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 _

S

saveAsBPSEQ(String, String) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
saveAsCT(String, String) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
saveAsDBN(String, String) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
savePath(JFileChooser) - Method in class fr.orsay.lri.varna.views.VueUI
 
saveRNA(String, VARNAConfig, double, SecStrDrawingProducer) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
saveRNADBN(String, String) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
saveRNAEPS(String, VARNAConfig) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
saveRNASVG(String, VARNAConfig) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
saveRNAXFIG(String, VARNAConfig) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
saveSelection() - Method in class fr.orsay.lri.varna.VARNAPanel
 
saveSession(String) - Method in class fr.orsay.lri.varna.VARNAPanel
 
saveToDisk(String) - Method in class fr.orsay.lri.varna.models.export.SecStrProducerGraphics
 
saveToJPEG(String) - Method in class fr.orsay.lri.varna.views.VueUI
 
saveToPNG(String) - Method in class fr.orsay.lri.varna.views.VueUI
 
scaleSlider - Variable in class fr.orsay.lri.varna.views.VueJPEG
 
SECOND_RNA_COLOR - Static variable in class fr.orsay.lri.varna.models.rna.ModeleBasesComparison
 
secondSequenceForComparisonOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
secondStructureForComparisonOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
SecStrDrawingProducer - Class in fr.orsay.lri.varna.models.export
 
SecStrDrawingProducer() - Constructor for class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
SecStrProducerGraphics - Class in fr.orsay.lri.varna.models.export
 
SecStrProducerGraphics(SecStrDrawingProducer) - Constructor for class fr.orsay.lri.varna.models.export.SecStrProducerGraphics
 
selectedBorder - Variable in class fr.orsay.lri.varna.components.ColorRenderer
 
sequence - Variable in class fr.orsay.lri.varna.models.templates.RNANodeValueTemplateSequence
The sequence this node came from.
sequenceAligner - Variable in class fr.orsay.lri.varna.models.treealign.RNATree2.ConvertToMapping
 
sequenceOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
serialVersionUID - Static variable in class fr.orsay.lri.varna.components.ActionRenderer
 
serialVersionUID - Static variable in class fr.orsay.lri.varna.components.AnnotationTableModel
 
serialVersionUID - Static variable in class fr.orsay.lri.varna.components.BaseSpecialColorEditor
 
serialVersionUID - Static variable in class fr.orsay.lri.varna.components.BaseTableModel
 
serialVersionUID - Static variable in class fr.orsay.lri.varna.components.ColorRenderer
 
serialVersionUID - Static variable in class fr.orsay.lri.varna.models.annotations.ChemProbAnnotation
 
serialVersionUID - Static variable in class fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation
 
serialVersionUID - Static variable in class fr.orsay.lri.varna.models.annotations.TextAnnotation
 
serialVersionUID - Static variable in class fr.orsay.lri.varna.models.FullBackup
 
serialVersionUID - Static variable in class fr.orsay.lri.varna.models.rna.Mapping
 
serialVersionUID - Static variable in class fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide
 
serialVersionUID - Static variable in class fr.orsay.lri.varna.models.rna.ModeleBasesComparison
 
serialVersionUID - Static variable in class fr.orsay.lri.varna.models.rna.ModeleBP
 
serialVersionUID - Static variable in class fr.orsay.lri.varna.models.rna.ModeleBPStyle
 
serialVersionUID - Static variable in class fr.orsay.lri.varna.models.rna.ModeleColorMap
 
serialVersionUID - Static variable in class fr.orsay.lri.varna.models.rna.ModeleStyleBase
 
serialVersionUID - Static variable in class fr.orsay.lri.varna.models.rna.RNA
 
serialVersionUID - Static variable in class fr.orsay.lri.varna.models.rna.StructureTemp
 
serialVersionUID - Static variable in class fr.orsay.lri.varna.models.rna.VARNAPoint
 
