35 #ifndef OPENMS_FORMAT_SEQUESTINFILE_H 
   36 #define OPENMS_FORMAT_SEQUESTINFILE_H 
   74     void store(
const String & filename);
 
   77     const String getEnzymeInfoAsString() 
const;
 
   80     const String & getDatabase() 
const;
 
   82     void setDatabase(
const String & database);
 
   85     const String & getNeutralLossesForIons() 
const;
 
   87     void setNeutralLossesForIons(
const String & neutral_losses_for_ions);
 
   90     const String & getIonSeriesWeights() 
const;
 
   92     void setIonSeriesWeights(
const String & ion_series_weights);
 
   95     const String & getPartialSequence() 
const;
 
   97     void setPartialSequence(
const String & partial_sequence);
 
  100     const String & getSequenceHeaderFilter() 
const;
 
  102     void setSequenceHeaderFilter(
const String & sequence_header_filter);
 
  105     const String & getProteinMassFilter() 
const;
 
  107     void setProteinMassFilter(
const String & protein_mass_filter);
 
  111     Real getPeakMassTolerance() 
const;
 
  113     void setPeakMassTolerance(
Real peak_mass_tolerance);
 
  116     Real getPrecursorMassTolerance() 
const;
 
  118     void setPrecursorMassTolerance(
Real precursor_mass_tolerance);
 
  121     Real getMatchPeakTolerance() 
const;
 
  123     void setMatchPeakTolerance(
Real match_peak_tolerance);
 
  126     Real getIonCutoffPercentage() 
const;
 
  128     void setIonCutoffPercentage(
Real ion_cutoff_percentage);
 
  131     Size getPeptideMassUnit() 
const;
 
  133     void setPeptideMassUnit(
Size peptide_mass_unit);
 
  136     Size getOutputLines() 
const;
 
  138     void setOutputLines(
Size output_lines);
 
  141     Size getEnzymeNumber() 
const;
 
  143     String getEnzymeName() 
const;
 
  148     Size getMaxAAPerModPerPeptide() 
const;
 
  150     void setMaxAAPerModPerPeptide(
Size max_aa_per_mod_per_peptide);
 
  153     Size getMaxModsPerPeptide() 
const;
 
  155     void setMaxModsPerPeptide(
Size max_mods_per_peptide);
 
  158     Size getNucleotideReadingFrame() 
const;
 
  170     void setNucleotideReadingFrame(
Size nucleotide_reading_frame);
 
  173     Size getMaxInternalCleavageSites() 
const;
 
  175     void setMaxInternalCleavageSites(
Size max_internal_cleavage_sites);
 
  178     Size getMatchPeakCount() 
const;
 
  180     void setMatchPeakCount(
Size match_peak_count);
 
  183     Size getMatchPeakAllowedError() 
const;
 
  185     void setMatchPeakAllowedError(
Size match_peak_allowed_error);
 
  189     bool getShowFragmentIons() 
const;
 
  191     void setShowFragmentIons(
bool show_fragments);
 
  194     bool getPrintDuplicateReferences() 
const;
 
  196     void setPrintDuplicateReferences(
bool print_duplicate_references);
 
  199     bool getRemovePrecursorNearPeaks() 
const;
 
  201     void setRemovePrecursorNearPeaks(
bool remove_precursor_near_peaks);
 
  204     bool getMassTypeParent() 
const;
 
  206     void setMassTypeParent(
bool mass_type_parent);
 
  209     bool getMassTypeFragment() 
const;
 
  211     void setMassTypeFragment(
bool mass_type_fragment);
 
  214     bool getNormalizeXcorr() 
const;
 
  216     void setNormalizeXcorr(
bool normalize_xcorr);
 
  219     bool getResiduesInUpperCase() 
const;
 
  221     void setResiduesInUpperCase(
bool residues_in_upper_case);
 
  226     void addEnzymeInfo(std::vector<String> & enzyme_info);
 
  229     const std::map<String, std::vector<String> > & getModifications() 
const;
 
