pyms.Mixins

Mixins for PyMassSpec Classes.

Classes:

GetIndexTimeMixin()	Mixin class for retention time attributes and methods.
IntensityArrayMixin()	Mixin class for intensity_array attribute.
MassListMixin()	Mixin class to add the mass_list property, which returns a copy of the internal _mass_list attribute.
MaxMinMassMixin()	Mixin class to add the min_mass and max_mass properties, which provide read-only access to the internal _min_mass and _max_mass attributes.
TimeListMixin()	Mixin class to add the time_list property, which returns a copy of the internal _time_list attribute.

class GetIndexTimeMixin

Bases: object

Mixin class for retention time attributes and methods.

Methods:

get_index_at_time(time)	Returns the nearest index corresponding to the given time.
get_time_at_index(ix)	Returns time at given index.

get_index_at_time(time)

Returns the nearest index corresponding to the given time.

Parameters:

time (float) – Time in seconds

Return type:

int

Returns:

Nearest index corresponding to given time

Authors:

Lewis Lee, Tim Erwin, Vladimir Likic

Changed in version 2.3.0: Now returns -1 if no index is found.

get_time_at_index(ix)

Returns time at given index.

Parameters:

ix (int)

Authors:

Lewis Lee, Vladimir Likic

Return type:

float

class IntensityArrayMixin

Bases: object

Mixin class for intensity_array attribute.

Attributes:

intensity_array	Returns a copy of the intensity array.
intensity_array_list	Returns a copy of the intensity array as a list of lists of floats.
intensity_matrix	Returns a copy of the intensity matrix.
matrix_list	Returns the intensity matrix as a list of lists of floats.

property intensity_array

Returns a copy of the intensity array.

Return type:

ndarray

Returns:

Matrix of intensity values.

Authors:

Andrew Isaac, Lewis Lee

property intensity_array_list

Returns a copy of the intensity array as a list of lists of floats.

Return type:

List[List[float]]

Returns:

Matrix of intensity values.

Author:

Andrew Isaac

property intensity_matrix

Returns a copy of the intensity matrix.

Return type:

ndarray

Returns:

Matrix of intensity values.

Author:

Andrew Isaac

property matrix_list

Returns the intensity matrix as a list of lists of floats.

Return type:

ndarray

Returns:

Matrix of intensity values

Author:

Andrew Isaac

class MassListMixin

Bases: MaxMinMassMixin

Mixin class to add the mass_list property, which returns a copy of the internal _mass_list attribute.

Attributes:

mass_list

Returns a list of the masses.

property mass_list

Returns a list of the masses.

Authors:

Qiao Wang, Andrew Isaac, Vladimir Likic

Return type:

List[float]

class MaxMinMassMixin

Bases: object

Mixin class to add the min_mass and max_mass properties, which provide read-only access to the internal _min_mass and _max_mass attributes.

Attributes:

max_mass	Returns the maximum m/z value in the spectrum.
min_mass	Returns the minimum m/z value in the spectrum.

property max_mass

Returns the maximum m/z value in the spectrum.

Author:

Andrew Isaac

Return type:

Optional[float]

property min_mass

Returns the minimum m/z value in the spectrum.

Author:

Andrew Isaac

Return type:

Optional[float]

class TimeListMixin

Bases: object

Mixin class to add the time_list property, which returns a copy of the internal _time_list attribute.

Attributes:

time_list

Returns a copy of the time list.

property time_list

Returns a copy of the time list.

Return type:

List[float]

Returns:

List of retention times

Authors:

Andrew Isaac, Lewis Lee, Vladimir Likic