serialVersionUID - Static variable in exception fr.orsay.lri.varna.models.templates.RNATemplateDrawingAlgorithmException
 
serialVersionUID - Static variable in exception fr.orsay.lri.varna.models.templates.RNATemplateMappingException
 
serialVersionUID - Static variable in exception fr.orsay.lri.varna.models.treealign.RNANodeValue2WrongTypeException
 
serialVersionUID - Static variable in exception fr.orsay.lri.varna.models.treealign.RNATree2Exception
 
serialVersionUID - Static variable in exception fr.orsay.lri.varna.models.treealign.TreeAlignException
 
serialVersionUID - Static variable in class fr.orsay.lri.varna.models.VARNAConfig
 
serialVersionUID - Static variable in class fr.orsay.lri.varna.VARNAPanel
 
serialVersionUID - Static variable in class fr.orsay.lri.varna.views.VueAboutPanel
 
serialVersionUID - Static variable in class fr.orsay.lri.varna.views.VueBases
 
serialVersionUID - Static variable in class fr.orsay.lri.varna.views.VueBPList.BPTableModel
 
serialVersionUID - Static variable in class fr.orsay.lri.varna.views.VueListeAnnotations
 
serialVersionUID - Static variable in class fr.orsay.lri.varna.views.VueLoadColorMapValues
 
serialVersionUID - Static variable in class fr.orsay.lri.varna.views.VueMenu
 
set_appartenance(int) - Method in class fr.orsay.lri.varna.models.rna.ModeleBasesComparison
Sets this base's related RNA.
set_base1(Character) - Method in class fr.orsay.lri.varna.models.rna.ModeleBasesComparison
Sets the base of the first RNA in this comparison base.
set_base2(Character) - Method in class fr.orsay.lri.varna.models.rna.ModeleBasesComparison
Sets the base of the second RNA in this comparison base.
set_base_inner_color(Color) - Method in class fr.orsay.lri.varna.models.rna.ModeleStyleBase
 
set_base_name_color(Color) - Method in class fr.orsay.lri.varna.models.rna.ModeleStyleBase
 
set_base_number_color(Color) - Method in class fr.orsay.lri.varna.models.rna.ModeleStyleBase
 
set_base_outline_color(Color) - Method in class fr.orsay.lri.varna.models.rna.ModeleStyleBase
 
set_c(String) - Method in class fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide
 
set_colored(Boolean) - Method in class fr.orsay.lri.varna.models.rna.ModeleBasesComparison
Sets the coloration authorization of this comparison base.
set_controleurMenu(ControleurMenu) - Method in class fr.orsay.lri.varna.views.VueMenu
 
set_itemOptionBondsColored(JCheckBoxMenuItem) - Method in class fr.orsay.lri.varna.views.VueMenu
 
set_itemOptionDashBaseColored(JCheckBoxMenuItem) - Method in class fr.orsay.lri.varna.views.VueMenu
 
set_itemOptionSpecialBaseColored(JCheckBoxMenuItem) - Method in class fr.orsay.lri.varna.views.VueMenu
 
set_itemShowWarnings(JCheckBoxMenuItem) - Method in class fr.orsay.lri.varna.views.VueMenu
 
set_listeBases(ArrayList<ModeleBase>) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
set_rotation(JMenuItem) - Method in class fr.orsay.lri.varna.views.VueMenu
 
set_selectedAnnotation(TextAnnotation) - Method in class fr.orsay.lri.varna.VARNAPanel
 
set_spaceBetweenBases(Double) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
setAjustement(int) - Method in class fr.orsay.lri.varna.models.rna.Motif
 
setAlignment(int[][]) - Method in class fr.orsay.lri.varna.models.treealign.ExampleDistance3.SequenceAlignResult
 
setAlignment(Tree<AlignedNode<ValueType1, ValueType2>>) - Method in class fr.orsay.lri.varna.models.treealign.TreeAlignResult
 
