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 _

G

GAP - Static variable in class fr.orsay.lri.varna.components.GradientEditorPanel
 
gapsBaseColorOpt - Static variable in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
generate_region(Connection) - Method in class fr.orsay.lri.varna.models.naView.NAView
Generates the coordinates for the base pairing region of a connection given the position of the starting base pair.
get_appartenance() - Method in class fr.orsay.lri.varna.models.rna.ModeleBasesComparison
Gets this base's related RNA.
get_base() - Method in class fr.orsay.lri.varna.models.export.CircleCommand
 
get_base() - Method in class fr.orsay.lri.varna.models.export.FillCircleCommand
 
get_base() - Method in class fr.orsay.lri.varna.models.export.TextCommand
 
get_base1() - Method in class fr.orsay.lri.varna.models.rna.ModeleBasesComparison
Return the base of the first RNA in this comparison base.
get_base2() - Method in class fr.orsay.lri.varna.models.rna.ModeleBasesComparison
Return the base of the second RNA in this comparison base.
get_base_inner_color() - Method in class fr.orsay.lri.varna.models.rna.ModeleStyleBase
 
get_base_name_color() - Method in class fr.orsay.lri.varna.models.rna.ModeleStyleBase
 
get_base_number_color() - Method in class fr.orsay.lri.varna.models.rna.ModeleStyleBase
 
get_base_outline_color() - Method in class fr.orsay.lri.varna.models.rna.ModeleStyleBase
 
get_c() - Method in class fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide
 
get_color() - Method in class fr.orsay.lri.varna.models.export.FillCircleCommand
 
get_color() - Method in class fr.orsay.lri.varna.models.export.FillPolygonCommand
 
get_colored() - Method in class fr.orsay.lri.varna.models.rna.ModeleBasesComparison
Allows to know if this comparison base is colored.
get_controleurMenu() - Method in class fr.orsay.lri.varna.views.VueMenu
 
get_controleurSpecialColorEditor() - Method in class fr.orsay.lri.varna.components.BaseSpecialColorEditor
 
get_dest() - Method in class fr.orsay.lri.varna.models.export.LineCommand
 
get_dims() - Method in class fr.orsay.lri.varna.models.export.RectangleCommand
 
get_drawMode() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
get_font() - Method in class fr.orsay.lri.varna.models.export.FontCommand
 
get_itemOptionBondsColored() - Method in class fr.orsay.lri.varna.views.VueMenu
 
get_itemOptionDashBaseColored() - Method in class fr.orsay.lri.varna.views.VueMenu
 
get_itemOptionSpecialBaseColored() - Method in class fr.orsay.lri.varna.views.VueMenu
 
get_itemShowWarnings() - Method in class fr.orsay.lri.varna.views.VueMenu
 
get_listeBases() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
get_orig() - Method in class fr.orsay.lri.varna.models.export.LineCommand
 
get_orig() - Method in class fr.orsay.lri.varna.models.export.RectangleCommand
 
get_points() - Method in class fr.orsay.lri.varna.models.export.FillPolygonCommand
 
get_points() - Method in class fr.orsay.lri.varna.models.export.PolygonCommand
 
get_radius() - Method in class fr.orsay.lri.varna.models.export.CircleCommand
 
get_radius() - Method in class fr.orsay.lri.varna.models.export.FillCircleCommand
 
get_rotation() - Method in class fr.orsay.lri.varna.views.VueMenu
 
get_selectedAnnotation() - Method in class fr.orsay.lri.varna.VARNAPanel
 
get_size() - Method in class fr.orsay.lri.varna.models.export.FontCommand
 
get_spaceBetweenBases() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
get_thickness() - Method in class fr.orsay.lri.varna.models.export.CircleCommand
 
get_thickness() - Method in class fr.orsay.lri.varna.models.export.FillCircleCommand
 
get_thickness() - Method in class fr.orsay.lri.varna.models.export.LineCommand
 
get_thickness() - Method in class fr.orsay.lri.varna.models.export.PolygonCommand
 
get_thickness() - Method in class fr.orsay.lri.varna.models.export.RectangleCommand
 
get_txt() - Method in class fr.orsay.lri.varna.models.export.TextCommand
 
get_vp() - Method in class fr.orsay.lri.varna.views.VueAnnotation
 
get_vp() - Method in class fr.orsay.lri.varna.views.VueBases
 
get_vp() - Method in class fr.orsay.lri.varna.views.VueBorder
 
get_vp() - Method in class fr.orsay.lri.varna.views.VueBPHeightIncrement
 
get_vp() - Method in class fr.orsay.lri.varna.views.VueBPThickness
 
get_vp() - Method in class fr.orsay.lri.varna.views.VueBPType
 
get_vp() - Method in class fr.orsay.lri.varna.views.VueChemProbAnnotation
 
get_vp() - Method in class fr.orsay.lri.varna.views.VueGlobalRotation
 
get_vp() - Method in class fr.orsay.lri.varna.views.VueHighlightRegionEdit
 
get_vp() - Method in class fr.orsay.lri.varna.views.VueListeAnnotations
 
get_vp() - Method in class fr.orsay.lri.varna.views.VueMenu
 
get_vp() - Method in class fr.orsay.lri.varna.views.VueNumPeriod
 
get_vp() - Method in class fr.orsay.lri.varna.views.VueSpaceBetweenBases
 
get_vp() - Method in class fr.orsay.lri.varna.views.VueStyleBP
 
get_vp() - Method in class fr.orsay.lri.varna.views.VueZoom
 
get_vueBases() - Method in class fr.orsay.lri.varna.components.BaseSpecialColorEditor
 
