Package transsys :: Class TranssysInstanceCollection
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Class TranssysInstanceCollection

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object --+
         |
        TranssysInstanceCollection

Abstract base class of collections of transsys instances which are all instances of the same transsys program. This base class provides generic functions for computing average concentrations, standard deviation of concentrations etc.

This class is abstract in the sense that the methods transsys_instance_list and get_transsys_program are implemented to raise exceptions. Subclasses must override (i.e. implement) these methods. In this sense, the methods are abstract.

Instance Methods [hide private]
 
__init__(self)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
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transsys_instance_list(self)
Return a list of all transsys instances in this collection.
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list of floats
get_factor_expression_list(self, factor)
Return a list of expression levels for a factor.
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write_table_header(self, f)
Write a header for a table of records describing the instances in this collection.
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write_table(self, f)
Write a table of records describing the instances in this collection.
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get_transsys_program(self)
Return the transsys program of which the instances.
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A CollectionStatistics instance or None
statistics(self)
Compute an instance of CollectionStatistics from this collection.
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Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __str__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self)
(Constructor)

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x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__
(inherited documentation)

transsys_instance_list(self)

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Return a list of all transsys instances in this collection.

Implementing subclasses are allowed to return a list of references to their transsys instances. Therefore, the instances in a list obtained by this method should be used for reading only. If modifications are required, the instances should be cloned.

get_factor_expression_list(self, factor)

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Return a list of expression levels for a factor.

Parameters:
  • factor (String @return list of expression levels) - the name of the factor, as a string
Returns: list of floats

write_table(self, f)

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Write a table of records describing the instances in this collection.

The output format should be suitable for reading by the R function read.table(file, header = TRUE).

Subclasses can override this method to add more information (e.g. symbol name, lattice coordinates etc.). In this case, remember to also override write_table_header accordingly.

statistics(self)

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Compute an instance of CollectionStatistics from this collection.

If the collection is empty, a CollectionStatistics instance containing None values for all statistics is produced.

Returns: A CollectionStatistics instance or None
A CollectionStatistics instance or None