setAncrage(ModeleBase) - Method in class fr.orsay.lri.varna.models.annotations.TextAnnotation
 
setAncrage(double, double) - Method in class fr.orsay.lri.varna.models.annotations.TextAnnotation
 
setAncrage(ArrayList<ModeleBase>, int) - Method in class fr.orsay.lri.varna.models.annotations.TextAnnotation
 
setAngle(double) - Method in class fr.orsay.lri.varna.models.naView.Connection
 
setAngleInDegres(double) - Method in class fr.orsay.lri.varna.models.annotations.TextAnnotation
 
setAngleInRadians(double) - Method in class fr.orsay.lri.varna.models.annotations.TextAnnotation
 
setAutoCenter(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the current state of auto centering mode.
setAutoFit(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setBackboneColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the color to be used for drawing backbone interactions.
setBackground(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the background color
setBackgroundColor(Color) - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
setBaseFontSize(Float) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the font size for displaying bases
setBaseFontStyle(int) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the font style for displaying bases
setBaseInnerColor(Color) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
setBaseInnerColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setBaseNameColor(Color) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
setBaseNameColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setBaseNumber(int) - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
 
setBaseNumbersColor(Color) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
setBaseNumbersColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setBaseOutlineColor(Color) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
setBaseOutlineColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setBases(ArrayList<ModeleBase>) - Method in class fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation
 
setBent(double) - Method in class fr.orsay.lri.varna.models.rna.ModeleBPStyle
 
setBondColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the color used to display hydrogen bonds (base pairings)
setBorderSize(Dimension) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the size of the border, i.e.
setBPHeightIncrement(double) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
setBPHeightIncrement(double) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the base pair height increment, i.e.
setBPStyle(VARNAConfig.BP_STYLE) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the base-pair representation style
setBroken(boolean) - Method in class fr.orsay.lri.varna.models.naView.Connection
 
setCaption(String) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
 
setCenter(Point2D.Double) - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
 
setCenter(int, double, double) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
setCenter(int, Point2D.Double) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
setCenterMotif() - Method in class fr.orsay.lri.varna.models.rna.Motif
 
setChecker(boolean) - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
 
setColor(Color) - Method in class fr.orsay.lri.varna.models.annotations.ChemProbAnnotation
 
setColor(Color) - Method in class fr.orsay.lri.varna.models.annotations.TextAnnotation
 
setColor(Color) - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
setColor(Color) - Method in class fr.orsay.lri.varna.models.export.SecStrProducerGraphics
 
setColor(Color) - Method in class fr.orsay.lri.varna.models.export.SwingGraphics
 
setColor(Color) - Method in interface fr.orsay.lri.varna.models.export.VueVARNAGraphics
 
setColorGapsBases(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
Toggles on/off using a special color used for drawing "Gaps" bases in comparison mode
setColorie(Boolean) - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
Sets this InterfaceBase color statement.
setColorie(Boolean) - Method in class fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide
 
setColorie(Boolean) - Method in class fr.orsay.lri.varna.models.rna.ModeleBasesComparison
 
setColorMap(ModeleColorMap) - Method in class fr.orsay.lri.varna.components.GradientEditorPanel
 
setColorMap(ModeleColorMap) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setColorMapCaption(String) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setColorMapMaxValue(double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setColorMapMinValue(double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setColorMapValues(Double[], ModeleColorMap) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
setColorMapValues(Double[], ModeleColorMap, boolean) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
setColorMapValues(Double[]) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setColorMapVisible(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setColorNonStandardBases(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
Toggles on/off using a special color used for drawing "non-standard" bases
setColorS(Color) - Method in class fr.orsay.lri.varna.models.export.PSExport
 
setColorS(Color) - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
setColorS(Color) - Method in class fr.orsay.lri.varna.models.export.XFIGExport
 
setConfig(VARNAConfig) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setConnection(int, Connection) - Method in class fr.orsay.lri.varna.models.naView.Loop
 
