1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
|
from libcpp cimport bool
from libcpp.map cimport map as libcpp_map
from libcpp.vector cimport vector as libcpp_vector
from String cimport *
from Types cimport *
cdef extern from "<OpenMS/FORMAT/SequestInfile.h>" namespace "OpenMS":
cdef cppclass SequestInfile "OpenMS::SequestInfile":
SequestInfile() nogil except +
SequestInfile(SequestInfile) nogil except +
bool operator==(SequestInfile &sequest_infile) nogil except +
void store(String &filename) nogil except +
String getEnzymeInfoAsString() nogil except +
String getDatabase() nogil except +
void setDatabase(String &database) nogil except +
String getNeutralLossesForIons() nogil except +
void setNeutralLossesForIons(String &neutral_losses_for_ions) nogil except +
String getIonSeriesWeights() nogil except +
void setIonSeriesWeights(String &ion_series_weights) nogil except +
String getPartialSequence() nogil except +
void setPartialSequence(String &partial_sequence) nogil except +
String getSequenceHeaderFilter() nogil except +
void setSequenceHeaderFilter(String &sequence_header_filter) nogil except +
String getProteinMassFilter() nogil except +
void setProteinMassFilter(String &protein_mass_filter) nogil except +
Real getPeakMassTolerance() nogil except +
void setPeakMassTolerance(Real peak_mass_tolerance) nogil except +
Real getPrecursorMassTolerance() nogil except +
void setPrecursorMassTolerance(Real precursor_mass_tolerance) nogil except +
Real getMatchPeakTolerance() nogil except +
void setMatchPeakTolerance(Real match_peak_tolerance) nogil except +
Real getIonCutoffPercentage() nogil except +
void setIonCutoffPercentage(Real ion_cutoff_percentage) nogil except +
Size getPeptideMassUnit() nogil except +
void setPeptideMassUnit(Size peptide_mass_unit) nogil except +
Size getOutputLines() nogil except +
void setOutputLines(Size output_lines) nogil except +
Size getEnzymeNumber() nogil except +
String getEnzymeName() nogil except +
Size setEnzyme(String enzyme_name) nogil except +
Size getMaxAAPerModPerPeptide() nogil except +
void setMaxAAPerModPerPeptide(Size max_aa_per_mod_per_peptide) nogil except +
Size getMaxModsPerPeptide() nogil except +
void setMaxModsPerPeptide(Size max_mods_per_peptide) nogil except +
Size getNucleotideReadingFrame() nogil except +
void setNucleotideReadingFrame(Size nucleotide_reading_frame) nogil except +
Size getMaxInternalCleavageSites() nogil except +
void setMaxInternalCleavageSites(Size max_internal_cleavage_sites) nogil except +
Size getMatchPeakCount() nogil except +
void setMatchPeakCount(Size match_peak_count) nogil except +
Size getMatchPeakAllowedError() nogil except +
void setMatchPeakAllowedError(Size match_peak_allowed_error) nogil except +
bool getShowFragmentIons() nogil except +
void setShowFragmentIons(bool show_fragments) nogil except +
bool getPrintDuplicateReferences() nogil except +
void setPrintDuplicateReferences(bool print_duplicate_references) nogil except +
bool getRemovePrecursorNearPeaks() nogil except +
void setRemovePrecursorNearPeaks(bool remove_precursor_near_peaks) nogil except +
bool getMassTypeParent() nogil except +
void setMassTypeParent(bool mass_type_parent) nogil except +
bool getMassTypeFragment() nogil except +
void setMassTypeFragment(bool mass_type_fragment) nogil except +
bool getNormalizeXcorr() nogil except +
void setNormalizeXcorr(bool normalize_xcorr) nogil except +
bool getResiduesInUpperCase() nogil except +
void setResiduesInUpperCase(bool residues_in_upper_case) nogil except +
void addEnzymeInfo(libcpp_vector[ String ] &enzyme_info) nogil except +
libcpp_map[ String, libcpp_vector[ String ] ] getModifications() nogil except + # wrap-ignore
void handlePTMs(String &modification_line, String &modifications_filename, bool monoisotopic) nogil except +
|
