emzed.ms_data.peak_map module

class emzed.ms_data.peak_map.BoundSpectrum(parent, scan_number)[source]

Bases: object

check()[source]
intensities

Property which fetches / updated value from/to db table on demand

ms_level

Property which fetches / updated value from/to db table on demand

mzs

Property which fetches / updated value from/to db table on demand

peaks

Property which fetches / updated value from/to db table on demand

polarity

Property which fetches / updated value from/to db table on demand

property precursors
rt

Property which fetches / updated value from/to db table on demand

property scan_number
unbind()[source]

dettaches spectrum from peakmap

class emzed.ms_data.peak_map.Chromatogram(rts, intensities)[source]

Bases: _Chromatogram

class emzed.ms_data.peak_map.ChromatogramType(value)[source]

Bases: Enum

An enumeration.

ABSORPTION_CHROMATOGRAM = 7
BASEPEAK_CHROMATOGRAM = 3
ELECTROMAGNETIC_RADIATION_CHROMATOGRAM = 6
EMISSION_CHROMATOGRAM = 8
MASS_CHROMATOGRAM = 0
SELECTED_ION_CURRENT_CHROMATOGRAM = 2
SELECTED_ION_MONITORING_CHROMATOGRAM = 4
SELECTED_REACTION_MONITORING_CHROMATOGRAM = 5
TOTAL_ION_CURRENT_CHROMATOGRAM = 1
class emzed.ms_data.peak_map.DbBackedProperty(get_function, set_function=None)[source]

Bases: object

Property which fetches / updated value from/to db table on demand

class emzed.ms_data.peak_map.ImmutableMSChromatograms(peakmap)[source]

Bases: object

class emzed.ms_data.peak_map.ImmutablePeakMap(conn, access_name, meta_data=None, info=None)[source]

Bases: DbBackedModel

chromatogram(mzmin=None, mzmax=None, rtmin=None, rtmax=None, ms_level=None, precursormzmin=None, precursormzmax=None)[source]
close()[source]
extract(mzmin=None, mzmax=None, rtmin=None, rtmax=None, imin=None, imax=None, mslevelmin=None, mslevelmax=None, precursormzmin=None, precursormzmax=None, *, target_db_file=None)[source]
extract_for_precursors(mzs, mz_tol, *, target_db_file=None)[source]
filter(predicate, target_db_file=None)[source]
get_dominating_peak_map()[source]
get_precursors_mzs()[source]
is_in_memory()[source]
is_open()[source]
classmethod load(path, *, target_db_file=None, overwrite=False)[source]
ms_levels()[source]
mz_range(ms_level=None)[source]
mz_ranges(ms_level=None)[source]
classmethod open(path)[source]
polarities()[source]
representing_mz_peak(mzmin, mzmax, rtmin, rtmax, ms_level=1)[source]
rt_range(ms_level=None)[source]
rt_ranges(ms_level=None)[source]
save(path, *, overwrite=False)[source]
scan_counts()[source]
split_by_precursors(mz_tol=0.0)[source]
summary()[source]
property unique_id
class emzed.ms_data.peak_map.ImmutableSpectra(peakmap, is_mutable=False)[source]

Bases: SpectraBase

add_spectrum(spectrum)[source]
class emzed.ms_data.peak_map.MSChromatogram(mz, precursor_mz, rts, intensities, type_)[source]

Bases: object

property available_types
property intensities
property mz
property precursor_mz
rt_range()[source]
property rts
property type
class emzed.ms_data.peak_map.MutableSpectra(peakmap)[source]

Bases: ImmutableSpectra

add_spectrum(spectrum)[source]
class emzed.ms_data.peak_map.PeakMap(conn, access_name, meta_data, info)[source]

Bases: ImmutablePeakMap

add_spectrum(spectrum)[source]
classmethod from_(pm, *, target_db_file=None)[source]
merge(other)[source]
spectra_for_modification()[source]

contextmanager. in this context one can change spectra attributes like rt, ms_level, peaks or polarity

class emzed.ms_data.peak_map.SpectraBase[source]

Bases: object

class emzed.ms_data.peak_map.Spectrum(scan_number, rt, ms_level, polarity, precursors, peaks)[source]

Bases: object

unbind()[source]

dettaches spectrum from peakmap

emzed.ms_data.peak_map.chromatogram(conn, access_name, mzmin, mzmax, rtmin, rtmax, ms_level, precursormzmin, precursormzmax)[source]
emzed.ms_data.peak_map.create_indices(conn, access_name)[source]
emzed.ms_data.peak_map.create_table(access_name='peakmap', conn=None)[source]
emzed.ms_data.peak_map.db_backed_property

alias of DbBackedProperty

emzed.ms_data.peak_map.extract_spectrum(mspec)[source]
emzed.ms_data.peak_map.insert_chromatogram(conn, access_name, mz, precursor_mz, peaks, type_)[source]
emzed.ms_data.peak_map.insert_peaks(conn, access_name, peaks, rt, ms_level, polarity, precursors, scan_number)[source]
emzed.ms_data.peak_map.insert_precursors(conn, access_name, scan_number, precursors)[source]
emzed.ms_data.peak_map.profile(fun)[source]
emzed.ms_data.peak_map.representing_mz_peak(conn, access_name, mzmin, mzmax, rtmin, rtmax, ms_level)[source]
emzed.ms_data.peak_map.to_openms_spectrum(s)[source]