setCoord(int, Point2D.Double) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
setCoord(int, double, double) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
setCoords(Point2D.Double) - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
 
setCurrentColor(Color) - Method in class fr.orsay.lri.varna.components.BaseSpecialColorEditor
 
setCustomColor(Color) - Method in class fr.orsay.lri.varna.models.rna.ModeleBPStyle
 
setDashedStroke() - Method in class fr.orsay.lri.varna.models.export.SecStrProducerGraphics
 
setDashedStroke() - Method in class fr.orsay.lri.varna.models.export.SwingGraphics
 
setDashedStroke() - Method in interface fr.orsay.lri.varna.models.export.VueVARNAGraphics
 
setData(ArrayList<Object>) - Method in class fr.orsay.lri.varna.views.VueListeAnnotations
 
setDecalage(double) - Method in class fr.orsay.lri.varna.models.rna.Motif
 
setDefaultBPColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the new color to be used for hydrogen bonds (base pairings)
setDepth(int) - Method in class fr.orsay.lri.varna.models.naView.Loop
 
setDestinationLink(Point2D.Double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setDistance(double) - Method in class fr.orsay.lri.varna.models.templates.RNATemplateMapping
 
setDistance(double) - Method in class fr.orsay.lri.varna.models.treealign.ExampleDistance3.SequenceAlignResult
 
setDistance(double) - Method in class fr.orsay.lri.varna.models.treealign.TreeAlignResult
 
setDrawBackbone(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setDrawMode(int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
setEdge3(ModeleBP.Edge) - Method in class fr.orsay.lri.varna.models.rna.ModeleBP
 
setEdge5(ModeleBP.Edge) - Method in class fr.orsay.lri.varna.models.rna.ModeleBP
 
setElementStructure(int, ModeleBP) - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
Sets this InterfaceBase associated structure element.
setElementStructure(int) - Method in class fr.orsay.lri.varna.models.rna.ModeleBasesComparison
Sets this InterfaceBase assiociated structure element.
setEnd(int) - Method in class fr.orsay.lri.varna.models.naView.Connection
 
setEnd1(int) - Method in class fr.orsay.lri.varna.models.naView.Region
 
setEnd2(int) - Method in class fr.orsay.lri.varna.models.naView.Region
 
setEndPosition(Point2D.Double) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
 
setErrorsOn(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets whether errors are to be displayed
setExtracted(boolean) - Method in class fr.orsay.lri.varna.models.naView.Base
 
setExtruded(boolean) - Method in class fr.orsay.lri.varna.models.naView.Connection
 
setFillColor(Color) - Method in class fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation
 
setFlatExteriorLoop(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setFlipped(boolean) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
 
setFont(Font) - Method in class fr.orsay.lri.varna.models.annotations.TextAnnotation
 
setFont(int, double) - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
setFont(Font) - Method in class fr.orsay.lri.varna.models.export.SecStrProducerGraphics
 
setFont(Font) - Method in class fr.orsay.lri.varna.models.export.SwingGraphics
 
setFont(Font) - Method in interface fr.orsay.lri.varna.models.export.VueVARNAGraphics
 
setFontS(int, double) - Method in class fr.orsay.lri.varna.models.export.PSExport
 
setFontS(int, double) - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
setFontS(int, double) - Method in class fr.orsay.lri.varna.models.export.SVGExport
 
setFontS(int, double) - Method in class fr.orsay.lri.varna.models.export.XFIGExport
 
setGapsBasesColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the color to use for 'Gaps' bases in comparison mode
setHasBeenPlaced(boolean) - Method in class fr.orsay.lri.varna.models.rna.ModeleStrand
 
setHelix(RNATemplate.RNATemplateHelix) - Method in class fr.orsay.lri.varna.models.templates.RNANodeValueTemplateBasePair
 
setHelix(RNATemplate.RNATemplateHelix) - Method in class fr.orsay.lri.varna.models.templates.RNANodeValueTemplateBrokenBasePair
 