getAjustement() - Method in class fr.orsay.lri.varna.models.rna.Motif
 
getAlignment() - Method in class fr.orsay.lri.varna.models.treealign.ExampleDistance3.SequenceAlignResult
The result array is a matrix of height 2 and width at most length(sequence A) + length(sequence B).
getAlignment() - Method in class fr.orsay.lri.varna.models.treealign.TreeAlignResult
 
getAllBPs() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getAllBPs() - Method in class fr.orsay.lri.varna.models.rna.RNAMLParser
 
getAllPartners(int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getAncestor(int) - Method in class fr.orsay.lri.varna.models.rna.Mapping
 
getAncestor(RNATemplate.RNATemplateElement) - Method in class fr.orsay.lri.varna.models.templates.RNATemplateMapping
If the given template element is in the mapping, return an ArrayList containing the corresponding base indexes, otherwise return null.
getAnchorPosition() - Method in class fr.orsay.lri.varna.models.annotations.ChemProbAnnotation
 
getAncrage() - Method in class fr.orsay.lri.varna.models.annotations.TextAnnotation
 
getAngle() - Method in class fr.orsay.lri.varna.models.naView.Connection
 
getAngle() - Method in class fr.orsay.lri.varna.views.VueGlobalRotation
 
getAngle() - Method in class fr.orsay.lri.varna.views.VueHighlightRegionEdit
 
getAngleInDegres() - Method in class fr.orsay.lri.varna.models.annotations.TextAnnotation
 
getAngleInRadians() - Method in class fr.orsay.lri.varna.models.annotations.TextAnnotation
 
getAnnotation(int, ModeleBase) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getAnnotations() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getAny() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate
Return an arbitrary element of the template, null if empty.
getAnyEndPoint() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate
Return an arbitrary endpoint of the template, null if empty.
getApproxCurveLength() - Method in class fr.orsay.lri.varna.models.CubicBezierCurve
Get the (exact) length of the approximation curve.
getArrayListMB() - Method in class fr.orsay.lri.varna.models.rna.ModeleStrand
 
getAuxBPs() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getAuxBPs(int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getAverageColor(ArrayList<Color>) - Static method in class fr.orsay.lri.varna.models.BaseList
 
getAverageInnerColor() - Method in class fr.orsay.lri.varna.models.BaseList
 
getAverageNameColor() - Method in class fr.orsay.lri.varna.models.BaseList
 
getAverageNumberColor() - Method in class fr.orsay.lri.varna.models.BaseList
 
getAverageOutlineColor() - Method in class fr.orsay.lri.varna.models.BaseList
 
getBackboneColor() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the color used to draw backbone bounds.
getBaseAt(int) - Method in class fr.orsay.lri.varna.models.rna.Motif
 
getBaseAt(int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getBaseAt(Point2D.Double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
getBaseContent(int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getBaseInnerColor(int, VARNAConfig) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getBaseList() - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw.PairedPortion
 
getBaseList() - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw.Portion
 
getBaseList() - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw.UnpairedPortion
 
getBaseNameColor(int, VARNAConfig) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getBaseNumber() - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
 
getBaseNumber(int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getBaseNumbers() - Method in class fr.orsay.lri.varna.models.rna.RNAMLParser
 
getBaseOuterColor(int, VARNAConfig) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getBasePairColor(ModeleBP, VARNAConfig) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getBasePairThickness(ModeleBP, VARNAConfig) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getBases() - Method in class fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation
 
getBases() - Method in class fr.orsay.lri.varna.models.BaseList
 
getBases() - Method in class fr.orsay.lri.varna.models.rna.ModeleBasesComparison
Gets the string representation of the two bases in this ModeleBasesComparison.
getBasesAt(Collection<? extends Integer>) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getBasesBetween(int, int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getBasesInRectangle(Rectangle) - Method in class fr.orsay.lri.varna.VARNAPanel
 
getBasesInRectangleDiff(Rectangle, Rectangle) - Method in class fr.orsay.lri.varna.VARNAPanel
 
getBBox() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getBent() - Method in class fr.orsay.lri.varna.models.rna.ModeleBPStyle
 
getBondColor() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the color used to display hydrogen bonds (base pairings)
getBorderSize() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the size of the border, i.e.
getBoundingBox() - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
getBoxPolice() - Method in class fr.orsay.lri.varna.views.VueFont
 
getBPHeightIncrement() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getBPHeightIncrement() - Method in class fr.orsay.lri.varna.VARNAPanel
For the LINE_MODE drawing algorithm, sets the base pair height increment, i.e.
getBPsAt(int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getBPStyle(int, int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getBPStyle() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the base-pair representation style
getButton() - Method in class fr.orsay.lri.varna.components.BaseSpecialColorEditor
 
getCaption() - Method in class fr.orsay.lri.varna.models.BaseList
 
getCaption() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
 
getCellEditorValue() - Method in class fr.orsay.lri.varna.components.ActionEditor
 
getCellEditorValue() - Method in class fr.orsay.lri.varna.components.BaseSpecialColorEditor
 
getCenter() - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
 
getCenter(int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getCenterPosition() - Method in class fr.orsay.lri.varna.models.annotations.TextAnnotation
 
getCentralStrand() - Method in class fr.orsay.lri.varna.models.rna.Motif
Find the central strand in a RNA star pattern
getChecker() - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
 
