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 _

D

data - Variable in class fr.orsay.lri.varna.components.AnnotationTableModel
 
data - Variable in class fr.orsay.lri.varna.components.BaseTableModel
 
data - Variable in class fr.orsay.lri.varna.views.VueBases
 
data - Variable in class fr.orsay.lri.varna.views.VueBaseValues
 
data - Variable in class fr.orsay.lri.varna.views.VueBPList
 
data - Variable in class fr.orsay.lri.varna.views.VueListeAnnotations
 
debug - Variable in class fr.orsay.lri.varna.models.naView.NAView
 
debugPrintArray(Object[]) - Method in class fr.orsay.lri.varna.models.rna.RNAMLParser
 
decalerBase(ModeleStrand, double) - Method in class fr.orsay.lri.varna.models.rna.Motif
 
decode(String) - Static method in class fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide
 
DEF1 - Variable in class fr.orsay.lri.varna.models.treealign.TreeAlign.Aligner
DEF1[i] is the distance between the empty forest and F1[i] (the forest of children of node i in the first tree).
DEF2 - Variable in class fr.orsay.lri.varna.models.treealign.TreeAlign.Aligner
Same as DEF1, but for second tree.
DEFAULT_AMOUNT - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
DEFAULT_BACKBONE_COLOR - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
DEFAULT_BACKGROUND_COLOR - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
DEFAULT_BASE_FONT - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
DEFAULT_BASE_OUTLINE_THICKNESS - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
DEFAULT_BOND_COLOR - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
DEFAULT_BP_INCREMENT - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
DEFAULT_BP_STYLE - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
DEFAULT_BP_THICKNESS - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
DEFAULT_COLOR - Static variable in class fr.orsay.lri.varna.models.annotations.ChemProbAnnotation
 
DEFAULT_COLOR - Static variable in class fr.orsay.lri.varna.models.rna.ModeleColorMap
 
DEFAULT_COLOR_MAP - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
DEFAULT_COLOR_MAP_FONT_COLOR - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
DEFAULT_COLOR_MAP_FONT_SIZE - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
DEFAULT_COLOR_MAP_HEIGHT - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
DEFAULT_COLOR_MAP_OUTLINE - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
DEFAULT_COLOR_MAP_STRIPE_WIDTH - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
DEFAULT_COLOR_MAP_WIDTH - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
DEFAULT_COLOR_MAP_X_OFFSET - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
DEFAULT_COLOR_MAP_Y_OFFSET - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
DEFAULT_DASH_BASE_COLOR - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
DEFAULT_DIST_NUMBERS - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
DEFAULT_DRAW_MODE - Static variable in class fr.orsay.lri.varna.models.rna.RNA
 
DEFAULT_FILL_COLOR - Static variable in class fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation
 
DEFAULT_HOVER_COLOR - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
DEFAULT_INTENSITY - Static variable in class fr.orsay.lri.varna.models.annotations.ChemProbAnnotation
 
DEFAULT_NUMBERS_FONT - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
DEFAULT_OUTLINE_COLOR - Static variable in class fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation
 
DEFAULT_PERIOD - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
DEFAULT_RADIUS - Static variable in class fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation
 
DEFAULT_RNA_COLOR - Static variable in class fr.orsay.lri.varna.models.rna.ModeleBasesComparison
 
DEFAULT_SPECIAL_BASE_COLOR - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
DEFAULT_TITLE_COLOR - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
DEFAULT_TITLE_FONT - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
DEFAULT_TYPE - Static variable in class fr.orsay.lri.varna.models.annotations.ChemProbAnnotation
 
DEFAULT_ZOOM - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
DEFAULTCOLOR - Static variable in class fr.orsay.lri.varna.models.annotations.TextAnnotation
default text color
defaultColorMap() - Static method in class fr.orsay.lri.varna.models.rna.ModeleColorMap
 
DEFAULTFONT - Static variable in class fr.orsay.lri.varna.models.annotations.TextAnnotation
default text font
DefaultMapping(int, int) - Static method in class fr.orsay.lri.varna.models.rna.Mapping
 
DefaultOutermostMapping(int, int) - Static method in class fr.orsay.lri.varna.models.rna.Mapping
 
defaultTangentVectorAngle - Static variable in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
 
defaultTangentVectorLength - Static variable in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
 
degree - Variable in class fr.orsay.lri.varna.models.treealign.TreeAlign.TreeData
The number of children of a node is called the node degree.
degrees - Variable in class fr.orsay.lri.varna.models.treealign.TreeAlign.TreeData
The number of children of a node is called the node degree.
delete(RNANodeValue2) - Method in class fr.orsay.lri.varna.models.templates.RNANodeValue2TemplateDistance
 
depth - Variable in class fr.orsay.lri.varna.models.naView.Loop
 
depth(Loop) - Method in class fr.orsay.lri.varna.models.naView.NAView
Determines the depth of loop, lp.
deriveStroke(BasicStroke, double) - Method in class fr.orsay.lri.varna.models.export.SwingGraphics
 
