semanticSBML.merge_logic.BioRelations.Local

Class Local

Instance Methods

__init__(self, merger=None)

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setNewId(self, element, merge_model)
set a unique id for an element, if id is aready unique, leave it, if not set a new one

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[str]

getMathElementNames(self, mathobj)
get a list of stings that are identifiers of sbml elements used in the inserted math obj this is a recursive function

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updateMathElementIDs(self, mathobj, merge_model, create_copy=True)
update all IDs in mathematical expressions with IDs of merged elements if the old element is merged

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(OriginElement,OriginElement)

chooseBestTuple(self, el1, el2)
reorder elements so that adding the second element to the tuple of the first gives a better result than adding the first element to the tuple of the second

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compareElements(self, el1, el2)
compare the annotations of two elements and return a similarity score

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compareLocation(self, el1, el2)

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bool

isAnnotationEqual(self, an1, an2, type)
return if 2 annotations can be considered equal

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getScoreMatrix(self, filename)
TODO triangular to square matrix

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updateId(self, libsbml_element, oldId, newId)

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_updateMathPointers(self, math, oldId, newId)

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_updateLocationPointers(self, libsbml_element, oldId, newId)

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_updateReactionPointers(self, libsbml_element, oldId, newId)

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setNewId(self, element, merge_model)

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set a unique id for an element, if id is aready unique, leave it, if not set a new one

Parameters:

element (MergedElement | OriginElement | libsmbl.(Species|...)) - merge(d) element or libsmbl element

getMathElementNames(self, mathobj)

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get a list of stings that are identifiers of sbml elements used in the inserted math obj this is a recursive function

Parameters:

mathobj (libSBML.math)

Returns: [str]

list of identifier strings

chooseBestTuple(self, el1, el2)

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reorder elements so that adding the second element to the tuple of the first gives a better result than adding the first element to the tuple of the second

Parameters:

el1 (OriginElement) - OriginElement that belongs to a MergeTuple

Returns: (OriginElement,OriginElement)

reorder list of the input

compareElements(self, el1, el2)

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compare the annotations of two elements and return a similarity score

Parameters:

el1 (libSBML base element or OriginElement) - element containing annotations
el2 (libSBML base element or OriginElement) - element containing annotations

isAnnotationEqual(self, an1, an2, type)

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return if 2 annotations can be considered equal

Parameters:

an1 (Annotation)
an2 (Annotation)

Returns: bool