getChemProbAnnotations() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getChildren() - Method in class fr.orsay.lri.varna.models.treealign.Tree
Returns the list of children.
getClip() - Method in class fr.orsay.lri.varna.VARNAPanel
 
getColor() - Method in class fr.orsay.lri.varna.models.annotations.ChemProbAnnotation
 
getColor() - Method in class fr.orsay.lri.varna.models.annotations.TextAnnotation
 
getColor() - Method in class fr.orsay.lri.varna.models.export.ColorCommand
 
getColor() - Method in class fr.orsay.lri.varna.models.export.SecStrProducerGraphics
 
getColor() - Method in class fr.orsay.lri.varna.models.export.SwingGraphics
 
getColor() - Method in interface fr.orsay.lri.varna.models.export.VueVARNAGraphics
 
getColor(Color) - Method in class fr.orsay.lri.varna.models.rna.ModeleBPStyle
Returns the current custom color if such a color is defined to be used (through setCustomColor), or returns the default color.
getColorAt(int) - Method in class fr.orsay.lri.varna.models.rna.ModeleColorMap
 
getColorChooser() - Method in class fr.orsay.lri.varna.components.BaseSpecialColorEditor
 
getColorCode(Color) - Method in class fr.orsay.lri.varna.models.export.XFIGExport
 
getColorForValue(double) - Method in class fr.orsay.lri.varna.models.rna.ModeleColorMap
 
getColorGapsBases() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns true if a special color is used for drawing "Gaps" bases in comparison mode
getColorie() - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
Gets this InterfaceBase color statement.
getColorie() - Method in class fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide
 
getColorie() - Method in class fr.orsay.lri.varna.models.rna.ModeleBasesComparison
 
getColorMap() - Method in class fr.orsay.lri.varna.components.GradientEditorPanel
 
getColorMap() - Method in enum fr.orsay.lri.varna.models.rna.ModeleColorMap.NamedColorMapTypes
 
getColorMap() - Method in class fr.orsay.lri.varna.VARNAPanel
 
getColorMap() - Method in class fr.orsay.lri.varna.views.VueColorMapStyle
 
getColorMapCaption() - Method in class fr.orsay.lri.varna.VARNAPanel
 
getColorMapHeight() - Method in class fr.orsay.lri.varna.VARNAPanel
 
getColorMapValues() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getColorMapVisible() - Method in class fr.orsay.lri.varna.VARNAPanel
 
getColorSpecialBases() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns true if a special color is used as inner color for non-standard base
getColumnClass(int) - Method in class fr.orsay.lri.varna.components.AnnotationTableModel
 
getColumnClass(int) - Method in class fr.orsay.lri.varna.components.BaseTableModel
 
getColumnClass(int) - Method in class fr.orsay.lri.varna.views.VueBaseValues.ValueTableModel
 
getColumnClass(int) - Method in class fr.orsay.lri.varna.views.VueBPList.BPTableModel
 
getColumnCount() - Method in class fr.orsay.lri.varna.components.AnnotationTableModel
 
getColumnCount() - Method in class fr.orsay.lri.varna.components.BaseTableModel
 
getColumnCount() - Method in class fr.orsay.lri.varna.views.VueBaseValues.ValueTableModel
 
getColumnCount() - Method in class fr.orsay.lri.varna.views.VueBPList.BPTableModel
 
getColumnName(int) - Method in class fr.orsay.lri.varna.components.AnnotationTableModel
 
getColumnName(int) - Method in class fr.orsay.lri.varna.components.BaseTableModel
 
getColumnName(int) - Method in class fr.orsay.lri.varna.views.VueBaseValues.ValueTableModel
 
getColumnName(int) - Method in class fr.orsay.lri.varna.views.VueBPList.BPTableModel
 
getConfig() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the current VARNA Panel configuration.
getConnection(int) - Method in class fr.orsay.lri.varna.models.naView.Loop
 
getContent() - Method in class fr.orsay.lri.varna.models.rna.ExtendedMB
 
getContent() - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
 
getContent() - Method in class fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide
 
getContent() - Method in class fr.orsay.lri.varna.models.rna.ModeleBasesComparison
 
getContents() - Method in class fr.orsay.lri.varna.models.BaseList
 
getCoords() - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
 
getCoords(int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getCurColorCode() - Method in class fr.orsay.lri.varna.models.export.XFIGExport
 
getCurFontSize() - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
getCurrentColor() - Method in class fr.orsay.lri.varna.components.BaseSpecialColorEditor
 
getCurrentColor() - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
getCurrentFont() - Method in class fr.orsay.lri.varna.models.export.SecStrDrawingProducer
 
getCustomColor() - Method in class fr.orsay.lri.varna.models.rna.ModeleBPStyle
 
getData() - Method in class fr.orsay.lri.varna.views.VueBases
 
getData() - Method in class fr.orsay.lri.varna.views.VueListeAnnotations
 
getDataAt(int) - Method in class fr.orsay.lri.varna.views.VueBases
 
getDecalage() - Method in class fr.orsay.lri.varna.models.rna.Motif
 
getDepth() - Method in class fr.orsay.lri.varna.models.naView.Loop
 
getDialog() - Method in class fr.orsay.lri.varna.components.BaseSpecialColorEditor
 
getDimension() - Method in class fr.orsay.lri.varna.views.VueBorder
 
getDirVector() - Method in class fr.orsay.lri.varna.models.annotations.ChemProbAnnotation
 