DET1 - Variable in class fr.orsay.lri.varna.models.treealign.TreeAlign.Aligner
DET1[i] is the distance between the empty tree and T1[i] (the subtree rooted at node i in the first tree).
DET2 - Variable in class fr.orsay.lri.varna.models.treealign.TreeAlign.Aligner
Same as DET1, but for second tree.
determine_depths() - Method in class fr.orsay.lri.varna.models.naView.NAView
Determine the depth of all loops.
determine_radius(Loop, double) - Method in class fr.orsay.lri.varna.models.naView.NAView
For the loop pointed to by lp, determine the radius of the loop that will ensure that each base around the loop will have a separation of at least lencut around the circle.
determineRadius(int, int, double) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
determineRadius(int, int, double, double, double) - Static method in class fr.orsay.lri.varna.models.rna.RNA
 
determineRadius(int, int, RNA) - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw
 
deviationBasePair() - Method in class fr.orsay.lri.varna.models.rna.Motif
 
DF1 - Variable in class fr.orsay.lri.varna.models.treealign.TreeAlign.Aligner
DF1[i][j_t] is DFL for (i,j,s,t) with s=0.
DF1Decisions1 - Variable in class fr.orsay.lri.varna.models.treealign.TreeAlign.Aligner
This arrays have the same shape as respectively DF1.
DF1Decisions2 - Variable in class fr.orsay.lri.varna.models.treealign.TreeAlign.Aligner
 
DF2 - Variable in class fr.orsay.lri.varna.models.treealign.TreeAlign.Aligner
DF2[j][i_s] is DFL for (i,j,s,t) with t=0.
DF2Decisions1 - Variable in class fr.orsay.lri.varna.models.treealign.TreeAlign.Aligner
This arrays have the same shape as respectively DF2.
DF2Decisions2 - Variable in class fr.orsay.lri.varna.models.treealign.TreeAlign.Aligner
 
dialog - Variable in class fr.orsay.lri.varna.components.BaseSpecialColorEditor
 
discardStacking() - Method in class fr.orsay.lri.varna.models.rna.RNAMLParser
 
disconnect() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement.EdgeEndPoint
Disconnect this endpoint from the other, ie.
disconnectFromAny() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement
Disconnect this endpoint from any other elements it may be connected to.
disconnectFromAny() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
 
disconnectFromAny() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
 
displayMenu() - Method in class fr.orsay.lri.varna.views.VueMenu
 
distance - Variable in class fr.orsay.lri.varna.models.templates.RNATemplateMapping
Alignment distance.
distance - Variable in class fr.orsay.lri.varna.models.treealign.ExampleDistance3.SequenceAlignResult
 
distance - Variable in class fr.orsay.lri.varna.models.treealign.TreeAlignResult
 
distanceFromAlignment(Tree<AlignedNode<ValueType1, ValueType2>>) - Method in class fr.orsay.lri.varna.models.treealign.TreeAlign
Takes a alignment, and compute the distance between the two original trees.
DL - Variable in class fr.orsay.lri.varna.models.treealign.TreeAlign.Aligner
Distances between labels.
document - Variable in class fr.orsay.lri.varna.models.templates.RNATemplate.ConvertToXml
 
dragDropEnd(DragSourceDropEvent) - Method in class fr.orsay.lri.varna.components.ReorderableJList
 
dragEnter(DragSourceDragEvent) - Method in class fr.orsay.lri.varna.components.ReorderableJList
 
dragEnter(DropTargetDragEvent) - Method in class fr.orsay.lri.varna.components.ReorderableJList
 
dragExit(DragSourceEvent) - Method in class fr.orsay.lri.varna.components.ReorderableJList
 
dragExit(DropTargetEvent) - Method in class fr.orsay.lri.varna.components.ReorderableJList
 
draggedIndex - Variable in class fr.orsay.lri.varna.components.ReorderableJList
 
dragGestureRecognized(DragGestureEvent) - Method in class fr.orsay.lri.varna.components.ReorderableJList
 
dragOver(DragSourceDragEvent) - Method in class fr.orsay.lri.varna.components.ReorderableJList
 
dragOver(DropTargetDragEvent) - Method in class fr.orsay.lri.varna.components.ReorderableJList
 
dragSource - Variable in class fr.orsay.lri.varna.components.ReorderableJList
 
draw(GeneralPath) - Method in class fr.orsay.lri.varna.models.export.SecStrProducerGraphics
 
draw(GeneralPath) - Method in class fr.orsay.lri.varna.models.export.SwingGraphics
 
draw(GeneralPath) - Method in interface fr.orsay.lri.varna.models.export.VueVARNAGraphics
 
