- saveSelection() - Method in class fr.orsay.lri.varna.VARNAPanel
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- saveSession(String) - Method in class fr.orsay.lri.varna.VARNAPanel
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- set_selectedAnnotation(TextAnnotation) - Method in class fr.orsay.lri.varna.VARNAPanel
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- setAutoCenter(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
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Sets the current state of auto centering mode.
- setBackboneColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
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Sets the color to be used for drawing backbone interactions.
- setBackground(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
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Sets the background color
- setBaseFontSize(Float) - Method in class fr.orsay.lri.varna.VARNAPanel
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Sets the font size for displaying bases
- setBaseFontStyle(int) - Method in class fr.orsay.lri.varna.VARNAPanel
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Sets the font style for displaying bases
- setBaseInnerColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
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- setBaseNameColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
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- setBaseNumbersColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
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- setBaseOutlineColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
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- setBondColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
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Sets the color used to display hydrogen bonds (base pairings)
- setBorderSize(Dimension) - Method in class fr.orsay.lri.varna.VARNAPanel
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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
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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
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Sets the base-pair representation style
- setColorGapsBases(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
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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
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- setColorMapCaption(String) - Method in class fr.orsay.lri.varna.VARNAPanel
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- setColorMapMaxValue(double) - Method in class fr.orsay.lri.varna.VARNAPanel
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- setColorMapMinValue(double) - Method in class fr.orsay.lri.varna.VARNAPanel
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- setColorMapValues(Double[]) - Method in class fr.orsay.lri.varna.VARNAPanel
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- setColorMapVisible(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
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- setColorNonStandardBases(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
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Toggles on/off using a special color used for drawing "non-standard"
bases
- setConfig(VARNAConfig) - Method in class fr.orsay.lri.varna.VARNAPanel
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- setDefaultBPColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
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Sets the new color to be used for hydrogen bonds (base pairings)
- setDestinationLink(Point2D.Double) - Method in class fr.orsay.lri.varna.VARNAPanel
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- setDrawBackbone(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
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- setErrorsOn(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
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Sets whether errors are to be displayed
- setFlatExteriorLoop(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
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- setGapsBasesColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
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Sets the color to use for 'Gaps' bases in comparison mode
- setHoverBase(ModeleBase) - Method in class fr.orsay.lri.varna.VARNAPanel
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- setLastSelectedPosition(Point2D.Double) - Method in class fr.orsay.lri.varna.VARNAPanel
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- setModifiable(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
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Toggles modifications on and off
- setNearestBase(Integer) - Method in class fr.orsay.lri.varna.VARNAPanel
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Sets the index of the currently selected base.
- setNonStandardBasesColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
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Sets the color used to draw non-standard bases
- setNumbersFontSize(Float) - Method in class fr.orsay.lri.varna.VARNAPanel
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Sets the font size for displaying base numbers
- setNumPeriod(int) - Method in class fr.orsay.lri.varna.VARNAPanel
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Sets the distance between consecutive base numbers.
- setOriginLink(Point2D.Double) - Method in class fr.orsay.lri.varna.VARNAPanel
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- setRealCoords(Point2D.Double[]) - Method in class fr.orsay.lri.varna.VARNAPanel
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Sets the coordinates of the currently displayed RNA
- setSelection(ArrayList<Integer>) - Method in class fr.orsay.lri.varna.VARNAPanel
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- setSelection(Collection<? extends ModeleBase>) - Method in class fr.orsay.lri.varna.VARNAPanel
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- setSelectionRectangle(Rectangle) - Method in class fr.orsay.lri.varna.VARNAPanel
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- setSequence(String) - Method in class fr.orsay.lri.varna.VARNAPanel
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- setShowNonCanonicalBP(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
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Toggles on/off displaying non-canonical base-pairs
- setShowNonPlanarBP(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
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Toggles on/off displaying "non-planar" base-pairs
- setShowWarnings(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
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Toggles on/off displaying warnings
- setTitle(String) - Method in class fr.orsay.lri.varna.VARNAPanel
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Sets the panel's title, giving a short description of the RNA secondary
structure.
- setTitleColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
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Sets the color used to draw the title
- setTitleFont(Font) - Method in class fr.orsay.lri.varna.VARNAPanel
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Sets the font used for rendering the title.
- setTitleFontColor(Color) - Method in class fr.orsay.lri.varna.VARNAPanel
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Sets the color to be used for the title.
- setTitleFontFamily(String) - Method in class fr.orsay.lri.varna.VARNAPanel
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Sets the new font family to be used for the title.
- setTitleFontSize(float) - Method in class fr.orsay.lri.varna.VARNAPanel
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Sets the new size of the title font.
- setTitleFontStyle(int) - Method in class fr.orsay.lri.varna.VARNAPanel
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Sets the new style of the title font.
- setTranslation(Point) - Method in class fr.orsay.lri.varna.VARNAPanel
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Sets the translation used for zooming in and out
- setUseBaseColorsForBPs(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
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Toggles on/off using base inner color for drawing base-pairs
- setZoom(Object) - Method in class fr.orsay.lri.varna.VARNAPanel
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Sets the current zoom factor
- setZoomIncrement(Object) - Method in class fr.orsay.lri.varna.VARNAPanel
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Sets the atomic zoom factor step, or increment.
- setZoomIncrement(double) - Method in class fr.orsay.lri.varna.VARNAPanel
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Sets the atomic zoom factor step, or increment.
- showRNA(RNA) - Method in class fr.orsay.lri.varna.VARNAPanel
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Sets the RNA to be displayed within this Panel.
- showRNA(RNA, VARNAConfig) - Method in class fr.orsay.lri.varna.VARNAPanel
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- showRNAInterpolated(RNA) - Method in class fr.orsay.lri.varna.VARNAPanel
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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
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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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