lineage.CellVar
===============

.. py:module:: lineage.CellVar

.. autoapi-nested-parse::

   This file contains the class for CellVar which holds the state and observation information in the hidden and observed trees respectively.



Classes
-------

.. autoapisummary::

   lineage.CellVar.Time
   lineage.CellVar.CellVar


Module Contents
---------------

.. py:class:: Time

   Class that stores all the time related observations in a neater format.
   This assists in pruning based on experimental time and obtaining
   attributes of the lineage as a whole like the average growth rate.


   .. py:attribute:: startT
      :type:  float


   .. py:attribute:: endT
      :type:  float


   .. py:attribute:: transition_time
      :type:  float
      :value: 0.0



.. py:class:: CellVar(parent = None, state = -1)

   Cell class.


   .. py:attribute:: parent
      :type:  CellVar | None


   .. py:attribute:: gen
      :type:  int


   .. py:attribute:: observed
      :type:  bool


   .. py:attribute:: state
      :type:  int


   .. py:attribute:: obs
      :type:  numpy.ndarray | list[Any]


   .. py:attribute:: time
      :type:  Time | None


   .. py:attribute:: left
      :type:  CellVar | None


   .. py:attribute:: right
      :type:  CellVar | None


   .. py:method:: divide(T, rng=None)

      Member function that performs division of a cell.
      Equivalent to adding another timestep in a Markov process.
      :param T: The array containing the likelihood of a cell switching states.



   .. py:method:: isLeafBecauseTerminal()

      Returns true when a cell is a leaf with no children.
      These are cells at the end of the tree.



   .. py:method:: isLeaf()

      Returns true when a cell is a leaf defined by the two conditions that determine
      whether a cell is a leaf. A cell only has to satisfy one of the conditions
      (an or statement) for it to be a leaf.