DRAW_MODE_CIRCULAR - Static variable in class fr.orsay.lri.varna.models.rna.RNA
Selects the "Feynman diagram" drawing algorithm that places the bases on a circle and draws the base-pairings as chords of the circle graph.
DRAW_MODE_LINEAR - Static variable in class fr.orsay.lri.varna.models.rna.RNA
Selects the linear algorithm.
DRAW_MODE_MOTIFVIEW - Static variable in class fr.orsay.lri.varna.models.rna.RNA
Selects the RNAView algorithm.
DRAW_MODE_NAVIEW - Static variable in class fr.orsay.lri.varna.models.rna.RNA
Selects the NAView algorithm.
DRAW_MODE_RADIATE - Static variable in class fr.orsay.lri.varna.models.rna.RNA
Selects the "tree drawing" algorithm.
DRAW_MODE_TEMPLATE - Static variable in class fr.orsay.lri.varna.models.rna.RNA
 
DRAW_MODE_VARNA_VIEW - Static variable in class fr.orsay.lri.varna.models.rna.RNA
 
drawAlongCurve(int, int, Point2D.Double, Point2D.Double, Point2D.Double, Point2D.Double, Point2D.Double[], Point2D.Double[]) - Method in class fr.orsay.lri.varna.models.rna.RNA
This functions draws the RNA sequence between (including) firstBase and lastBase along a curve.
drawArc(Point2D.Double, double, double, double, double) - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
drawArc(double, double, double, double, double, double) - Method in class fr.orsay.lri.varna.models.export.SecStrProducerGraphics
 
drawArc(double, double, double, double, double, double) - Method in class fr.orsay.lri.varna.models.export.SwingGraphics
 
drawArc(double, double, double, double, double, double) - Method in interface fr.orsay.lri.varna.models.export.VueVARNAGraphics
 
drawArcS(Point2D.Double, double, double, double, double) - Method in class fr.orsay.lri.varna.models.export.PSExport
 
drawArcS(Point2D.Double, double, double, double, double) - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
drawArcS(Point2D.Double, double, double, double, double) - Method in class fr.orsay.lri.varna.models.export.SVGExport
 
drawArcS(Point2D.Double, double, double, double, double) - Method in class fr.orsay.lri.varna.models.export.XFIGExport
 
drawBackbone(VueVARNAGraphics, Point2D.Double[], double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
drawBackboneOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
drawBase(VueVARNAGraphics, int, Point2D.Double[], Point2D.Double[], double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
drawBasePair(SecStrDrawingProducer, Point2D.Double, Point2D.Double, ModeleBP, VARNAConfig) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
drawBasePair(VueVARNAGraphics, Point2D.Double, Point2D.Double, ModeleBP, double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
drawBBox(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
Toggles on/off a rectangular outline of the bounding box.
drawBorder(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
Toggles on/off a rectangular outline of the border.
drawChemProbAnnotation(SecStrDrawingProducer, ChemProbAnnotation, Point2D.Double, double, double) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
drawChemProbAnnotation(VueVARNAGraphics, ChemProbAnnotation, Point2D.Double, double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
drawCircle(double, double, double, double) - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
drawCircle(double, double, double) - Method in class fr.orsay.lri.varna.models.export.SecStrProducerGraphics
 
drawCircle(double, double, double) - Method in class fr.orsay.lri.varna.models.export.SwingGraphics
 
drawCircle(double, double, double) - Method in interface fr.orsay.lri.varna.models.export.VueVARNAGraphics
 
drawCircleS(Point2D.Double, double, double) - Method in class fr.orsay.lri.varna.models.export.PSExport
 
drawCircleS(Point2D.Double, double, double) - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
drawCircleS(Point2D.Double, double, double) - Method in class fr.orsay.lri.varna.models.export.SVGExport
 
drawCircleS(Point2D.Double, double, double) - Method in class fr.orsay.lri.varna.models.export.XFIGExport
 
drawColorMap(VARNAConfig, SecStrDrawingProducer) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
drawColorMap(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
 