getDistance() - Method in class fr.orsay.lri.varna.models.templates.RNATemplateMapping
 
getDistance() - Method in class fr.orsay.lri.varna.models.treealign.ExampleDistance3.SequenceAlignResult
 
getDistance() - Method in class fr.orsay.lri.varna.models.treealign.TreeAlignResult
 
getDrawBackbone() - Method in class fr.orsay.lri.varna.VARNAPanel
 
getDrawMode() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getDrawMode() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the current algorithm used for drawing the structure
getDrawn() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getEdge3() - Method in class fr.orsay.lri.varna.views.VueBPType
 
getEdge5() - Method in class fr.orsay.lri.varna.views.VueBPType
 
getEdgePartner3() - Method in class fr.orsay.lri.varna.models.rna.ModeleBP
 
getEdgePartner5() - Method in class fr.orsay.lri.varna.models.rna.ModeleBP
 
getEDIT() - Static method in class fr.orsay.lri.varna.components.BaseSpecialColorEditor
 
getElement() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement.EdgeEndPoint
Returns the endpoint on which this edge endpoint is.
getElementStructure() - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
Gets this InterfaceBase associated structure element.
getElementStructure() - Method in class fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide
 
getElementStructure() - Method in class fr.orsay.lri.varna.models.rna.ModeleBasesComparison
Gets this InterfaceBase assiociated structure element.
getEnd() - Method in class fr.orsay.lri.varna.models.naView.Connection
 
getEnd1() - Method in class fr.orsay.lri.varna.models.naView.Region
 
getEnd2() - Method in class fr.orsay.lri.varna.models.naView.Region
 
getEndAngle() - Method in class fr.orsay.lri.varna.models.export.ArcCommand
 
getEndChoose() - Method in class fr.orsay.lri.varna.components.GradientEditorPanel
 
getEndPointFromPosition(RNATemplate.EdgeEndPointPosition) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement
Get the EdgeEndPoint object corresponding to the the given position on this endpoint.
getEndPointFromPosition(RNATemplate.EdgeEndPointPosition) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
 
getEndPointFromPosition(RNATemplate.EdgeEndPointPosition) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
 
getEndPosition() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
 
getEndRemove() - Method in class fr.orsay.lri.varna.components.GradientEditorPanel
 
getExtendedRNABBox() - Method in class fr.orsay.lri.varna.VARNAPanel
 
getFillColor() - Method in class fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation
 
getFirst() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate
The first endpoint (in sequence order) of the template.
getFirstEndPoint() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate
The first endpoint edge endpoint (in sequence order) of the template.
getFlatExteriorLoop() - Method in class fr.orsay.lri.varna.VARNAPanel
 
getFont() - Method in class fr.orsay.lri.varna.models.annotations.TextAnnotation
 
getFont() - Method in class fr.orsay.lri.varna.views.VueFont
 
getFullName() - Static method in class fr.orsay.lri.varna.models.VARNAConfig
 
getGapsBasesColor() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the color used to draw 'Gaps' bases in comparison mode
getHeight() - Method in class fr.orsay.lri.varna.models.export.ArcCommand
 
getHeight() - Method in class fr.orsay.lri.varna.views.VueBorder
 
getHelix(int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getHelix() - Method in class fr.orsay.lri.varna.models.templates.RNANodeValueTemplateBasePair
 
getHelix() - Method in class fr.orsay.lri.varna.models.templates.RNANodeValueTemplateBrokenBasePair
 
getHelixCountOnLoop(int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getHelixDescription() - Method in class fr.orsay.lri.varna.models.annotations.TextAnnotation
 
getHelixInterval(int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getHighlightedVersion(Color, Color) - Method in class fr.orsay.lri.varna.VARNAPanel
 
getHighlightRegion() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getId() - Method in enum fr.orsay.lri.varna.models.rna.ModeleColorMap.NamedColorMapTypes
 
getIn() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
 
getIn1() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
 
getIn1EndPoint() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement
Get the the IN endpoint in the case of a sequence and the IN1 endpoint in the case of an helix.
getIn1EndPoint() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
 
getIn1EndPoint() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
 
getIn1Is() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
 
getIn2() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
 
getIncrement() - Method in class fr.orsay.lri.varna.views.VueBPHeightIncrement
 
getIndex() - Method in class fr.orsay.lri.varna.models.rna.ExtendedMB
 
getIndex() - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
The internal index for this Base
getIndex() - Method in class fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide
 
getIndex() - Method in class fr.orsay.lri.varna.models.rna.ModeleBasesComparison
 
getIndex3() - Method in class fr.orsay.lri.varna.models.rna.ModeleBP
 
getIndex5() - Method in class fr.orsay.lri.varna.models.rna.ModeleBP
 
getIndexFromBaseNumber(int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getIndices() - Method in class fr.orsay.lri.varna.models.BaseList
 
getInnerHeight() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the "real pixels" height of the drawing surface for our RNA.
getInnerWidth() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the "real pixels" width of the drawing surface for our RNA.
getInTangentVectorAngle() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
 
getInTangentVectorLength() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
 
getIntensity() - Method in class fr.orsay.lri.varna.models.annotations.ChemProbAnnotation
 
getIntervDroite() - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
 
getIntervDroiteEx() - Method in class fr.orsay.lri.varna.models.rna.ExtendedMB
 
getIntervGauche() - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
 
getIntervGaucheEx() - Method in class fr.orsay.lri.varna.models.rna.ExtendedMB
 
getLastSelectedPosition() - Method in class fr.orsay.lri.varna.VARNAPanel
 
getLeftBasePosition() - Method in class fr.orsay.lri.varna.models.treealign.RNANodeValue
 
