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R

rad - Variable in class fr.orsay.lri.varna.views.VueHighlightRegionEdit
 
radius - Variable in class fr.orsay.lri.varna.models.naView.Loop
 
radius - Variable in class fr.orsay.lri.varna.models.naView.Radloop
 
RADIUS_REDUCTION_FACTOR - Variable in class fr.orsay.lri.varna.models.naView.NAView
 
Radloop - Class in fr.orsay.lri.varna.models.naView
 
Radloop() - Constructor for class fr.orsay.lri.varna.models.naView.Radloop
 
read_in_bases(ArrayList<Integer>) - Method in class fr.orsay.lri.varna.models.naView.NAView
 
readMappingFromAlignment(String, String) - Static method in class fr.orsay.lri.varna.models.rna.Mapping
 
readValues(Reader, ModeleColorMap) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
readValues(Reader) - Method in class fr.orsay.lri.varna.VARNAPanel
 
reajustement() - Method in class fr.orsay.lri.varna.models.rna.Motif
 
RectangleCommand - Class in fr.orsay.lri.varna.models.export
 
RectangleCommand(Point2D.Double, Point2D.Double, double) - Constructor for class fr.orsay.lri.varna.models.export.RectangleCommand
 
redColorMap() - Static method in class fr.orsay.lri.varna.models.rna.ModeleColorMap
 
redo() - Method in class fr.orsay.lri.varna.models.VARNAEdits.AddBPEdit
 
redo() - Method in class fr.orsay.lri.varna.models.VARNAEdits.BasesShiftEdit
 
redo() - Method in class fr.orsay.lri.varna.models.VARNAEdits.HelixFlipEdit
 
redo() - Method in class fr.orsay.lri.varna.models.VARNAEdits.HelixRotateEdit
 
redo() - Method in class fr.orsay.lri.varna.models.VARNAEdits.RedrawEdit
 
redo() - Method in class fr.orsay.lri.varna.models.VARNAEdits.RemoveBPEdit
 
redo() - Method in class fr.orsay.lri.varna.models.VARNAEdits.RotateRNAEdit
 
redo() - Method in class fr.orsay.lri.varna.models.VARNAEdits.SingleBaseMoveEdit
 
redo() - Method in class fr.orsay.lri.varna.VARNAPanel
 
redrawMenu() - Method in class fr.orsay.lri.varna.views.VueMenu
 
reflectCoordinates() - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw.HelixEmbedding
 
refreshCode() - Method in class fr.orsay.lri.varna.views.VueColorMapStyle
 
region - Variable in class fr.orsay.lri.varna.models.naView.Base
 
region - Variable in class fr.orsay.lri.varna.models.naView.Connection
 
Region - Class in fr.orsay.lri.varna.models.naView
 
Region() - Constructor for class fr.orsay.lri.varna.models.naView.Region
 
regions - Variable in class fr.orsay.lri.varna.models.naView.NAView
 
remainingNodes - Variable in class fr.orsay.lri.varna.models.treealign.Tree.DFSPrefixIterator
 
remove() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNAIterator
 
remove() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.VertexIterator
 
remove() - Method in class fr.orsay.lri.varna.models.treealign.Tree.DFSPrefixIterator
 
REMOVE - Static variable in class fr.orsay.lri.varna.views.VueListeAnnotations
if this view is for removing annoted texts
REMOVE_HEIGHT - Static variable in class fr.orsay.lri.varna.components.GradientEditorPanel
 
removeAll(BaseList) - Method in class fr.orsay.lri.varna.models.BaseList
Returns, in a new BaseList, the list consisting of the current BaseList minus the list passed as argument.
removeAnnotation(TextAnnotation) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
removeAnnotation(String) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
removeAnnotation(TextAnnotation) - Method in class fr.orsay.lri.varna.VARNAPanel
 
removeBackgroundColor() - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
removeBase(ModeleBase) - Method in class fr.orsay.lri.varna.models.BaseList
 
removeBP(ModeleBP) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
removeChemProbAnnotation(ChemProbAnnotation) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
removeColorMap() - Method in class fr.orsay.lri.varna.VARNAPanel
 
removedHelixes - Variable in class fr.orsay.lri.varna.models.templates.RNATemplate.ConvertToTree
 
