cobramod.error
==============

.. py:module:: cobramod.error

.. autoapi-nested-parse::

   Errors for CobraMod

   This module creates special errors for CobraMod. Read each error for their
   explanation.



Attributes
----------

.. autoapisummary::

   cobramod.error.debug_log


Exceptions
----------

.. autoapisummary::

   cobramod.error.UserInterruption
   cobramod.error.NoDelimiter
   cobramod.error.GraphKeyError
   cobramod.error.FoundInPairError
   cobramod.error.NodeAttributeError
   cobramod.error.WrongParserError
   cobramod.error.WrongDataError
   cobramod.error.WrongSyntax
   cobramod.error.PatternNotFound
   cobramod.error.NoIntersectFound
   cobramod.error.NoGeneInformation
   cobramod.error.SuperpathwayException
   cobramod.error.UnbalancedReaction


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

.. py:data:: debug_log

.. py:exception:: UserInterruption

   Bases: :py:obj:`Exception`


   Exception that is used if the input of a user interrupts the program flow.


.. py:exception:: NoDelimiter(string)

   Bases: :py:obj:`Exception`


   Simple Error that should be raised when a string does not include the
   delimiter "|"


.. py:exception:: GraphKeyError

   Bases: :py:obj:`Exception`


   Simple Error that should be raised when a value is missing as key in a
   graph


.. py:exception:: FoundInPairError

   Bases: :py:obj:`Exception`


   Simple Error that is raised when the pair of a PairDictionary has already
   given key name.


.. py:exception:: NodeAttributeError

   Bases: :py:obj:`Exception`


   Simple Error that should be raised when a
   :func:`cobramod.visualization.Node` cannot identify its type.


.. py:exception:: WrongParserError

   Bases: :py:obj:`Exception`


   Simple Error that should be raised if a method cannot handle the parsing.


.. py:exception:: WrongDataError

   Bases: :py:obj:`Exception`


   Simple Error that should be raised if COBRApy object is not the correct
   one.


.. py:exception:: WrongSyntax

   Bases: :py:obj:`Exception`


   Simple Error that should be raised if a specific syntax is invalid. For
   instance, when strings do not have a certain number of items when splitted.


.. py:exception:: PatternNotFound

   Bases: :py:obj:`Exception`


   Simple error that should be raised when a pattern is not found in a item.
   e.g. a substring.


.. py:exception:: NoIntersectFound

   Bases: :py:obj:`Exception`


   Simple error that should be raised when no intersect is found between two
   sets.


.. py:exception:: NoGeneInformation

   Bases: :py:obj:`Exception`


   Simple error that should be raised when given object has no gene
   information in the database.


.. py:exception:: SuperpathwayException

   Bases: :py:obj:`Exception`


   Simple Warning that should be raised if a pathway is identified as a
   Superpathway


.. py:exception:: UnbalancedReaction(identifier, dict_balance)

   Bases: :py:obj:`Exception`


   Simple Error that should be raised if a reaction has wrong mass balance.