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S

saveSelection() - Method in class fr.orsay.lri.varna.VARNAPanel
 
saveSession(String) - Method in class fr.orsay.lri.varna.VARNAPanel
 
set_selectedAnnotation(TextAnnotation) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setAutoCenter(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the current state of auto centering mode.
setBackboneColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the color to be used for drawing backbone interactions.
setBackground(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the background color
setBaseFontSize(Float) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the font size for displaying bases
setBaseFontStyle(int) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the font style for displaying bases
setBaseInnerColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setBaseNameColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setBaseNumbersColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setBaseOutlineColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setBondColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the color used to display hydrogen bonds (base pairings)
setBorderSize(Dimension) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the size of the border, i.e. the empty space between the end of the drawing area and the actual border.
setBPHeightIncrement(double) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the base pair height increment, i.e. the vertical distance between two arcs to be used in LINE_MODE.
setBPStyle(VARNAConfig.BP_STYLE) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the base-pair representation style
setColorGapsBases(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
Toggles on/off using a special color used for drawing "Gaps" bases in comparison mode
setColorMap(ModeleColorMap) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setColorMapCaption(String) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setColorMapMaxValue(double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setColorMapMinValue(double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setColorMapValues(Double[]) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setColorMapVisible(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setColorNonStandardBases(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
Toggles on/off using a special color used for drawing "non-standard" bases
setConfig(VARNAConfig) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setDefaultBPColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the new color to be used for hydrogen bonds (base pairings)
setDestinationLink(Point2D.Double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setDrawBackbone(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setErrorsOn(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets whether errors are to be displayed
setFlatExteriorLoop(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setGapsBasesColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the color to use for 'Gaps' bases in comparison mode
setHoverBase(ModeleBase) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setLastSelectedPosition(Point2D.Double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setModifiable(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
Toggles modifications on and off
setNearestBase(Integer) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the index of the currently selected base.
setNonStandardBasesColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the color used to draw non-standard bases
setNumbersFontSize(Float) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the font size for displaying base numbers
setNumPeriod(int) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the distance between consecutive base numbers.
setOriginLink(Point2D.Double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setRealCoords(Point2D.Double[]) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the coordinates of the currently displayed RNA
setSelection(ArrayList<Integer>) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setSelection(Collection<? extends ModeleBase>) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setSelectionRectangle(Rectangle) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setSequence(String) - Method in class fr.orsay.lri.varna.VARNAPanel
 
setShowNonCanonicalBP(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
Toggles on/off displaying non-canonical base-pairs
setShowNonPlanarBP(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
Toggles on/off displaying "non-planar" base-pairs
setShowWarnings(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
Toggles on/off displaying warnings
setTitle(String) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the panel's title, giving a short description of the RNA secondary structure.
setTitleColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the color used to draw the title
setTitleFont(Font) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the font used for rendering the title.
setTitleFontColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the color to be used for the title.
setTitleFontFamily(String) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the new font family to be used for the title.
setTitleFontSize(float) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the new size of the title font.
setTitleFontStyle(int) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the new style of the title font.
setTranslation(Point) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the translation used for zooming in and out
setUseBaseColorsForBPs(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
Toggles on/off using base inner color for drawing base-pairs
setZoom(Object) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the current zoom factor
setZoomIncrement(Object) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the atomic zoom factor step, or increment.
setZoomIncrement(double) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the atomic zoom factor step, or increment.
showRNA(RNA) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the RNA to be displayed within this Panel.
showRNA(RNA, VARNAConfig) - Method in class fr.orsay.lri.varna.VARNAPanel
 
showRNAInterpolated(RNA) - Method in class fr.orsay.lri.varna.VARNAPanel
Simply displays (does not redraw) a secondary structure , using an interpolated transition between the previous one and the new one.
showRNAInterpolated(RNA, Mapping) - Method in class fr.orsay.lri.varna.VARNAPanel
Simply displays (does not redraw) a secondary structure , using an interpolated transition between the previous one and the new one.
showRNAInterpolated(RNA, VARNAConfig, Mapping) - Method in class fr.orsay.lri.varna.VARNAPanel
 
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