Package transsys
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Package transsys

source code

transsys module

Classes: ExpressionNode Base class for nodes in an expression tree

Functions: dot_attribute_string xxx?

Submodules [hide private]

Classes [hide private]
  ExpressionNode
Base class for nodes in expression trees.
  ExpressionNodeValue
Expression node holding a constant floating point value.
  ExpressionNodeIdentifier
Node representing an identifier, i.e.
  ExpressionNodeBinary
  ExpressionNodeAdd
  ExpressionNodeSubtract
  ExpressionNodeMult
  ExpressionNodeDiv
  ExpressionNodeLower
  ExpressionNodeLowerEqual
  ExpressionNodeGreater
  ExpressionNodeGreaterEqual
  ExpressionNodeEqual
  ExpressionNodeUnequal
  ExpressionNodeNot
  ExpressionNodeAnd
  ExpressionNodeOr
  ExpressionNodeFunction
  ExpressionNodeUniformRandom
  ExpressionNodeGaussianRandom
  ExpressionNodePower
  ExpressionNodeLogarithm
  ExpressionNodeAtan
  PromoterElement
  PromoterElementConstitutive
  PromoterElementLink
  PromoterElementActivate
  PromoterElementRepress
  Factor
Class representing a transsys factor.
  Gene
Class to represent a gene.
  TranssysProgram
Class to represent a transsys program.
  GraphicsPrimitive
  GraphicsPrimitiveMove
  GraphicsPrimitivePush
  GraphicsPrimitivePop
  GraphicsPrimitiveTurn
  GraphicsPrimitiveRoll
  GraphicsPrimitiveBank
  GraphicsPrimitiveSphere
  GraphicsPrimitiveCylinder
  GraphicsPrimitiveBox
  GraphicsPrimitiveColor
  Symbol
  Assignment
  LhsSymbol
  ProductionElement
  Rule
  LsysProgram
  TranssysInstance
  CollectionStatistics
Aggregate statistics computed from a TranssysInstanceCollection.
  TranssysInstanceCollection
Abstract base class of collections of transsys instances which are all instances of the same transsys program.
  SimpleCollection
A very simple, container-like implementation of the abstract TranssysInstanceCollection base class.
  TimeSeries
  SymbolInstance
  LsysSymbolString
  DotParameters
  CyclicSequence
A convenience class for use with RandomTranssysParameters.
  RandomTranssysParameters
A factory for generating "random" transsys programs.
  TranssysProgramScanner
  TranssysProgramParser
  ArrayIntensityFunction
A basic intensity function which computes the intensity by taking the expression level and adding background and noise
  ArraySeries
Functions [hide private]
 
dot_attribute_string(d)
Produce an attribute list in the dot language
source code
 
_comment_lines(clines, prefix='') source code
 
write_lsys_code(f, lines) source code
 
write_random_transsys(f, name, rtp) source code
 
expression_level_dict(transsys_filename, num_timesteps, sampling_period, initial_levels=None) source code
Variables [hide private]
  required_clib_api_version = '350'