Class: RNA

RNA()

new RNA()

Properties:
Name Type Description
cy cytoscape cytoscape drawing
baseList Array Array of ModelBase
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Classes

RNA

Methods

addBP(i, j)

Add additional basepair (i, j) The function check whether (i, j) fit planar unless the flag noplanar is set
Parameters:
Name Type Description
i int | ModelBase index of ModelBase object of i
j int | ModelBase index of ModelBase object of j
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addBPAux(i)

Add aux basepair (i, j)
Parameters:
Name Type Description
i int | ModelBase -
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applyBasesStyle(style, …bases)

Apply base style to given bases The function assigns a number (the order) to given ModelBaseStyle object Bases will be grouped with class `basegroup${number}`
Parameters:
Name Type Attributes Description
style ModelBaseStyle base style to apply
bases ModelBase | int <repeatable>
 bases (could be either ModelBase object or the index in baseList) to apply on
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cyOfBPs()

Return basepair to draw in cytoscape format
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cyOfBackbones()

Return backbones to draw in cytoscape format
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cyOfBaseNum()

Return base number to draw in cytoscape format
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cyOfBases()

Return bases to draw in cytoscape format
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elOfAuxBPs()

Returns aux basepair in cytoscape edge element list with classes set to basepair and auxbp
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elOfBackbones()

Returns backbone in cytoscape edge element list with classes set to backbone
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elOfBases()

Returns bases in cytoscape node element list
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elOfPlanarBPs()

Returns planar basepair in cytoscape edge element list with classes set to basepair and planarbp
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elOfSingleBP()

Returns cytoscape edge element for one single bp
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setConfig(cfg)

Set drawing configuration
Parameters:
Name Type Description
cfg VARNAConfig configuration to draw
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styleOfBPs()

Return basepair style in cytoscape format
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styleOfBackbones()

Return backbone style in cytoscape format
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styleOfBases()

Returns base style in cytoscape style
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(static) fromDBN(dbn, seq)

Construct from given dbn and seq. At most one can be empty
Parameters:
Name Type Description
dbn string secondary structure in dbn
seq string RNA sequence
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