|
||||||||||
PREV NEXT | FRAMES NO FRAMES |
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)
|
|
||||||||||
PREV NEXT | FRAMES NO FRAMES |