setHoverBase(ModeleBase) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setIn1Is(RNATemplate.In1Is) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
 
setInTangentVectorAngle(double) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
 
setInTangentVectorLength(double) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
 
setIntensity(double) - Method in class fr.orsay.lri.varna.models.annotations.ChemProbAnnotation
 
setIntervDroite(boolean) - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
 
setIntervDroiteEx(boolean) - Method in class fr.orsay.lri.varna.models.rna.ExtendedMB
 
setIntervGauche(boolean) - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
 
setIntervGaucheEx(boolean) - Method in class fr.orsay.lri.varna.models.rna.ExtendedMB
 
setLastSelectedPosition(Point2D.Double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setLeftBasePosition(int) - Method in class fr.orsay.lri.varna.models.treealign.RNANodeValue
 
setLeftNode(Tree<OriginalNodeValueType1>) - Method in class fr.orsay.lri.varna.models.treealign.AlignedNode
 
setLeftNucleotide(String) - Method in class fr.orsay.lri.varna.models.treealign.RNANodeValue
 
setLength(int) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
 
setLength(int) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
 
setLevelPosition(int) - Method in class fr.orsay.lri.varna.models.rna.ModeleStrand
 
setLimited(boolean) - Method in class fr.orsay.lri.varna.views.VueAnnotation
 
setLoop(Loop) - Method in class fr.orsay.lri.varna.models.naView.Connection
 
setLoopnumber(int) - Method in class fr.orsay.lri.varna.models.naView.Radloop
 
setMark(boolean) - Method in class fr.orsay.lri.varna.models.naView.Loop
 
setMate(int) - Method in class fr.orsay.lri.varna.models.naView.Base
 
setMaxValue(double) - Method in class fr.orsay.lri.varna.models.rna.ModeleColorMap
 
setMinValue(double) - Method in class fr.orsay.lri.varna.models.rna.ModeleColorMap
 
setModifiable(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
Toggles modifications on and off
setName(String) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
setNconnection(int) - Method in class fr.orsay.lri.varna.models.naView.Loop
 
setNearestBase(Integer) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the index of the currently selected base.
setNext(Radloop) - Method in class fr.orsay.lri.varna.models.naView.Radloop
 
setNode(RNANodeValue) - Method in class fr.orsay.lri.varna.models.treealign.RNANodeValue2
 
setNodes(List<RNANodeValue>) - Method in class fr.orsay.lri.varna.models.treealign.RNANodeValue2
 
setNonStandardBasesColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the color used to draw non-standard bases
setNull(boolean) - Method in class fr.orsay.lri.varna.models.naView.Connection
 
setNumber(int) - Method in class fr.orsay.lri.varna.models.naView.Loop
 
setNumbersFontSize(Float) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the font size for displaying base numbers
setNumPeriod(int) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the distance between consecutive base numbers.
setNumStrand(int) - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
 
setOrigin(RNANodeValue.Origin) - Method in class fr.orsay.lri.varna.models.treealign.RNANodeValue
 
setOriginLink(Point2D.Double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setOut(boolean) - Method in class fr.orsay.lri.varna.models.annotations.ChemProbAnnotation
 
setOutlineColor(Color) - Method in class fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation
 
setOutTangentVectorAngle(double) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
 
setOutTangentVectorLength(double) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
 
setPanel(JPanel) - Method in class fr.orsay.lri.varna.views.VueManualInput
 
setPartner3(ModeleBase) - Method in class fr.orsay.lri.varna.models.rna.ModeleBP
 
setPartner5(ModeleBase) - Method in class fr.orsay.lri.varna.models.rna.ModeleBP
 
setPlainStroke() - Method in class fr.orsay.lri.varna.models.export.SecStrProducerGraphics
 
setPlainStroke() - Method in class fr.orsay.lri.varna.models.export.SwingGraphics
 
