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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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