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 _

F

f(double, double) - Static method in class fr.orsay.lri.varna.models.rna.RNA.ComputeArcCenter
 
f(RNANodeValue2, RNANodeValueTemplate) - Method in class fr.orsay.lri.varna.models.templates.RNANodeValue2TemplateDistance
 
f(RNANodeValue2, RNANodeValue2) - Method in class fr.orsay.lri.varna.models.treealign.ExampleDistance2
 
f(RNANodeValue2, RNANodeValue2) - Method in class fr.orsay.lri.varna.models.treealign.ExampleDistance3
 
f(ValueType1, ValueType2) - Method in interface fr.orsay.lri.varna.models.treealign.TreeAlignLabelDistanceAsymmetric
Returns the substitution cost between v1 and v2.
FACTOR - Variable in class fr.orsay.lri.varna.views.VueBPThickness
 
FILE_TYPE_BPSEQ - Static variable in class fr.orsay.lri.varna.models.rna.RNA
 
FILE_TYPE_CT - Static variable in class fr.orsay.lri.varna.models.rna.RNA
 
FILE_TYPE_DBN - Static variable in class fr.orsay.lri.varna.models.rna.RNA
 
FILE_TYPE_RNAML - Static variable in class fr.orsay.lri.varna.models.rna.RNA
 
FILE_TYPE_UNKNOWN - Static variable in class fr.orsay.lri.varna.models.rna.RNA
 
fileAux - Variable in class fr.orsay.lri.varna.views.VueLoadColorMapValues
 
fileCB - Variable in class fr.orsay.lri.varna.views.VueLoadColorMapValues
 
fileMenu() - Method in class fr.orsay.lri.varna.views.VueMenu
 
fileTxt - Variable in class fr.orsay.lri.varna.views.VueLoadColorMapValues
 
fill(GeneralPath) - Method in class fr.orsay.lri.varna.models.export.SecStrProducerGraphics
 
fill(GeneralPath) - Method in class fr.orsay.lri.varna.models.export.SwingGraphics
 
fill(GeneralPath) - Method in interface fr.orsay.lri.varna.models.export.VueVARNAGraphics
 
fillCircle(double, double, double, double, Color) - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
fillCircle(double, double, double) - Method in class fr.orsay.lri.varna.models.export.SecStrProducerGraphics
 
fillCircle(double, double, double) - Method in class fr.orsay.lri.varna.models.export.SwingGraphics
 
fillCircle(double, double, double) - Method in interface fr.orsay.lri.varna.models.export.VueVARNAGraphics
 
FillCircleCommand - Class in fr.orsay.lri.varna.models.export
 
FillCircleCommand(Point2D.Double, double, double, Color) - Constructor for class fr.orsay.lri.varna.models.export.FillCircleCommand
 
fillCircleS(Point2D.Double, double, double, Color) - Method in class fr.orsay.lri.varna.models.export.PSExport
 
fillCircleS(Point2D.Double, double, double, Color) - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
fillCircleS(Point2D.Double, double, double, Color) - Method in class fr.orsay.lri.varna.models.export.SVGExport
 
fillCircleS(Point2D.Double, double, double, Color) - Method in class fr.orsay.lri.varna.models.export.XFIGExport
 
fillPolygon(GeneralPath, Color) - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
fillPolygon(double[], double[], Color) - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
FillPolygonCommand - Class in fr.orsay.lri.varna.models.export
 
FillPolygonCommand(Point2D.Double[], Color) - Constructor for class fr.orsay.lri.varna.models.export.FillPolygonCommand
 
fillPolygonS(Point2D.Double[], Color) - Method in class fr.orsay.lri.varna.models.export.PSExport
 
fillPolygonS(Point2D.Double[], Color) - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
fillPolygonS(Point2D.Double[], Color) - Method in class fr.orsay.lri.varna.models.export.SVGExport
 
fillPolygonS(Point2D.Double[], Color) - Method in class fr.orsay.lri.varna.models.export.XFIGExport
 
fillRect(double, double, double, double) - Method in class fr.orsay.lri.varna.models.export.SecStrProducerGraphics
 
fillRect(double, double, double, double) - Method in class fr.orsay.lri.varna.models.export.SwingGraphics
 
fillRect(double, double, double, double) - Method in interface fr.orsay.lri.varna.models.export.VueVARNAGraphics
 
fillRectangle(double, double, double, double, Color) - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
fillRoundRect(double, double, double, double, double, double) - Method in class fr.orsay.lri.varna.models.export.SecStrProducerGraphics
 
fillRoundRect(double, double, double, double, double, double) - Method in class fr.orsay.lri.varna.models.export.SwingGraphics
 
fillRoundRect(double, double, double, double, double, double) - Method in interface fr.orsay.lri.varna.models.export.VueVARNAGraphics
 