getLeftNode() - Method in class fr.orsay.lri.varna.models.treealign.AlignedNode
 
getLeftNucleotide() - Method in class fr.orsay.lri.varna.models.treealign.RNANodeValue
 
getLeftOffset() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the "real pixels" x-coordinate of the RNA.
getLength() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
 
getLength() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
 
getLevelPosition() - Method in class fr.orsay.lri.varna.models.rna.ModeleStrand
 
getListBasesMotif() - Method in class fr.orsay.lri.varna.models.rna.Motif
 
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class fr.orsay.lri.varna.components.ReorderableJList.ReorderableListCellRenderer
 
getListeAnnotations() - Method in class fr.orsay.lri.varna.VARNAPanel
 
getListeBasesToString() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getListStrand() - Method in class fr.orsay.lri.varna.models.rna.Motif
 
getListStrands() - Method in class fr.orsay.lri.varna.models.rna.StructureTemp
 
getLocalOutline(RNA) - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw.PairedPortion
 
getLoop() - Method in class fr.orsay.lri.varna.models.naView.Connection
 
getLoopBases(int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getLoopDescription() - Method in class fr.orsay.lri.varna.models.annotations.TextAnnotation
 
getLoopnumber() - Method in class fr.orsay.lri.varna.models.naView.Radloop
 
getMate() - Method in class fr.orsay.lri.varna.models.naView.Base
 
getMaxColor() - Method in class fr.orsay.lri.varna.models.rna.ModeleColorMap
 
getMaxIndex() - Method in class fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation
 
getMaxValue() - Method in class fr.orsay.lri.varna.models.rna.ModeleColorMap
 
getMB(int) - Method in class fr.orsay.lri.varna.models.rna.ModeleStrand
 
getMinColor() - Method in class fr.orsay.lri.varna.models.rna.ModeleColorMap
 
getMinIndex() - Method in class fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation
 
getMinValue() - Method in class fr.orsay.lri.varna.models.rna.ModeleColorMap
 
getMode() - Method in class fr.orsay.lri.varna.views.VueBases
 
getMultiLoop(int) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getN() - Method in class fr.orsay.lri.varna.models.CubicBezierCurve
The number of lines approximating the Bezier curve.
getName() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getName() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement
 
getName() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
 
getName() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
 
getNbColumns() - Method in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
getNbRows() - Method in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
getNconnection() - Method in class fr.orsay.lri.varna.models.naView.Loop
 
getNearestBase() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the index of the currently selected base, defaulting to the closest base to the last mouse-click.
getNext() - Method in class fr.orsay.lri.varna.models.naView.Radloop
 
getNextEndPoint() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement.EdgeEndPoint
Get the next endpoint.
getNextEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement
Provided endpoint is an endpoint of this endpoint, get the next endpoint, either on this same endpoint, or or the connected endpoint.
getNextEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
 
getNextEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
 
getNode() - Method in class fr.orsay.lri.varna.models.treealign.RNANodeValue2
In case of a single node, return it.
getNodes() - Method in class fr.orsay.lri.varna.models.treealign.RNANodeValue2
In case of multiple nodes, return them.
getNonCrossingStruct() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getNonOverlappingStruct() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getNonStandardBasesColor() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the color used to draw non-standard bases
getNormalVector() - Method in class fr.orsay.lri.varna.models.annotations.ChemProbAnnotation
 
getNumBases() - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw.PairedPortion
 
getNumBases() - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw.Portion
 
getNumBases() - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw.UnpairedPortion
 
getNumber() - Method in class fr.orsay.lri.varna.models.naView.Loop
 
getNumbers() - Method in class fr.orsay.lri.varna.models.BaseList
 
getNumColors() - Method in class fr.orsay.lri.varna.models.rna.ModeleColorMap
 
getNumPeriod() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the current numbering period.
getNumPeriod() - Method in class fr.orsay.lri.varna.views.VueNumPeriod
 
getNumPortions() - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw.RNATree
 
getNumStrand() - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
 
getOffsetPanel() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the shifting of the origin of the Panel in zoom mode
getOrientation() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getOrientation() - Method in class fr.orsay.lri.varna.VARNAPanel
 
getOrigin() - Method in class fr.orsay.lri.varna.models.treealign.RNANodeValue
 
getOrigine() - Method in class fr.orsay.lri.varna.models.export.ArcCommand
 
getOtherElement() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement.EdgeEndPoint
Returns the endpoint at the other endpoint of the edge.
getOtherEndPoint() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement.EdgeEndPoint
Returns the other endpoint of the edge.
getOut() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
 
getOut1() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
 
getOut2() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
 
getOutline(RNA) - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw.PairedPortion
 
getOutline(RNA, boolean) - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw.PairedPortion
 
getOutline(RNA) - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw.Portion
 
getOutline(RNA) - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw.RNATree
 
getOutline(RNA) - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw.UnpairedPortion
 
getOutlineColor() - Method in class fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation
 
