass_unit);

    Size getOutputLines() const;
    void setOutputLines(Size output_lines);

    Size getEnzymeNumber() const;
    String getEnzymeName() const;
    Size setEnzyme(String enzyme_name);

    Size getMaxAAPerModPerPeptide() const;
    void setMaxAAPerModPerPeptide(Size max_aa_per_mod_per_peptide);

    Size getMaxModsPerPeptide() const;
    void setMaxModsPerPeptide(Size max_mods_per_peptide);

    Size getNucleotideReadingFrame() const;
    void setNucleotideReadingFrame(Size nucleotide_reading_frame);

    Size getMaxInternalCleavageSites() const;
    void setMaxInternalCleavageSites(Size max_internal_cleavage_sites);

    Size getMatchPeakCount() const;
    void setMatchPeakCount(Size match_peak_count);

    Size getMatchPeakAllowedError() const;
    void setMatchPeakAllowedError(Size match_peak_allowed_error);


    bool getShowFragmentIons() const;
    void setShowFragmentIons(bool show_fragments);

    bool getPrintDuplicateReferences() const;
    void setPrintDuplicateReferences(bool print_duplicate_references);

    bool getRemovePrecursorNearPeaks() const;
    void setRemovePrecursorNearPeaks(bool remove_precursor_near_peaks);

    bool getMassTypeParent() const;
    void setMassTypeParent(bool mass_type_parent);

    bool getMassTypeFragment() const;
    void setMassTypeFragment(bool mass_type_fragment);

    bool getNormalizeXcorr() const;
    void setNormalizeXcorr(bool normalize_xcorr);

    bool getResiduesInUpperCase() const;
    void setResiduesInUpperCase(bool residues_in_upper_case);

    void addEnzymeInfo(std::vector<String> & enzyme_info);

    const std::map<String, std::vector<String> > & getModifications() const;

    void handlePTMs(const String & modification_line, const String & modifications_filename, const bool monoisotopic);

protected:
    const std::map<String, std::vector<String> > & getEnzymeInfo_() const;

    void setStandardEnzymeInfo_();

    std::map<String, std::vector<String> > enzyme_info_;            
    String database_;         
    String snd_database_;         
    String neutral_losses_for_ions_;         
    String ion_series_weights_;        
    String partial_sequence_;         
    String sequence_header_filter_;        
    String protein_mass_filter_;

    float precursor_mass_tolerance_;        
    float peak_mass_tolerance_;        
    float match_peak_tolerance_;        
    float ion_cutoff_percentage_;        

    Size peptide_mass_unit_;        
    Size output_lines_;        
    Size enzyme_number_;        
    Size max_AA_per_mod_per_peptide_;        
    Size max_mods_per_peptide_;        
    Size nucleotide_reading_frame_;        
    Size max_internal_cleavage_sites_;        
    Size match_peak_count_;        
    Size match_peak_allowed_error_;        


    bool show_fragment_ions_;        
    bool print_duplicate_references_;        
    bool remove_precursor_near_peaks_;        
    bool mass_type_parent_;        
    bool mass_type_fragment_;        
    bool normalize_xcorr_;        
    bool residues_in_upper_case_;        

    std::map<String, std::vector<String> > PTMname_residues_mass_type_;           
  };

} // namespace OpenMS