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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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