setPlainStroke() - Method in interface fr.orsay.lri.varna.models.export.VueVARNAGraphics
 
setPositionInHelix(int) - Method in class fr.orsay.lri.varna.models.templates.RNANodeValueTemplateBasePair
 
setPositionInHelix(int) - Method in class fr.orsay.lri.varna.models.templates.RNANodeValueTemplateBrokenBasePair
 
setPrev(Radloop) - Method in class fr.orsay.lri.varna.models.naView.Radloop
 
setRadius(double) - Method in class fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation
 
setRadius(double) - Method in class fr.orsay.lri.varna.models.naView.Loop
 
setRadius(double) - Method in class fr.orsay.lri.varna.models.naView.Radloop
 
setRealCoords(Point2D.Double[]) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the coordinates of the currently displayed RNA
setRegion(Region) - Method in class fr.orsay.lri.varna.models.naView.Base
 
setRegion(Region) - Method in class fr.orsay.lri.varna.models.naView.Connection
 
setRightBasePosition(int) - Method in class fr.orsay.lri.varna.models.treealign.RNANodeValue
 
setRightNode(Tree<OriginalNodeValueType2>) - Method in class fr.orsay.lri.varna.models.treealign.AlignedNode
 
setRightNucleotide(String) - Method in class fr.orsay.lri.varna.models.treealign.RNANodeValue
 
setRNA(String, String) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
setRNA(String[], int[]) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
setRNA(List<String>, int[]) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
setRNA(List<String>, int[], int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
setRNA(String[], int[], int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
setRNA(String, String, ArrayList<Integer>) - Method in class fr.orsay.lri.varna.models.rna.RNA
Sets the RNA to be drawn.
setRNA(List<String>, String) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
setRNA(RNA) - Method in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
setScale(double) - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
setScaleFactor(double) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the scale factor used by the autofitting function
setSelection(ArrayList<Integer>) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setSelection(Collection<? extends ModeleBase>) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setSelectionRectangle(Rectangle) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setSequence(String) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
setSequence(List<String>) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
setSequence(RNATemplate.RNATemplateUnpairedSequence) - Method in class fr.orsay.lri.varna.models.templates.RNANodeValueTemplateSequence
 
setSequence(String) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setShowNonCanonicalBP(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
Toggles on/off displaying non-canonical base-pairs
setShowNonPlanarBP(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
Toggles on/off displaying "non-planar" base-pairs
setShowWarnings(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
Toggles on/off displaying warnings
setSpecialTableModel(BaseTableModel) - Method in class fr.orsay.lri.varna.views.VueBases
 
setSpecialTableModel(AnnotationTableModel) - Method in class fr.orsay.lri.varna.views.VueListeAnnotations
 
setStart(int) - Method in class fr.orsay.lri.varna.models.naView.Connection
 
setStart1(int) - Method in class fr.orsay.lri.varna.models.naView.Region
 
setStart2(int) - Method in class fr.orsay.lri.varna.models.naView.Region
 
setStartPosition(Point2D.Double) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
 
setStericity(ModeleBP.Stericity) - Method in class fr.orsay.lri.varna.models.rna.ModeleBP
 
setStrandLeft(boolean) - Method in class fr.orsay.lri.varna.models.rna.ModeleStrand
 
setStrandRight(boolean) - Method in class fr.orsay.lri.varna.models.rna.ModeleStrand
 
setStrokeThickness(double) - Method in class fr.orsay.lri.varna.models.export.SecStrProducerGraphics
 
setStrokeThickness(double) - Method in class fr.orsay.lri.varna.models.export.SwingGraphics
 
setStrokeThickness(double) - Method in interface fr.orsay.lri.varna.models.export.VueVARNAGraphics
 
setStyle(ModeleBPStyle) - Method in class fr.orsay.lri.varna.models.rna.ModeleBP
 
setStyleBase(ModeleStyleBase) - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
Sets this InterfaceBase style.
setStyleBP(ModeleBP) - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
Sets the base pair type for this element.
setTable(JTable) - Method in class fr.orsay.lri.varna.views.VueBases
 