getOutTangentVectorAngle() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
 
getOutTangentVectorLength() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
 
getP0() - Method in class fr.orsay.lri.varna.models.CubicBezierCurve
 
getP1() - Method in class fr.orsay.lri.varna.models.CubicBezierCurve
 
getP2() - Method in class fr.orsay.lri.varna.models.CubicBezierCurve
 
getP3() - Method in class fr.orsay.lri.varna.models.CubicBezierCurve
 
getPanel() - Method in class fr.orsay.lri.varna.views.VueAnnotation
 
getPanel() - Method in class fr.orsay.lri.varna.views.VueBorder
 
getPanel() - Method in class fr.orsay.lri.varna.views.VueBPHeightIncrement
 
getPanel() - Method in class fr.orsay.lri.varna.views.VueBPThickness
 
getPanel() - Method in class fr.orsay.lri.varna.views.VueBPType
 
getPanel() - Method in class fr.orsay.lri.varna.views.VueChemProbAnnotation
 
getPanel() - Method in class fr.orsay.lri.varna.views.VueFont
 
getPanel() - Method in class fr.orsay.lri.varna.views.VueGlobalRotation
 
getPanel() - Method in class fr.orsay.lri.varna.views.VueHighlightRegionEdit
 
getPanel() - Method in class fr.orsay.lri.varna.views.VueJPEG
 
getPanel() - Method in class fr.orsay.lri.varna.views.VueManualInput
 
getPanel() - Method in class fr.orsay.lri.varna.views.VueNumPeriod
 
getPanel() - Method in class fr.orsay.lri.varna.views.VueSpaceBetweenBases
 
getPanel() - Method in class fr.orsay.lri.varna.views.VueStyleBP
 
getPanel() - Method in class fr.orsay.lri.varna.views.VueZoom
 
getParamEncoding() - Method in class fr.orsay.lri.varna.models.rna.ModeleColorMap
 
getParameterInfo() - Static method in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
getParameterValue(String, String) - Method in interface fr.orsay.lri.varna.interfaces.InterfaceParameterLoader
 
getParentTemplate() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement
Returns the template to which this endpoint belongs.
getPartner(int) - Method in class fr.orsay.lri.varna.models.rna.Mapping
 
getPartner(ModeleBase) - Method in class fr.orsay.lri.varna.models.rna.ModeleBP
 
getPartner(int) - Method in class fr.orsay.lri.varna.models.templates.RNATemplateMapping
If the given base index is in the mapping, return the corresponding template element, otherwise return null.
getPartner3() - Method in class fr.orsay.lri.varna.models.rna.ModeleBP
 
getPartner5() - Method in class fr.orsay.lri.varna.models.rna.ModeleBP
 
getPopup() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the popup menu used for user mouse iteractions
getPopupMenu() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns this panel's UI menu
getPortion(int) - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw.RNATree
 
getPosition() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement.EdgeEndPoint
Get the position on the endpoint where this endpoint is.
getPositionFromEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement
The inverse of getEndPointFromPosition.
getPositionFromEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
 
getPositionFromEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
 
getPositionInHelix() - Method in class fr.orsay.lri.varna.models.templates.RNANodeValueTemplateBasePair
 
getPositionInHelix() - Method in class fr.orsay.lri.varna.models.templates.RNANodeValueTemplateBrokenBasePair
 
getPresentationName() - Method in class fr.orsay.lri.varna.models.VARNAEdits.AddBPEdit
 
getPresentationName() - Method in class fr.orsay.lri.varna.models.VARNAEdits.BasesShiftEdit
 
getPresentationName() - Method in class fr.orsay.lri.varna.models.VARNAEdits.HelixFlipEdit
 
getPresentationName() - Method in class fr.orsay.lri.varna.models.VARNAEdits.HelixRotateEdit
 
getPresentationName() - Method in class fr.orsay.lri.varna.models.VARNAEdits.RedrawEdit
 
getPresentationName() - Method in class fr.orsay.lri.varna.models.VARNAEdits.RemoveBPEdit
 
getPresentationName() - Method in class fr.orsay.lri.varna.models.VARNAEdits.RotateRNAEdit
 
getPresentationName() - Method in class fr.orsay.lri.varna.models.VARNAEdits.SingleBaseMoveEdit
 
getPrev() - Method in class fr.orsay.lri.varna.models.naView.Radloop
 
getPreviousEndPoint() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement.EdgeEndPoint
Same as getNextEndPoint(), but with the previous endpoint.
getPreviousEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement
Provided endpoint is an endpoint of this endpoint, get the previous endpoint, either on this same endpoint, or or the connected endpoint.
getPreviousEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
 
getPreviousEndPoint(RNATemplate.RNATemplateElement.EdgeEndPoint) - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
 
getQualitySlider() - Method in class fr.orsay.lri.varna.views.VueJPEG
 
getRadius() - Method in class fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation
 
getRadius() - Method in class fr.orsay.lri.varna.models.naView.Loop
 
getRadius() - Method in class fr.orsay.lri.varna.models.naView.Radloop
 
getReader() - Method in class fr.orsay.lri.varna.views.VueLoadColorMapValues
 
getRealCoords() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the coordinates of the currently displayed RNA
getRegion() - Method in class fr.orsay.lri.varna.models.naView.Base
 
getRegion() - Method in class fr.orsay.lri.varna.models.naView.Connection
 
getRGBString(Color) - Method in class fr.orsay.lri.varna.models.export.SVGExport
 
getRightBasePosition() - Method in class fr.orsay.lri.varna.models.treealign.RNANodeValue
 
getRightNode() - Method in class fr.orsay.lri.varna.models.treealign.AlignedNode
 
getRightNucleotide() - Method in class fr.orsay.lri.varna.models.treealign.RNANodeValue
 