removeElement(RNATemplate.RNATemplateElement) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate
Remove the element from the template.
removeElementStructure() - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
 
removeEntry(int) - Method in class fr.orsay.lri.varna.components.GradientEditorPanel
 
removeFromSelection(int) - Method in class fr.orsay.lri.varna.VARNAPanel
 
removeHighlightRegion(HighlightRegionAnnotation) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
removeHighlightRegion(HighlightRegionAnnotation) - Method in class fr.orsay.lri.varna.VARNAPanel
 
removeLink() - Method in class fr.orsay.lri.varna.VARNAPanel
 
removePseudoKnots() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RemovePseudoKnots
 
removePseudoKnotsAux() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RemovePseudoKnots
We compute helixesStructWithoutPseudoKnots from helixesStruct by replacing values by -1 for the helixes we cut (the bases are become non-paired).
removeSelectedAnnotation() - Method in class fr.orsay.lri.varna.VARNAPanel
 
removeSelectionMenu() - Method in class fr.orsay.lri.varna.views.VueMenu
 
removeSelectionRectangle() - Method in class fr.orsay.lri.varna.VARNAPanel
 
renderAnnotations(SecStrDrawingProducer, double, double, VARNAConfig) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
renderAnnotations(VueVARNAGraphics, double, double, double, double, double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
renderComponent(VueVARNAGraphics, boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
Draws current RNA structure in a given Graphics "device".
renderRegionHighlights(SecStrDrawingProducer, Point2D.Double[], Point2D.Double[]) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
renderRNA(VueVARNAGraphics, Rectangle2D.Double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
ReorderableJList - Class in fr.orsay.lri.varna.components
 
ReorderableJList() - Constructor for class fr.orsay.lri.varna.components.ReorderableJList
 
ReorderableJList.ReorderableListCellRenderer - Class in fr.orsay.lri.varna.components
 
ReorderableJList.ReorderableListCellRenderer() - Constructor for class fr.orsay.lri.varna.components.ReorderableJList.ReorderableListCellRenderer
 
ReorderableJList.RJLTransferable - Class in fr.orsay.lri.varna.components
 
ReorderableJList.RJLTransferable(Object) - Constructor for class fr.orsay.lri.varna.components.ReorderableJList.RJLTransferable
 
replaceChildrenListBy(List<Tree<T>>) - Method in class fr.orsay.lri.varna.models.treealign.Tree
This method replaces the list of children of a tree with the list given as argument.
replaceEntry(int, Color, double) - Method in class fr.orsay.lri.varna.components.GradientEditorPanel
 
rescale(double, double) - Method in class fr.orsay.lri.varna.models.rna.ModeleColorMap
 
rescaleColorMap(ModeleColorMap) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
reset() - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
reset() - Method in class fr.orsay.lri.varna.VARNAPanel
Resets the visual aspects (Zoom factor, shift) for the Panel.
resetAnnotationHighlight() - Method in class fr.orsay.lri.varna.VARNAPanel
Stops highlighting bases
resetBoundingBox() - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
resetListeAnnotations() - Method in class fr.orsay.lri.varna.VARNAPanel
 
resolveEntity(String, String) - Method in class fr.orsay.lri.varna.models.rna.RNAMLParser
 
restoreSelection() - Method in class fr.orsay.lri.varna.VARNAPanel
 
restoreThicknesses() - Method in class fr.orsay.lri.varna.views.VueBPThickness
 
retainAll(BaseList) - Method in class fr.orsay.lri.varna.models.BaseList
Returns, in a new BaseList, the intersection of the current BaseList and of the argument.
retrieveParametersValues() - Method in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
revdata - Variable in class fr.orsay.lri.varna.views.VueBases
 
rightBasePosition - Variable in class fr.orsay.lri.varna.models.treealign.RNANodeValue
 
rightNode - Variable in class fr.orsay.lri.varna.models.treealign.AlignedNode
 
rightNucleotide - Variable in class fr.orsay.lri.varna.models.treealign.RNANodeValue
 
rlphead - Variable in class fr.orsay.lri.varna.models.naView.NAView
 
rna - Variable in class fr.orsay.lri.varna.models.FullBackup
 
RNA - Class in fr.orsay.lri.varna.models.rna
The RNA model which contain the base list and the draw algorithm mode
RNA() - Constructor for class fr.orsay.lri.varna.models.rna.RNA
 