  242     void handlePTMs(
const String & modification_line, 
const String & modifications_filename, 
const bool monoisotopic);
 
  246     const std::map<String, std::vector<String> > & getEnzymeInfo_() 
const;
 
  249     void setStandardEnzymeInfo_();
 
  271     Size max_internal_cleavage_sites_;        
 
  299 #endif // OPENMS_FORMAT_SEQUESTINFILE_H 
bool normalize_xcorr_
whether to display normalized xcorr values 
Definition: SequestInfile.h:291
String database_
database used 
Definition: SequestInfile.h:252
bool residues_in_upper_case_
whether residues are in upper case 
Definition: SequestInfile.h:292
Real precursor_mass_tolerance_
tolerance for matching a theoretical to an experimental peptide 
Definition: SequestInfile.h:260
float Real
Real type. 
Definition: Types.h:109
A more convenient string class. 
Definition: String.h:56
Size enzyme_number_
number of the enzyme used for cleavage 
Definition: SequestInfile.h:267
String ion_series_weights_
weights for the a-; b-; c-; d-; v-; w-; x-; y- and z-ion series; space delimited 
Definition: SequestInfile.h:255
String neutral_losses_for_ions_
whether neutral losses are considered for the a-; b- and y-ions (e.g. 011 for b- and y-ions) ...
Definition: SequestInfile.h:254
std::map< String, std::vector< String > > PTMname_residues_mass_type_
the modification names map to the affected residues, the mass change and the type ...
Definition: SequestInfile.h:294
String partial_sequence_
space-delimited list of sequence parts that have to occur in the theortical spectra ...
Definition: SequestInfile.h:256
bool mass_type_parent_
mass type of the parent peak (0 - monoisotopic; 1 - average) 
Definition: SequestInfile.h:289
Size nucleotide_reading_frame_
Definition: SequestInfile.h:270
Real match_peak_tolerance_
minimum distance between two experimental peaks 
Definition: SequestInfile.h:262
Real peak_mass_tolerance_
tolerance for matching a theoretical to an experimental peak 
Definition: SequestInfile.h:261
Real ion_cutoff_percentage_
cutoff of the ratio matching theoretical peaks/theoretical peaks 
Definition: SequestInfile.h:263
bool remove_precursor_near_peaks_
whether peaks near (15 amu) the precursor peak are removed 
Definition: SequestInfile.h:288
String snd_database_
second database used 
Definition: SequestInfile.h:253
Size match_peak_allowed_error_
number of peaks that may lack this test 
Definition: SequestInfile.h:283
Size max_AA_per_mod_per_peptide_
maximum number of amino acids containing the same modification in a peptide 
Definition: SequestInfile.h:268
Size max_mods_per_peptide_
maximum number of modifications per peptide 
Definition: SequestInfile.h:269
Size output_lines_
number of peptides to be displayed 
Definition: SequestInfile.h:266
bool show_fragment_ions_
whether to display fragment ions 
Definition: SequestInfile.h:286
Size match_peak_count_
number of the top abundant peaks to match with theoretical one 
Definition: SequestInfile.h:282
std::map< String, std::vector< String > > enzyme_info_
an endline-delimited list of enzymes; each with cutting direction 0 (N to C) /1; cuts after (list of ...
Definition: SequestInfile.h:251
bool print_duplicate_references_
whether all proteins containing a found peptide should be displayed 
Definition: SequestInfile.h:287
String protein_mass_filter_
Definition: SequestInfile.h:258
size_t Size
Size type e.g. used as variable which can hold result of size() 
Definition: Types.h:144
Sequest input file adapter. 
Definition: SequestInfile.h:52
String sequence_header_filter_
space-delimited list of sequences that have to occur or be absend (preceeded by a tilde) in a protein...
Definition: SequestInfile.h:257
Size peptide_mass_unit_
peptide mass unit (0 = amu; 1 = mmu; 2 = ppm) 
Definition: SequestInfile.h:265
bool mass_type_fragment_
mass type of fragment peaks (0 - monoisotopic; 1 - average) 
Definition: SequestInfile.h:290