- drawBackbone(VueVARNAGraphics, Point2D.Double[], double, double) - Method in class fr.orsay.lri.varna.VARNAPanel
-
- drawBBox(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
-
Toggles on/off a rectangular outline of the bounding box.
- drawBorder(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
-
Toggles on/off a rectangular outline of the border.
- drawColorMap(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
-
- drawRegionHighlightsAnnotation(VueVARNAGraphics, Point2D.Double[], Point2D.Double[], double) - Method in class fr.orsay.lri.varna.VARNAPanel
-
- drawRNA(String, String) - Method in class fr.orsay.lri.varna.VARNAPanel
-
Sets the RNA secondary structure to be drawn in this panel, using the
default layout algorithm.
- drawRNA(RNA, int) - Method in class fr.orsay.lri.varna.VARNAPanel
-
Sets the RNA secondary structure to be drawn in this panel, using a given
layout algorithm.
- drawRNA() - Method in class fr.orsay.lri.varna.VARNAPanel
-
Redraws the current RNA.
- drawRNA(RNA) - Method in class fr.orsay.lri.varna.VARNAPanel
-
Sets the RNA secondary structure to be drawn in this panel, using the
current drawing algorithm.
- drawRNA(String, String, int) - Method in class fr.orsay.lri.varna.VARNAPanel
-
Sets the RNA secondary structure to be drawn in this panel, using a given
layout algorithm.
- drawRNA(Reader, int) - Method in class fr.orsay.lri.varna.VARNAPanel
-
- drawRNA(String, String, String, String, int) - Method in class fr.orsay.lri.varna.VARNAPanel
-
When comparison mode is ON, sets the two RNA secondary structure to be
drawn in this panel, using a given layout algorithm.
- drawRNAInterpolated(String, String) - Method in class fr.orsay.lri.varna.VARNAPanel
-
Draws a secondary structure of RNA using the default drawing algorithm
and displays it, using an interpolated transition between the previous
one and the new one.
- drawRNAInterpolated(String, String, int) - Method in class fr.orsay.lri.varna.VARNAPanel
-
Draws a secondary structure of RNA using a given algorithm and displays
it, using an interpolated transition between the previous one and the new
one.
- drawRNAInterpolated(String, String, Mapping) - Method in class fr.orsay.lri.varna.VARNAPanel
-
Draws a secondary structure of RNA using the default drawing algorithm
and displays it, using an interpolated transition between the previous
one and the new one.
- drawRNAInterpolated(String, String, int, Mapping) - Method in class fr.orsay.lri.varna.VARNAPanel
-
Draws a secondary structure of RNA using a given drawing algorithm and
displays it, using an interpolated transition between the previous one
and the new one.
- drawRNAInterpolated(RNA) - Method in class fr.orsay.lri.varna.VARNAPanel
-
Draws a secondary structure of RNA using the default drawing algorithm
and displays it, using an interpolated transition between the previous
one and the new one.
- drawRNAInterpolated(RNA, Mapping) - Method in class fr.orsay.lri.varna.VARNAPanel
-
Draws a secondary structure of RNA using the default drawing algorithm
and displays it, using an interpolated transition between the previous
one and the new one.
- drawRNAInterpolated(RNA, int, Mapping) - Method in class fr.orsay.lri.varna.VARNAPanel
-
Draws a secondary structure of RNA using a given drawing algorithm and
displays it, using an interpolated transition between the previous one
and the new one.
- get_selectedAnnotation() - Method in class fr.orsay.lri.varna.VARNAPanel
-
- getBackboneColor() - Method in class fr.orsay.lri.varna.VARNAPanel
-
Returns the color used to draw backbone bounds.
- getBaseAt(Point2D.Double) - Method in class fr.orsay.lri.varna.VARNAPanel
-
- getBasesInRectangle(Rectangle) - Method in class fr.orsay.lri.varna.VARNAPanel
-
- getBasesInRectangleDiff(Rectangle, Rectangle) - Method in class fr.orsay.lri.varna.VARNAPanel
-
- 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. the empty space between the end of
the drawing area
- getBPHeightIncrement() - Method in class fr.orsay.lri.varna.VARNAPanel
-
For the LINE_MODE drawing algorithm, sets the base pair height increment,
i.e. the vertical distance between two nested arcs.