drawColorMap(VueVARNAGraphics, double, Rectangle2D.Double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
drawColorMapOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
drawHelixLikeTemplateHelix(int[], RNATemplate.RNATemplateHelix, Point2D.Double[], Point2D.Double[], double, Map<RNATemplate.RNATemplateHelix, Point2D.Double>) - Method in class fr.orsay.lri.varna.models.rna.RNA
Draw the given helix (given as a *SORTED* array of indexes) like defined in the given template helix.
drawHelixLikeTemplateHelixOLD(int[], RNATemplate.RNATemplateHelix, Point2D.Double[], Point2D.Double[], double, Map<RNATemplate.RNATemplateHelix, Point2D.Double>) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
drawLine(double, double, double, double, double) - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
drawLine(double, double, double, double) - Method in class fr.orsay.lri.varna.models.export.SecStrProducerGraphics
 
drawLine(double, double, double, double) - Method in class fr.orsay.lri.varna.models.export.SwingGraphics
 
drawLine(double, double, double, double) - Method in interface fr.orsay.lri.varna.models.export.VueVARNAGraphics
 
drawLineS(Point2D.Double, Point2D.Double, double) - Method in class fr.orsay.lri.varna.models.export.PSExport
 
drawLineS(Point2D.Double, Point2D.Double, double) - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
drawLineS(Point2D.Double, Point2D.Double, double) - Method in class fr.orsay.lri.varna.models.export.SVGExport
 
drawLineS(Point2D.Double, Point2D.Double, double) - Method in class fr.orsay.lri.varna.models.export.XFIGExport
 
drawLoop(int, int, double, double, double, Point2D.Double[], Point2D.Double[]) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
drawMOTIFView() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
drawNCOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
drawOnBezierCurve(int[], Point2D.Double, Point2D.Double, Point2D.Double, Point2D.Double, Point2D.Double[], Point2D.Double[]) - Method in class fr.orsay.lri.varna.models.rna.RNA
A Bezier curve can be defined by four points, see http://en.wikipedia.org/wiki/Bezier_curve#Cubic_B.C3.A9zier_curves Here we give this four points and an array of bases indexes (which must be indexes in this RNA sequence) which will be moved to be on the Bezier curve.
drawOnStraightLine(int[], Point2D.Double, Point2D.Double, Point2D.Double[], Point2D.Double[]) - Method in class fr.orsay.lri.varna.models.rna.RNA
Like drawOnBezierCurve(), but on a straight line.
drawPage(Graphics2D) - Method in class fr.orsay.lri.varna.views.PrintPanel
This method draws the page both on the screen and the printer graphics context.
drawPolygon(double[], double[], double) - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
drawPolygon(GeneralPath, double) - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
drawPolygonS(Point2D.Double[], double) - Method in class fr.orsay.lri.varna.models.export.PSExport
 
drawPolygonS(Point2D.Double[], double) - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
drawPolygonS(Point2D.Double[], double) - Method in class fr.orsay.lri.varna.models.export.SVGExport
 
drawPolygonS(Point2D.Double[], double) - Method in class fr.orsay.lri.varna.models.export.XFIGExport
 
drawRect(double, double, double, double) - Method in class fr.orsay.lri.varna.models.export.SecStrProducerGraphics
 
drawRect(double, double, double, double) - Method in class fr.orsay.lri.varna.models.export.SwingGraphics
 
drawRect(double, double, double, double) - Method in interface fr.orsay.lri.varna.models.export.VueVARNAGraphics
 
drawRectangle(double, double, double, double, double) - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
drawRectangleS(Point2D.Double, Point2D.Double, double) - Method in class fr.orsay.lri.varna.models.export.PSExport
 
drawRectangleS(Point2D.Double, Point2D.Double, double) - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
drawRectangleS(Point2D.Double, Point2D.Double, double) - Method in class fr.orsay.lri.varna.models.export.SVGExport
 
drawRectangleS(Point2D.Double, Point2D.Double, double) - Method in class fr.orsay.lri.varna.models.export.XFIGExport
 
drawRegionHighlightsAnnotation(VueVARNAGraphics, Point2D.Double[], Point2D.Double[], double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
drawRNA(VARNAConfig) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
drawRNA(int, VARNAConfig) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
drawRNA(double, RNA) - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw
 
drawRNA(String, String) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the RNA secondary structure to be drawn in this panel, using the default layout algorithm.
drawRNA(RNA, int) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the RNA secondary structure to be drawn in this panel, using a given layout algorithm.
drawRNA() - Method in class fr.orsay.lri.varna.VARNAPanel
Redraws the current RNA.
drawRNA(RNA) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the RNA secondary structure to be drawn in this panel, using the current drawing algorithm.
drawRNA(String, String, int) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the RNA secondary structure to be drawn in this panel, using a given layout algorithm.
drawRNA(Reader, int) - Method in class fr.orsay.lri.varna.VARNAPanel
 
