emzed.ms_data.peak_map module

class emzed.ms_data.peak_map.BoundSpectrum(parent, scan_number)

Bases: object

check()

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()

dettaches spectrum from peakmap

class emzed.ms_data.peak_map.Chromatogram(rts, intensities)

Bases: _Chromatogram

class emzed.ms_data.peak_map.ChromatogramType(value)

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)

Bases: object

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

class emzed.ms_data.peak_map.ImmutableMSChromatograms(peakmap)

Bases: object

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

Bases: DbBackedModel

chromatogram(mzmin=None, mzmax=None, rtmin=None, rtmax=None, ms_level=None, precursormzmin=None, precursormzmax=None)

close()

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)

extract_for_precursors(mzs, mz_tol, *, target_db_file=None)

filter(predicate, target_db_file=None)

get_dominating_peak_map()

get_precursors_mzs()

is_in_memory()

is_open()

classmethod load(path, *, target_db_file=None, overwrite=False)

ms_levels()

mz_range(ms_level=None)

mz_ranges(ms_level=None)

classmethod open(path)

polarities()

representing_mz_peak(mzmin, mzmax, rtmin, rtmax, ms_level=1)

rt_range(ms_level=None)

rt_ranges(ms_level=None)

save(path, *, overwrite=False)

scan_counts()

split_by_precursors(mz_tol=0.0)

summary()

property unique_id

class emzed.ms_data.peak_map.ImmutableSpectra(peakmap, is_mutable=False)

Bases: SpectraBase

add_spectrum(spectrum)

class emzed.ms_data.peak_map.MSChromatogram(mz, precursor_mz, rts, intensities, type_)

Bases: object

property available_types

property intensities

property mz

property precursor_mz

rt_range()

property rts

property type

class emzed.ms_data.peak_map.MutableSpectra(peakmap)

Bases: ImmutableSpectra

add_spectrum(spectrum)

class emzed.ms_data.peak_map.PeakMap(conn, access_name, meta_data, info)

Bases: ImmutablePeakMap

add_spectrum(spectrum)

classmethod from_(pm, *, target_db_file=None)

merge(other)

spectra_for_modification()

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

class emzed.ms_data.peak_map.SpectraBase

Bases: object

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

Bases: object

unbind()

dettaches spectrum from peakmap

emzed.ms_data.peak_map.chromatogram(conn, access_name, mzmin, mzmax, rtmin, rtmax, ms_level, precursormzmin, precursormzmax)

emzed.ms_data.peak_map.create_indices(conn, access_name)

emzed.ms_data.peak_map.create_table(access_name='peakmap', conn=None)

emzed.ms_data.peak_map.db_backed_property

alias of DbBackedProperty

emzed.ms_data.peak_map.extract_spectrum(mspec)

emzed.ms_data.peak_map.insert_chromatogram(conn, access_name, mz, precursor_mz, peaks, type_)

emzed.ms_data.peak_map.insert_peaks(conn, access_name, peaks, rt, ms_level, polarity, precursors, scan_number)

emzed.ms_data.peak_map.insert_precursors(conn, access_name, scan_number, precursors)

emzed.ms_data.peak_map.profile(fun)

emzed.ms_data.peak_map.representing_mz_peak(conn, access_name, mzmin, mzmax, rtmin, rtmax, ms_level)

emzed.ms_data.peak_map.to_openms_spectrum(s)