RNA(String) - Constructor for class fr.orsay.lri.varna.models.rna.RNA
 
RNA(RNA) - Constructor for class fr.orsay.lri.varna.models.rna.RNA
 
rna - Variable in class fr.orsay.lri.varna.models.treealign.RNATree.ConvertToTree
 
RNA.ComputeArcCenter - Class in fr.orsay.lri.varna.models.rna
 
RNA.ComputeArcCenter() - Constructor for class fr.orsay.lri.varna.models.rna.RNA.ComputeArcCenter
 
RNA.DrawRNATemplateMethod - Class in fr.orsay.lri.varna.models.rna
What to do in case some helices are of a different length in the template and the actual helix.
RNA.DrawRNATemplateMethod() - Constructor for class fr.orsay.lri.varna.models.rna.RNA.DrawRNATemplateMethod
 
RNAForest2FromRNAForest(List<Tree<RNANodeValue>>) - Static method in class fr.orsay.lri.varna.models.treealign.RNATree2
 
RNAForest2FromRNAForestCommitNonPaired(List<Tree<RNANodeValue2>>, List<RNANodeValue>) - Static method in class fr.orsay.lri.varna.models.treealign.RNATree2
 
rnaIterator() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate
Iterates over the elements of the template, in the sequence order.
RNAMLParser - Class in fr.orsay.lri.varna.models.rna
 
RNAMLParser() - Constructor for class fr.orsay.lri.varna.models.rna.RNAMLParser
 
RNAMLParser.BPTemp - Class in fr.orsay.lri.varna.models.rna
 
RNAMLParser.BPTemp(int, int, String, String, String) - Constructor for class fr.orsay.lri.varna.models.rna.RNAMLParser.BPTemp
 
RNAMLParser.HelixTemp - Class in fr.orsay.lri.varna.models.rna
 
RNAMLParser.HelixTemp(int, int, int, String) - Constructor for class fr.orsay.lri.varna.models.rna.RNAMLParser.HelixTemp
 
RNANodeValue - Class in fr.orsay.lri.varna.models.treealign
We use the following convention: If the node is marked by a couple (n,m) these integers are stored in leftBasePosition and rightBasePosition (ie.
RNANodeValue() - Constructor for class fr.orsay.lri.varna.models.treealign.RNANodeValue
 
RNANodeValue.Origin - Enum in fr.orsay.lri.varna.models.treealign
 
RNANodeValue.Origin() - Constructor for enum fr.orsay.lri.varna.models.treealign.RNANodeValue.Origin
 
RNANodeValue2 - Class in fr.orsay.lri.varna.models.treealign
In this model, nodes are either: 1.
RNANodeValue2(boolean) - Constructor for class fr.orsay.lri.varna.models.treealign.RNANodeValue2
 
RNANodeValue2TemplateDistance - Class in fr.orsay.lri.varna.models.templates
Distance between an RNANodeValue2 and an RNANodeValueTemplate.
RNANodeValue2TemplateDistance() - Constructor for class fr.orsay.lri.varna.models.templates.RNANodeValue2TemplateDistance
 
RNANodeValue2WrongTypeException - Exception in fr.orsay.lri.varna.models.treealign
 
RNANodeValue2WrongTypeException() - Constructor for exception fr.orsay.lri.varna.models.treealign.RNANodeValue2WrongTypeException
 
RNANodeValueTemplate - Class in fr.orsay.lri.varna.models.templates
An node from an RNA template is either a sequence of non-paired bases, a base pair originally belonging to an helix, or a single base originally belonging to an helix but which was broken in order to remove pseudoknots.
RNANodeValueTemplate() - Constructor for class fr.orsay.lri.varna.models.templates.RNANodeValueTemplate
 
RNANodeValueTemplateBasePair - Class in fr.orsay.lri.varna.models.templates
See RNANodeValueTemplate.
RNANodeValueTemplateBasePair() - Constructor for class fr.orsay.lri.varna.models.templates.RNANodeValueTemplateBasePair
 