fillShow - Variable in class fr.orsay.lri.varna.views.VueHighlightRegionEdit
 
find3Prime(int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
find5Prime(int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
find_center_for_arc(double, double) - Method in class fr.orsay.lri.varna.models.naView.NAView
Given n points to be placed equidistantly and equiangularly on a polygon which has a chord of length, b, find the distance, h, from the midpoint of the chord for the center of polygon.
find_central_loop() - Method in class fr.orsay.lri.varna.models.naView.NAView
Find node of greatest branching that is deepest.
find_ic_middle(int, int, Connection, Connection, Loop) - Method in class fr.orsay.lri.varna.models.naView.NAView
Finds the middle of a set of connected connectors.
find_regions() - Method in class fr.orsay.lri.varna.models.naView.NAView
Identifies the regions in the structure.
findAll() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
findBulge(int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
findHelix(int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
findLoop(int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
findLoopBackward(int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
findLoopForward(int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
findNonPairedBaseGroup(Integer) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
findPair(int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
findStem(int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
fireHoverChanged(ModeleBase, ModeleBase) - Method in class fr.orsay.lri.varna.VARNAPanel
 
fireLayoutChanged() - Method in class fr.orsay.lri.varna.VARNAPanel
 
fireLayoutChanged(Hashtable<Integer, Point2D.Double>) - Method in class fr.orsay.lri.varna.VARNAPanel
 
fireSelectionChanged(BaseList, BaseList) - Method in class fr.orsay.lri.varna.VARNAPanel
 
fireSequenceChanged(int, String, String) - Method in class fr.orsay.lri.varna.VARNAPanel
 
fireStructureChanged(Set<ModeleBP>, Set<ModeleBP>, Set<ModeleBP>) - Method in class fr.orsay.lri.varna.VARNAPanel
 
fireUINewStructure() - Method in class fr.orsay.lri.varna.VARNAPanel
 
FIRST_RNA_COLOR - Static variable in class fr.orsay.lri.varna.models.rna.ModeleBasesComparison
 
firstSequenceForComparisonOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
firstStructureForComparisonOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
flatExteriorLoopOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
flipped - Variable in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
Tells whether the helix is flipped.
focusGained(FocusEvent) - Method in class fr.orsay.lri.varna.components.VARNAConsole
 
focusLost(FocusEvent) - Method in class fr.orsay.lri.varna.components.VARNAConsole
 
font - Variable in class fr.orsay.lri.varna.views.VueFont
 
FONT_COURIER - Static variable in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
FONT_COURIER_BOLD - Static variable in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
FONT_COURIER_BOLD_OBLIQUE - Static variable in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
FONT_COURIER_OBLIQUE - Static variable in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
FONT_HELVETICA - Static variable in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
FONT_HELVETICA_BOLD - Static variable in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
FONT_HELVETICA_BOLD_OBLIQUE - Static variable in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
FONT_HELVETICA_OBLIQUE - Static variable in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
FONT_TIMES_BOLD - Static variable in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
FONT_TIMES_BOLD_ITALIC - Static variable in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
FONT_TIMES_ITALIC - Static variable in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
FONT_TIMES_ROMAN - Static variable in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
FontCommand - Class in fr.orsay.lri.varna.models.export
 
FontCommand(int, double) - Constructor for class fr.orsay.lri.varna.models.export.FontCommand
 
fontName(int) - Method in class fr.orsay.lri.varna.models.export.PSExport
 
footerS() - Method in class fr.orsay.lri.varna.models.export.PSExport
 
footerS() - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
footerS() - Method in class fr.orsay.lri.varna.models.export.SVGExport
 
footerS() - Method in class fr.orsay.lri.varna.models.export.XFIGExport
 
fprime(double, double) - Static method in class fr.orsay.lri.varna.models.rna.RNA.ComputeArcCenter
d/dc f(c,delta)
fr.orsay.lri.varna - package fr.orsay.lri.varna
 
fr.orsay.lri.varna.components - package fr.orsay.lri.varna.components
 
fr.orsay.lri.varna.interfaces - package fr.orsay.lri.varna.interfaces
 
fr.orsay.lri.varna.models - package fr.orsay.lri.varna.models
 
fr.orsay.lri.varna.models.annotations - package fr.orsay.lri.varna.models.annotations
 
fr.orsay.lri.varna.models.export - package fr.orsay.lri.varna.models.export
 
fr.orsay.lri.varna.models.naView - package fr.orsay.lri.varna.models.naView
 
fr.orsay.lri.varna.models.rna - package fr.orsay.lri.varna.models.rna
 
fr.orsay.lri.varna.models.templates - package fr.orsay.lri.varna.models.templates
 
fr.orsay.lri.varna.models.treealign - package fr.orsay.lri.varna.models.treealign
 
fr.orsay.lri.varna.views - package fr.orsay.lri.varna.views
 
fromXMLDocument(Document) - Static method in class fr.orsay.lri.varna.models.templates.RNATemplate
 
fromXMLFile(File) - Static method in class fr.orsay.lri.varna.models.templates.RNATemplate
 
FullBackup - Class in fr.orsay.lri.varna.models
 
FullBackup(VARNAConfig, RNA, String) - Constructor for class fr.orsay.lri.varna.models.FullBackup
 

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 _