drawRNA(String, String, String, String, int) - Method in class fr.orsay.lri.varna.VARNAPanel
When comparison mode is ON, sets the two RNA secondary structure to be drawn in this panel, using a given layout algorithm.
drawRNACircle() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
drawRNAInterpolated(String, String) - Method in class fr.orsay.lri.varna.VARNAPanel
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.
drawRNAInterpolated(String, String, int) - Method in class fr.orsay.lri.varna.VARNAPanel
Draws a secondary structure of RNA using a given algorithm and displays it, using an interpolated transition between the previous one and the new one.
drawRNAInterpolated(String, String, Mapping) - Method in class fr.orsay.lri.varna.VARNAPanel
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.
drawRNAInterpolated(String, String, int, Mapping) - Method in class fr.orsay.lri.varna.VARNAPanel
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.
drawRNAInterpolated(RNA) - Method in class fr.orsay.lri.varna.VARNAPanel
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.
drawRNAInterpolated(RNA, Mapping) - Method in class fr.orsay.lri.varna.VARNAPanel
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.
drawRNAInterpolated(RNA, int, Mapping) - Method in class fr.orsay.lri.varna.VARNAPanel
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.
drawRNALine() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
drawRNANAView() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
drawRNARadiate(VARNAConfig) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
drawRNARadiate(double, boolean) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
drawRNATemplate(RNATemplate) - Method in class fr.orsay.lri.varna.models.rna.RNA
Same as below, with default helixLengthAdjustmentMethod.
drawRNATemplate(RNATemplate, int) - Method in class fr.orsay.lri.varna.models.rna.RNA
Draw this RNA like the given template.
drawRNAVARNAView() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
drawRoundRect(double, double, double, double, double, double) - Method in class fr.orsay.lri.varna.models.export.SecStrProducerGraphics
 
drawRoundRect(double, double, double, double, double, double) - Method in class fr.orsay.lri.varna.models.export.SwingGraphics
 
drawRoundRect(double, double, double, double, double, double) - Method in interface fr.orsay.lri.varna.models.export.VueVARNAGraphics
 
drawString(String, double, double) - Method in class fr.orsay.lri.varna.models.export.SwingGraphics
 
drawStringCentered(String, double, double) - Method in class fr.orsay.lri.varna.models.export.SecStrProducerGraphics
 
drawStringCentered(String, double, double) - Method in class fr.orsay.lri.varna.models.export.SwingGraphics
 
drawStringCentered(String, double, double) - Method in interface fr.orsay.lri.varna.models.export.VueVARNAGraphics
 
drawStringOutline(VueVARNAGraphics, String, double, double, double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
drawSymbol(SecStrDrawingProducer, double, double, double, double, double, boolean, ModeleBP.Edge, double) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
drawSymbol(VueVARNAGraphics, double, double, double, double, double, boolean, ModeleBP.Edge) - Method in class fr.orsay.lri.varna.VARNAPanel
 
drawTertiaryOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
drawText(double, double, String) - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
drawTextS(Point2D.Double, String) - Method in class fr.orsay.lri.varna.models.export.PSExport
 
drawTextS(Point2D.Double, String) - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
drawTextS(Point2D.Double, String) - Method in class fr.orsay.lri.varna.models.export.SVGExport
 
drawTextS(Point2D.Double, String) - Method in class fr.orsay.lri.varna.models.export.XFIGExport
 
drawTree(double, double, VARNASecDraw.RNATree, double, RNA) - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw
 
drop(DropTargetDropEvent) - Method in class fr.orsay.lri.varna.components.ReorderableJList
 
dropActionChanged(DragSourceDragEvent) - Method in class fr.orsay.lri.varna.components.ReorderableJList
 
dropActionChanged(DropTargetDragEvent) - Method in class fr.orsay.lri.varna.components.ReorderableJList
 
dropTarget - Variable in class fr.orsay.lri.varna.components.ReorderableJList
 
dropTargetIndex - Variable in class fr.orsay.lri.varna.components.ReorderableJList
 
DT - Variable in class fr.orsay.lri.varna.models.treealign.TreeAlign.Aligner
Distances between subtrees.
DTDecisions1 - Variable in class fr.orsay.lri.varna.models.treealign.TreeAlign.Aligner
This array has the same shape as DT, but is used to remember which case gave the minimum, so that we can later compute the alignment.
DTDecisions2 - Variable in class fr.orsay.lri.varna.models.treealign.TreeAlign.Aligner
 
dump_loops() - Method in class fr.orsay.lri.varna.models.naView.NAView
Displays all the loops.

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 _