RNANodeValueTemplateBrokenBasePair - Class in fr.orsay.lri.varna.models.templates
See RNANodeValueTemplate.
RNANodeValueTemplateBrokenBasePair() - Constructor for class fr.orsay.lri.varna.models.templates.RNANodeValueTemplateBrokenBasePair
 
RNANodeValueTemplateSequence - Class in fr.orsay.lri.varna.models.templates
See RNANodeValueTemplate.
RNANodeValueTemplateSequence() - Constructor for class fr.orsay.lri.varna.models.templates.RNANodeValueTemplateSequence
 
RNATemplate - Class in fr.orsay.lri.varna.models.templates
A model for RNA templates.
RNATemplate() - Constructor for class fr.orsay.lri.varna.models.templates.RNATemplate
 
RNATemplate.ConvertToTree - Class in fr.orsay.lri.varna.models.templates
 
RNATemplate.ConvertToTree(Set<RNATemplate.RNATemplateHelix>) - Constructor for class fr.orsay.lri.varna.models.templates.RNATemplate.ConvertToTree
 
RNATemplate.ConvertToXml - Class in fr.orsay.lri.varna.models.templates
 
RNATemplate.ConvertToXml() - Constructor for class fr.orsay.lri.varna.models.templates.RNATemplate.ConvertToXml
 
RNATemplate.EdgeEndPointPosition - Enum in fr.orsay.lri.varna.models.templates
Position of an endpoint on an endpoint.
RNATemplate.EdgeEndPointPosition() - Constructor for enum fr.orsay.lri.varna.models.templates.RNATemplate.EdgeEndPointPosition
 
RNATemplate.In1Is - Enum in fr.orsay.lri.varna.models.templates
For an helix, tells us whether IN1/OUT1 is the 5' strand (the first strand we meet if we follow the RNA sequence) or the 3' strand (the second we meet if we follow the RNA sequence).
RNATemplate.In1Is() - Constructor for enum fr.orsay.lri.varna.models.templates.RNATemplate.In1Is
 
RNATemplate.LoadFromXml - Class in fr.orsay.lri.varna.models.templates
 
RNATemplate.LoadFromXml(Document) - Constructor for class fr.orsay.lri.varna.models.templates.RNATemplate.LoadFromXml
 
RNATemplate.MakeEdgeList - Class in fr.orsay.lri.varna.models.templates
 
RNATemplate.MakeEdgeList() - Constructor for class fr.orsay.lri.varna.models.templates.RNATemplate.MakeEdgeList
 
RNATemplate.RemovePseudoKnots - Class in fr.orsay.lri.varna.models.templates
 
RNATemplate.RemovePseudoKnots() - Constructor for class fr.orsay.lri.varna.models.templates.RNATemplate.RemovePseudoKnots
 
RNATemplate.RNAIterator - Class in fr.orsay.lri.varna.models.templates
To get an iterator of this class, use rnaIterator().
RNATemplate.RNAIterator() - Constructor for class fr.orsay.lri.varna.models.templates.RNATemplate.RNAIterator
 
RNATemplate.RNATemplateElement - Class in fr.orsay.lri.varna.models.templates
An endpoint of an RNA template, it can be an helix or a sequence of non-paired bases.
RNATemplate.RNATemplateElement() - Constructor for class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement
When the endpoint is created, it is added to the list of elements in this template.
RNATemplate.RNATemplateElement.EdgeEndPoint - Class in fr.orsay.lri.varna.models.templates
An edge endpoint is where an edge can connect.
RNATemplate.RNATemplateElement.EdgeEndPoint() - Constructor for class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement.EdgeEndPoint
 
RNATemplate.RNATemplateHelix - Class in fr.orsay.lri.varna.models.templates
An helix in an RNA template.
RNATemplate.RNATemplateHelix(String) - Constructor for class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
 
RNATemplate.RNATemplateUnpairedSequence - Class in fr.orsay.lri.varna.models.templates
A sequence of non-paired bases in an RNA template.
RNATemplate.RNATemplateUnpairedSequence(String) - Constructor for class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
 
RNATemplate.VertexIterator - Class in fr.orsay.lri.varna.models.templates
 
RNATemplate.VertexIterator() - Constructor for class fr.orsay.lri.varna.models.templates.RNATemplate.VertexIterator
 
