Uses of Class
fr.orsay.lri.varna.models.rna.RNA

Packages that use RNA

fr.orsay.lri.varna
fr.orsay.lri.varna.interfaces
fr.orsay.lri.varna.models
fr.orsay.lri.varna.models.annotations
fr.orsay.lri.varna.models.rna
fr.orsay.lri.varna.models.templates
fr.orsay.lri.varna.models.treealign

Uses of RNA in fr.orsay.lri.varna

Fields in fr.orsay.lri.varna declared as RNA

private RNA

VARNAPanel._RNA

Methods in fr.orsay.lri.varna that return RNA

RNA	VARNAPanel.getRNA() Returns the current RNA model

Methods in fr.orsay.lri.varna with parameters of type RNA

void	VARNAPanel.drawRNA(RNA r) Sets the RNA secondary structure to be drawn in this panel, using the current drawing algorithm.
void	VARNAPanel.drawRNA(RNA r, int drawMode) Sets the RNA secondary structure to be drawn in this panel, using a given layout algorithm.
void	VARNAPanel.drawRNAInterpolated(RNA target) Draws a secondary structure of RNA using the default drawing algorithm and displays it, using an interpolated transition between the previous one and the new one.
void	VARNAPanel.drawRNAInterpolated(RNA target, int drawMode, Mapping m) Draws a secondary structure of RNA using a given drawing algorithm and displays it, using an interpolated transition between the previous one and the new one.
void	VARNAPanel.drawRNAInterpolated(RNA target, Mapping m) Draws a secondary structure of RNA using the default drawing algorithm and displays it, using an interpolated transition between the previous one and the new one.
void	VARNAPanel.showRNA(RNA r) Sets the RNA to be displayed within this Panel.
void	VARNAPanel.showRNA(RNA t, VARNAConfig cfg)
void	VARNAPanel.showRNAInterpolated(RNA target) Simply displays (does not redraw) a secondary structure , using an interpolated transition between the previous one and the new one.
void	VARNAPanel.showRNAInterpolated(RNA target, Mapping m) Simply displays (does not redraw) a secondary structure , using an interpolated transition between the previous one and the new one.
void	VARNAPanel.showRNAInterpolated(RNA target, VARNAConfig cfg, Mapping m)

Constructors in fr.orsay.lri.varna with parameters of type RNA

VARNAPanel(RNA r)
Creates a VARNAPanel instance, and displays an RNA.

Uses of RNA in fr.orsay.lri.varna.interfaces

Methods in fr.orsay.lri.varna.interfaces with parameters of type RNA

void	InterfaceVARNAListener.onUINewStructure(VARNAConfig v, RNA r)

Uses of RNA in fr.orsay.lri.varna.models

Fields in fr.orsay.lri.varna.models declared as RNA

private RNA	VARNAConfigLoader._defaultRNA
RNA	FullBackup.rna

Methods in fr.orsay.lri.varna.models with parameters of type RNA

void	VARNAConfigLoader.setRNA(RNA r)

Constructors in fr.orsay.lri.varna.models with parameters of type RNA

FullBackup(VARNAConfig c, RNA r, String n)

Uses of RNA in fr.orsay.lri.varna.models.annotations

Constructors in fr.orsay.lri.varna.models.annotations with parameters of type RNA

HighlightRegionAnnotation(RNA r, int startIndex, int stopIndex)

Uses of RNA in fr.orsay.lri.varna.models.rna

Fields in fr.orsay.lri.varna.models.rna declared as RNA

(package private) RNA	VARNASecDraw.HelixEmbedding._r
private RNA	Motif._rna

Methods in fr.orsay.lri.varna.models.rna that return RNA

RNA	RNA.clone()

Methods in fr.orsay.lri.varna.models.rna with parameters of type RNA

private void	VARNASecDraw.buildTree(int i, int j, VARNASecDraw.RNATree parent, RNA r)
double	VARNASecDraw.determineRadius(int numHelices, int numUnpaired, RNA r)
VARNASecDraw.RNATree	VARNASecDraw.drawRNA(double dirAngle, RNA r)
void	VARNASecDraw.drawTree(double x0, double y0, VARNASecDraw.RNATree t, double dir, RNA r)
GeneralPath	VARNASecDraw.PairedPortion.getLocalOutline(RNA r)
abstract GeneralPath	VARNASecDraw.Portion.getOutline(RNA r)
GeneralPath	VARNASecDraw.UnpairedPortion.getOutline(RNA r)
GeneralPath	VARNASecDraw.PairedPortion.getOutline(RNA r)
GeneralPath	VARNASecDraw.RNATree.getOutline(RNA r)
GeneralPath	VARNASecDraw.PairedPortion.getOutline(RNA r, boolean local)
private void	VARNASecDraw.HelixEmbedding.placeTerminalLoop(ArrayList<ModeleBase> mbl, RNA r)
void	VARNASecDraw.predrawTree(double x0, double y0, VARNASecDraw.RNATree t, double dir, RNA r, VARNASecDraw.HelixEmbedding parent, ArrayList<VARNASecDraw.HelixEmbedding> all)

Constructors in fr.orsay.lri.varna.models.rna with parameters of type RNA

Motif(RNA rna, ArrayList<ModeleBase> listeBases)

RNA(RNA r)

VARNASecDraw.HelixEmbedding(Point2D.Double support, VARNASecDraw.PairedPortion p, RNA r, VARNASecDraw.HelixEmbedding parent)

Uses of RNA in fr.orsay.lri.varna.models.templates

Methods in fr.orsay.lri.varna.models.templates that return RNA

RNA	RNATemplate.toRNA() Generate an RNA sequence that exactly matches the template.

Methods in fr.orsay.lri.varna.models.templates with parameters of type RNA

static TreeAlignResult<RNANodeValue2,RNANodeValueTemplate>	RNATemplateAlign.alignRNAWithTemplate(RNA rna, RNATemplate template) Align the given RNA with the given RNA template.
static RNATemplateMapping	RNATemplateAlign.makeTemplateMapping(TreeAlignResult<RNANodeValue2,RNANodeValueTemplate> alignResult, RNA rna) This method takes an alignment between a tree of RNANodeValue2 of RNANodeValue and a tree of RNANodeValue2 of RNANodeValueTemplate, and the original RNA object that was used to create the first tree in the alignment.
static RNATemplateMapping	RNATemplateAlign.mapRNAWithTemplate(RNA rna, RNATemplate template) Map an RNA with an RNATemplate using tree alignment.
String	RNATemplateMapping.showCompact(RNA r)

Uses of RNA in fr.orsay.lri.varna.models.treealign

Fields in fr.orsay.lri.varna.models.treealign declared as RNA

private RNA

RNATree.ConvertToTree.rna

Methods in fr.orsay.lri.varna.models.treealign with parameters of type RNA

static Tree<RNANodeValue2>	RNATree2.RNATree2FromRNA(RNA rna) Convert an RNA object into a RNA tree with RNANodeValue2.
static Tree<RNANodeValue>	RNATree.RNATreeFromRNA(RNA rna) Convert an RNA object into a RNA tree.

Constructors in fr.orsay.lri.varna.models.treealign with parameters of type RNA

RNATree.ConvertToTree(RNA rna)