getRNA() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the current RNA model
getRNAOffset() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the vector bringing the logical coordinate of left-top-most point in the panel to the left-top-most point of the RNA.
getRowCount() - Method in class fr.orsay.lri.varna.components.AnnotationTableModel
 
getRowCount() - Method in class fr.orsay.lri.varna.components.BaseTableModel
 
getRowCount() - Method in class fr.orsay.lri.varna.views.VueBaseValues.ValueTableModel
 
getRowCount() - Method in class fr.orsay.lri.varna.views.VueBPList.BPTableModel
 
getSafeBPStyle(String, VARNAConfig.BP_STYLE) - Method in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
getSafeColor(String) - Static method in class fr.orsay.lri.varna.models.rna.ModeleStyleBase
 
getSafeColor(String, Color) - Static method in class fr.orsay.lri.varna.models.VARNAConfigLoader
 
getScaleFactor() - Method in class fr.orsay.lri.varna.VARNAPanel
Gets the scale factor used by the autofitting function
getScaleSlider() - Method in class fr.orsay.lri.varna.views.VueJPEG
 
getSecStrBPs() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getSelection() - Method in class fr.orsay.lri.varna.VARNAPanel
 
getSelectionIndices() - Method in class fr.orsay.lri.varna.VARNAPanel
 
getSeq() - Method in class fr.orsay.lri.varna.models.rna.RNA
Returns the raw nucleotides sequence for the displayed RNA
getSequence() - Method in class fr.orsay.lri.varna.models.rna.RNAMLParser
 
getSequence() - Method in class fr.orsay.lri.varna.models.templates.RNANodeValueTemplateSequence
 
getSerialVersionUID() - Static method in class fr.orsay.lri.varna.components.BaseSpecialColorEditor
 
getSerialVersionUID() - Static method in class fr.orsay.lri.varna.views.VueMenu
 
getShape(Point2D.Double[], Point2D.Double[], double) - Method in class fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation
 
getShape() - Method in class fr.orsay.lri.varna.models.rna.VARNASecDraw.HelixEmbedding
 
getShowNonCanonicalBP() - Method in class fr.orsay.lri.varna.VARNAPanel
Return the current display status for non-canonical base-pairs
getShowNonPlanarBP() - Method in class fr.orsay.lri.varna.VARNAPanel
Return the current display status for non-planar base-pairs
getShowWarnings() - Method in class fr.orsay.lri.varna.VARNAPanel
Get current warning display status
getSize() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getSizeSlider() - Method in class fr.orsay.lri.varna.views.VueFont
 
getSourceElems() - Method in class fr.orsay.lri.varna.models.rna.Mapping
 
getSourceElemsAsSet() - Method in class fr.orsay.lri.varna.models.templates.RNATemplateMapping
Return a set containing all the base indexes in the mapping.
getSpace() - Method in class fr.orsay.lri.varna.views.VueSpaceBetweenBases
 
getSpawnPoint() - Method in class fr.orsay.lri.varna.views.VueMenu
 
getSpecialTableModel() - Method in class fr.orsay.lri.varna.views.VueBases
 
getSpecialTableModel() - Method in class fr.orsay.lri.varna.views.VueListeAnnotations
 
getStart() - Method in class fr.orsay.lri.varna.models.naView.Connection
 
getStart1() - Method in class fr.orsay.lri.varna.models.naView.Region
 
getStart2() - Method in class fr.orsay.lri.varna.models.naView.Region
 
getStartAngle() - Method in class fr.orsay.lri.varna.models.export.ArcCommand
 
getStartChoose() - Method in class fr.orsay.lri.varna.components.GradientEditorPanel
 
getStartPosition() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix
 
getStartRemove() - Method in class fr.orsay.lri.varna.components.GradientEditorPanel
 
getStericity() - Method in class fr.orsay.lri.varna.models.rna.ModeleBP
 
getStericity() - Method in class fr.orsay.lri.varna.views.VueBPType
 
getStrand(int) - Method in class fr.orsay.lri.varna.models.rna.StructureTemp
 
getStrandLeft() - Method in class fr.orsay.lri.varna.models.rna.ModeleStrand
 
getStrandRight() - Method in class fr.orsay.lri.varna.models.rna.ModeleStrand
 
getStringDimension(String) - Method in class fr.orsay.lri.varna.models.export.SecStrProducerGraphics
 
getStringDimension(String) - Method in class fr.orsay.lri.varna.models.export.SwingGraphics
 
getStringDimension(String) - Method in interface fr.orsay.lri.varna.models.export.VueVARNAGraphics
 
getStripeHeight() - Method in class fr.orsay.lri.varna.components.GradientEditorPanel
 
getStructBPSEQ() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getStructCT() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getStructDBN() - Method in class fr.orsay.lri.varna.models.rna.RNA
Returns the RNA secondary structure displayed by this panel as a well-parenthesized word, accordingly to the DBN format
getStructDBN(boolean) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getStructDBN(int[]) - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getStructureAux() - Method in class fr.orsay.lri.varna.models.rna.RNA
 
getStyle() - Method in class fr.orsay.lri.varna.models.rna.ModeleBP
 
getStyle() - Method in class fr.orsay.lri.varna.views.VueStyleBP
 
getStyleBase() - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
Gets this InterfaceBase style.
getStyleBase() - Method in class fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide
 
getStyleBase() - Method in class fr.orsay.lri.varna.models.rna.ModeleBasesComparison
Return the display style associated to this comparison base.
getStyleBP() - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
Gets the base pair type for this element.
getStylesBox() - Method in class fr.orsay.lri.varna.views.VueFont
 
getTable() - Method in class fr.orsay.lri.varna.views.VueBases
 
getTable() - Method in class fr.orsay.lri.varna.views.VueListeAnnotations
 
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class fr.orsay.lri.varna.components.ActionEditor
 
