Extends
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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createCy(container)
Create cytoscape drawing
Parameters:
| Name | Type | Description |
|---|---|---|
container |
Element | where to draw cytoscape |
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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
- Inherited From:
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styleOfBackbones()
Return backbone style in cytoscape format
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styleOfBases()
Returns base style in cytoscape style
- Inherited From:
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(static) fromEBIJson(n, data, seq)
Create Drawing from ebi basepair interaction json
Parameters:
| Name | Type | Description |
|---|---|---|
n |
int | RNA length |
data |
json | basepair interaction produced by FR3D |
seq |
string | sequence |
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