setTable(JTable) - Method in class fr.orsay.lri.varna.views.VueListeAnnotations
 
setTexte(String) - Method in class fr.orsay.lri.varna.models.annotations.TextAnnotation
 
setThickness(double) - Method in class fr.orsay.lri.varna.models.rna.ModeleBPStyle
 
setTitle(String) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the panel's title, giving a short description of the RNA secondary structure.
setTitleColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the color used to draw the title
setTitleFont(Font) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the font used for rendering the title.
setTitleFontColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the color to be used for the title.
setTitleFontFamily(String) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the new font family to be used for the title.
setTitleFontSize(float) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the new size of the title font.
setTitleFontStyle(int) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the new style of the title font.
setTitleHeight(int) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the height taken by the title
setTranslation(Point) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the translation used for zooming in and out
setType(ChemProbAnnotation.ChemProbAnnotationType) - Method in class fr.orsay.lri.varna.models.annotations.ChemProbAnnotation
 
setUseBaseColorsForBPs(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
Toggles on/off using base inner color for drawing base-pairs
setValue(double) - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
 
setValue(T) - Method in class fr.orsay.lri.varna.models.treealign.Tree
 
setValueAt(Object, int, int) - Method in class fr.orsay.lri.varna.components.AnnotationTableModel
 
setValueAt(Object, int, int) - Method in class fr.orsay.lri.varna.components.BaseTableModel
 
setValueAt(Object, int, int) - Method in class fr.orsay.lri.varna.views.VueBaseValues.ValueTableModel
 
setValueAt(Object, int, int) - Method in class fr.orsay.lri.varna.views.VueBPList.BPTableModel
 
setVertex3(Point2D.Double) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
 
setVertex5(Point2D.Double) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
 
setX(double) - Method in class fr.orsay.lri.varna.models.naView.Base
 
setX(double) - Method in class fr.orsay.lri.varna.models.naView.Loop
 
setXrad(double) - Method in class fr.orsay.lri.varna.models.naView.Connection
 
setY(double) - Method in class fr.orsay.lri.varna.models.naView.Base
 
setY(double) - Method in class fr.orsay.lri.varna.models.naView.Loop
 
setYrad(double) - Method in class fr.orsay.lri.varna.models.naView.Connection
 
setZoom(Object) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the current zoom factor
setZoomIncrement(Object) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the atomic zoom factor step, or increment.
setZoomIncrement(double) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the atomic zoom factor step, or increment.
shouldFlip(int, Point2D.Double) - Method in class fr.orsay.lri.varna.views.VueUI
Tests if an helix needs to be flipped.
shouldSelectCell(EventObject) - Method in class fr.orsay.lri.varna.components.ActionEditor
 
show() - Method in class fr.orsay.lri.varna.views.VueAnnotation
shows the dialog which add it to the VARNAPanel for previsualization.
show() - Method in class fr.orsay.lri.varna.views.VueChemProbAnnotation
 
show() - Method in class fr.orsay.lri.varna.views.VueHighlightRegionEdit
 
show(Component, int, int) - Method in class fr.orsay.lri.varna.views.VueMenu
 
showCompact(RNA) - Method in class fr.orsay.lri.varna.models.templates.RNATemplateMapping
 
showRNA(RNA) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the RNA to be displayed within this Panel.
showRNA(RNA, VARNAConfig) - Method in class fr.orsay.lri.varna.VARNAPanel
 
showRNAInterpolated(RNA) - Method in class fr.orsay.lri.varna.VARNAPanel
Simply displays (does not redraw) a secondary structure , using an interpolated transition between the previous one and the new one.
showRNAInterpolated(RNA, Mapping) - Method in class fr.orsay.lri.varna.VARNAPanel
Simply displays (does not redraw) a secondary structure , using an interpolated transition between the previous one and the new one.
showRNAInterpolated(RNA, VARNAConfig, Mapping) - Method in class fr.orsay.lri.varna.VARNAPanel
 
