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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
Overview
Package
Class
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