RNATemplateAlign - Class in fr.orsay.lri.varna.models.templates
This class is about the alignment between a tree of RNANodeValue2 and a tree of RNANodeValueTemplate.
RNATemplateAlign() - Constructor for class fr.orsay.lri.varna.models.templates.RNATemplateAlign
 
RNATemplateDrawingAlgorithmException - Exception in fr.orsay.lri.varna.models.templates
Exception thrown in case of failure of the template-based RNA drawing algorithm.
RNATemplateDrawingAlgorithmException(String) - Constructor for exception fr.orsay.lri.varna.models.templates.RNATemplateDrawingAlgorithmException
 
RNATemplateMapping - Class in fr.orsay.lri.varna.models.templates
A RNATemplateMapping is a mapping between bases in an RNA sequence and elements in a RNA template.
RNATemplateMapping() - Constructor for class fr.orsay.lri.varna.models.templates.RNATemplateMapping
 
RNATemplateMappingException - Exception in fr.orsay.lri.varna.models.templates
This exception is thrown when we discover that a template is invalid (it contains impossible connections between elements).
RNATemplateMappingException(String) - Constructor for exception fr.orsay.lri.varna.models.templates.RNATemplateMappingException
 
RNATemplateMappingException() - Constructor for exception fr.orsay.lri.varna.models.templates.RNATemplateMappingException
 
RNATree - Class in fr.orsay.lri.varna.models.treealign
This class contains all functions that are specific to trees (class Tree) of RNA.
RNATree() - Constructor for class fr.orsay.lri.varna.models.treealign.RNATree
 
RNATree.ConvertToMapping - Class in fr.orsay.lri.varna.models.treealign
 
RNATree.ConvertToMapping() - Constructor for class fr.orsay.lri.varna.models.treealign.RNATree.ConvertToMapping
 
RNATree.ConvertToTree - Class in fr.orsay.lri.varna.models.treealign
 
RNATree.ConvertToTree(RNA) - Constructor for class fr.orsay.lri.varna.models.treealign.RNATree.ConvertToTree
 
RNATree2 - Class in fr.orsay.lri.varna.models.treealign
This class contains all functions that are specific to trees (class Tree) of RNA, with RNANodeValue2.
RNATree2() - Constructor for class fr.orsay.lri.varna.models.treealign.RNATree2
 
RNATree2.ConvertToMapping - Class in fr.orsay.lri.varna.models.treealign
 
RNATree2.ConvertToMapping() - Constructor for class fr.orsay.lri.varna.models.treealign.RNATree2.ConvertToMapping
 
RNATree2Exception - Exception in fr.orsay.lri.varna.models.treealign
 
RNATree2Exception(String) - Constructor for exception fr.orsay.lri.varna.models.treealign.RNATree2Exception
 
RNATree2FromRNA(RNA) - Static method in class fr.orsay.lri.varna.models.treealign.RNATree2
Convert an RNA object into a RNA tree with RNANodeValue2.
RNATree2FromRNATree(Tree<RNANodeValue>) - Static method in class fr.orsay.lri.varna.models.treealign.RNATree2
Convert from RNANodeValue model to RNANodeValue2 model, ie.
RNATreeFromRNA(RNA) - Static method in class fr.orsay.lri.varna.models.treealign.RNATree
Convert an RNA object into a RNA tree.
RNAVIZ_BP_STYLE - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
rockNRollColorMap() - Static method in class fr.orsay.lri.varna.models.rna.ModeleColorMap
 
root - Variable in class fr.orsay.lri.varna.models.naView.NAView
 
rootDegree() - Method in class fr.orsay.lri.varna.models.treealign.Tree
Returns the number of children of the root node.
rotate(double) - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw.HelixEmbedding
 
rotateHelix(Point2D.Double, int, int, double) - Method in class fr.orsay.lri.varna.views.VueUI
 
rotatePoint(Point2D.Double, Point2D.Double, double) - Method in class fr.orsay.lri.varna.views.VueUI
 
rotationOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
rotationSlider - Variable in class fr.orsay.lri.varna.views.VueAnnotation
 
rotationSlider - Variable in class fr.orsay.lri.varna.views.VueGlobalRotation
 
run() - Method in class fr.orsay.lri.varna.views.VueAboutPanel.AboutAnimator
 

A B C D E F G H I K L M N O P Q R S T U V W X Y Z _