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)