- getBPStyle() - Method in class fr.orsay.lri.varna.VARNAPanel
-
Returns the base-pair representation style
- getColorGapsBases() - Method in class fr.orsay.lri.varna.VARNAPanel
-
Returns true if a special color is used for drawing "Gaps" bases in
comparison mode
- getColorMap() - Method in class fr.orsay.lri.varna.VARNAPanel
-
- getColorMapCaption() - Method in class fr.orsay.lri.varna.VARNAPanel
-
- 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
- getConfig() - Method in class fr.orsay.lri.varna.VARNAPanel
-
Returns the current VARNA Panel configuration.
- getDrawBackbone() - Method in class fr.orsay.lri.varna.VARNAPanel
-
- getDrawMode() - Method in class fr.orsay.lri.varna.VARNAPanel
-
Returns the current algorithm used for drawing the structure
- getExtendedRNABBox() - Method in class fr.orsay.lri.varna.VARNAPanel
-
- getFlatExteriorLoop() - Method in class fr.orsay.lri.varna.VARNAPanel
-
- getGapsBasesColor() - Method in class fr.orsay.lri.varna.VARNAPanel
-
Returns the color used to draw 'Gaps' bases in comparison mode
- 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.
- getLastSelectedPosition() - Method in class fr.orsay.lri.varna.VARNAPanel
-
- getLeftOffset() - Method in class fr.orsay.lri.varna.VARNAPanel
-
Returns the "real pixels" x-coordinate of the RNA.
- getListeAnnotations() - Method in class fr.orsay.lri.varna.VARNAPanel
-
- getNearestAnnotation(int, int) - Method in class fr.orsay.lri.varna.VARNAPanel
-
- 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.
- getNearestBase(int, int, boolean, boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
-
- getNearestBase(int, int) - Method in class fr.orsay.lri.varna.VARNAPanel
-
- getNearestBaseIndex(int, int, boolean, boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
-
- getNonStandardBasesColor() - Method in class fr.orsay.lri.varna.VARNAPanel
-
Returns the color used to draw non-standard bases
- getNumPeriod() - Method in class fr.orsay.lri.varna.VARNAPanel
-
Returns the current numbering period.
- 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.VARNAPanel
-
- 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
- getRealCoords() - Method in class fr.orsay.lri.varna.VARNAPanel
-
Returns the coordinates of the currently displayed RNA
- getRNA() - Method in class fr.orsay.lri.varna.VARNAPanel
-
Returns the current RNA model
- getSelection() - Method in class fr.orsay.lri.varna.VARNAPanel
-
- getSelectionIndices() - Method in class fr.orsay.lri.varna.VARNAPanel
-
- 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
- getSpaceBetweenBases() - Method in class fr.orsay.lri.varna.VARNAPanel
-
- 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.
- getTopOffset() - Method in class fr.orsay.lri.varna.VARNAPanel
-
Returns the "real pixels" y-coordinate of the RNA.
- getTranslation() - Method in class fr.orsay.lri.varna.VARNAPanel
-
Returns the translation used for zooming in and out
- getUseBaseColorsForBPs() - Method in class fr.orsay.lri.varna.VARNAPanel
-
Returns true if current base color is used as inner color for drawing
base-pairs
- getVARNAUI() - Method in class fr.orsay.lri.varna.VARNAPanel
-
Returns the view associated with user interactions
- getViewClip() - Method in class fr.orsay.lri.varna.VARNAPanel
-
- getZoom() - Method in class fr.orsay.lri.varna.VARNAPanel
-
Returns the current zoom factor
- getZoomedInTranslationBox() - Method in class fr.orsay.lri.varna.VARNAPanel
-
- getZoomIncrement() - Method in class fr.orsay.lri.varna.VARNAPanel
-
Returns the atomic zoom factor step, or increment.
- globalRescale(double) - Method in class fr.orsay.lri.varna.VARNAPanel
-
- globalRotation(Double) - Method in class fr.orsay.lri.varna.VARNAPanel
-
Rotates the RNA coordinates by a certain angle
- 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
-
- setDrawOutlineBases(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
- setFillBases(boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
-
- 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
- setSpaceBetweenBases(double) - Method in class fr.orsay.lri.varna.VARNAPanel
-
- 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
-