SIMPLE_BP_STYLE - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
singleNode - Variable in class fr.orsay.lri.varna.models.treealign.RNANodeValue2
Says whether we have a single node or a list of nodes.
size() - Method in class fr.orsay.lri.varna.models.BaseList
 
size - Variable in class fr.orsay.lri.varna.models.treealign.TreeAlign.TreeData
The tree size (number of nodes).
sizeSlider - Variable in class fr.orsay.lri.varna.views.VueFont
 
sizeStrand() - Method in class fr.orsay.lri.varna.models.rna.ModeleStrand
 
sizeStruct() - Method in class fr.orsay.lri.varna.models.rna.StructureTemp
 
spaceSlider - Variable in class fr.orsay.lri.varna.views.VueBPHeightIncrement
 
spaceSlider - Variable in class fr.orsay.lri.varna.views.VueSpaceBetweenBases
 
specialTableModel - Variable in class fr.orsay.lri.varna.views.VueBases
 
specialTableModel - Variable in class fr.orsay.lri.varna.views.VueListeAnnotations
 
standardParam(double) - Method in class fr.orsay.lri.varna.models.CubicBezierCurve
The standard exact cubic Bezier curve parametrization.
start - Variable in class fr.orsay.lri.varna.models.naView.Connection
 
startAngle - Variable in class fr.orsay.lri.varna.models.export.ArcCommand
 
startDocument() - Method in class fr.orsay.lri.varna.models.rna.RNAMLParser
 
startElement(String, String, String, Attributes) - Method in class fr.orsay.lri.varna.models.rna.RNAMLParser
 
startPosition - Variable in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
Position of the helix start point, ie.
stateChanged(ChangeEvent) - Method in class fr.orsay.lri.varna.views.VueBPThickness
 
stateChanged(ChangeEvent) - Method in class fr.orsay.lri.varna.views.VueChemProbAnnotation
 
stateChanged(ChangeEvent) - Method in class fr.orsay.lri.varna.views.VueHighlightRegionEdit
 
stateChanged(ChangeEvent) - Method in class fr.orsay.lri.varna.views.VueZoom
 
stopCellEditing() - Method in class fr.orsay.lri.varna.components.ActionEditor
 
strandLeft - Variable in class fr.orsay.lri.varna.models.rna.ModeleStrand
 
strandRight - Variable in class fr.orsay.lri.varna.models.rna.ModeleStrand
 
structureOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
StructureTemp - Class in fr.orsay.lri.varna.models.rna
 
StructureTemp() - Constructor for class fr.orsay.lri.varna.models.rna.StructureTemp
 
styleIntToString(int) - Method in class fr.orsay.lri.varna.views.VueFont
 
stylesBox - Variable in class fr.orsay.lri.varna.views.VueFont
 
StyleToInteger(String) - Static method in class fr.orsay.lri.varna.models.rna.ModeleStyleBase
Find the font style integer from a string.
subtreeToGraphviz(Tree<? extends GraphvizDrawableNodeValue>) - Static method in class fr.orsay.lri.varna.models.treealign.TreeGraphviz
 
supportedFlavors - Static variable in class fr.orsay.lri.varna.components.ReorderableJList
 
SVGExport - Class in fr.orsay.lri.varna.models.export
 
SVGExport() - Constructor for class fr.orsay.lri.varna.models.export.SVGExport
 
SwingGraphics - Class in fr.orsay.lri.varna.models.export
 
SwingGraphics(Graphics2D) - Constructor for class fr.orsay.lri.varna.models.export.SwingGraphics
 
symmetric(Point2D.Double, Point2D.Double, Point2D.Double[]) - Static method in class fr.orsay.lri.varna.models.rna.RNA
Compute the symmetric of all the points in the points array relative to the line that goes through p and has director vector v.

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