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class fr.orsay.lri.varna.components.BaseSpecialColorEditor
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class fr.orsay.lri.varna.components.ActionRenderer
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class fr.orsay.lri.varna.components.ColorRenderer
 
getTargetElems() - Method in class fr.orsay.lri.varna.models.rna.Mapping
 
getTargetElemsAsSet() - Method in class fr.orsay.lri.varna.models.templates.RNATemplateMapping
Return a set containing all the template elements in the mapping.
getTextAnnotation() - Method in class fr.orsay.lri.varna.views.VueAnnotation
 
getTexte() - Method in class fr.orsay.lri.varna.models.annotations.TextAnnotation
 
getThickness(double) - Method in class fr.orsay.lri.varna.models.rna.ModeleBPStyle
 
getThickness() - Method in class fr.orsay.lri.varna.views.VueBPThickness
 
getTitle() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the title of this panel
getTitleColor() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the color used to draw the title
getTitleFont() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the font currently used for rendering the title.
getTitleHeight() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the height taken by the title
getTopOffset() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the "real pixels" y-coordinate of the RNA.
getTransferData(DataFlavor) - Method in class fr.orsay.lri.varna.components.ReorderableJList.RJLTransferable
 
getTransferDataFlavors() - Method in class fr.orsay.lri.varna.components.ReorderableJList.RJLTransferable
 
getTranslation() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the translation used for zooming in and out
getTseq() - Method in class fr.orsay.lri.varna.views.VueManualInput
 
getTstr() - Method in class fr.orsay.lri.varna.views.VueManualInput
 
getType() - Method in class fr.orsay.lri.varna.models.annotations.ChemProbAnnotation
 
getType() - Method in class fr.orsay.lri.varna.models.annotations.TextAnnotation
 
getUseBaseColorsForBPs() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns true if current base color is used as inner color for drawing base-pairs
getValue() - Method in class fr.orsay.lri.varna.models.rna.ModeleBase
 
getValue() - Method in class fr.orsay.lri.varna.models.treealign.Tree
 
getValueAt(int, int) - Method in class fr.orsay.lri.varna.components.AnnotationTableModel
 
getValueAt(int, int) - Method in class fr.orsay.lri.varna.components.BaseTableModel
 
getValueAt(int) - Method in class fr.orsay.lri.varna.models.rna.ModeleColorMap
 
getValueAt(int, int) - Method in class fr.orsay.lri.varna.views.VueBaseValues.ValueTableModel
 
getValueAt(int, int) - Method in class fr.orsay.lri.varna.views.VueBPList.BPTableModel
 
getVARNAUI() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the view associated with user interactions
getVertex3() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
 
getVertex5() - Method in class fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence
 
getWidth() - Method in class fr.orsay.lri.varna.models.export.ArcCommand
 
getWidth() - Method in class fr.orsay.lri.varna.views.VueBorder
 
getX() - Method in class fr.orsay.lri.varna.models.naView.Base
 
getX() - Method in class fr.orsay.lri.varna.models.naView.Loop
 
getX() - Method in class fr.orsay.lri.varna.models.rna.VARNAPoint
 
getXPos(int) - Method in class fr.orsay.lri.varna.components.GradientEditorPanel
 
getXrad() - Method in class fr.orsay.lri.varna.models.naView.Connection
 
getY() - Method in class fr.orsay.lri.varna.models.naView.Base
 
getY() - Method in class fr.orsay.lri.varna.models.naView.Loop
 
getY() - Method in class fr.orsay.lri.varna.models.rna.VARNAPoint
 
getYrad() - Method in class fr.orsay.lri.varna.models.naView.Connection
 
getZoom() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the current zoom factor
getZoom() - Method in class fr.orsay.lri.varna.views.VueZoom
 
getZoomAmount() - Method in class fr.orsay.lri.varna.views.VueZoom
 
getZoomIncrement() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the atomic zoom factor step, or increment.
globalRotation(Double) - Method in class fr.orsay.lri.varna.models.rna.RNA
Rotates the RNA coordinates by a certain angle
globalRotation(Double) - Method in class fr.orsay.lri.varna.VARNAPanel
Rotates the RNA coordinates by a certain angle
gracefulStop() - Method in class fr.orsay.lri.varna.views.VueAboutPanel.AboutAnimator
 
gracefulStop() - Method in class fr.orsay.lri.varna.views.VueAboutPanel
 
GradientEditorPanel - Class in fr.orsay.lri.varna.components
 
GradientEditorPanel(ModeleColorMap) - Constructor for class fr.orsay.lri.varna.components.GradientEditorPanel
 
GraphicElement - Class in fr.orsay.lri.varna.models.export
 
GraphicElement() - Constructor for class fr.orsay.lri.varna.models.export.GraphicElement
 
GraphvizDrawableNodeValue - Interface in fr.orsay.lri.varna.models.treealign
A tree can be displayed using graphviz (using class TreeGraphviz) if the node values in the tree implement this interface.
greenColorMap() - Static method in class fr.orsay.lri.varna.models.rna.ModeleColorMap
 
guessFileTypeFromExtension(String) - Static method in class fr.orsay.lri.varna.models.rna.RNA
 

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