- get_selectedAnnotation() - Method in class fr.orsay.lri.varna.VARNAPanel
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- getBackboneColor() - Method in class fr.orsay.lri.varna.VARNAPanel
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Returns the color used to draw backbone bounds.
- getBaseAt(Point2D.Double) - Method in class fr.orsay.lri.varna.VARNAPanel
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- getBasesInRectangle(Rectangle) - Method in class fr.orsay.lri.varna.VARNAPanel
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- getBasesInRectangleDiff(Rectangle, Rectangle) - Method in class fr.orsay.lri.varna.VARNAPanel
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- getBondColor() - Method in class fr.orsay.lri.varna.VARNAPanel
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Returns the color used to display hydrogen bonds (base pairings)
- getBorderSize() - Method in class fr.orsay.lri.varna.VARNAPanel
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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
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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
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Returns the base-pair representation style
- getColorGapsBases() - Method in class fr.orsay.lri.varna.VARNAPanel
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Returns true if a special color is used for drawing "Gaps" bases in
comparison mode
- getColorMap() - Method in class fr.orsay.lri.varna.VARNAPanel
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- getColorMapCaption() - Method in class fr.orsay.lri.varna.VARNAPanel
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- getColorMapVisible() - Method in class fr.orsay.lri.varna.VARNAPanel
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- getColorSpecialBases() - Method in class fr.orsay.lri.varna.VARNAPanel
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Returns true if a special color is used as inner color for non-standard
base
- getConfig() - Method in class fr.orsay.lri.varna.VARNAPanel
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Returns the current VARNA Panel configuration.
- getDrawBackbone() - Method in class fr.orsay.lri.varna.VARNAPanel
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- getDrawMode() - Method in class fr.orsay.lri.varna.VARNAPanel
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Returns the current algorithm used for drawing the structure
- getExtendedRNABBox() - Method in class fr.orsay.lri.varna.VARNAPanel
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- getFlatExteriorLoop() - Method in class fr.orsay.lri.varna.VARNAPanel
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- getGapsBasesColor() - Method in class fr.orsay.lri.varna.VARNAPanel
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Returns the color used to draw 'Gaps' bases in comparison mode
- getInnerHeight() - Method in class fr.orsay.lri.varna.VARNAPanel
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Returns the "real pixels" height of the drawing surface for our RNA.
- getInnerWidth() - Method in class fr.orsay.lri.varna.VARNAPanel
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Returns the "real pixels" width of the drawing surface for our RNA.
- getLastSelectedPosition() - Method in class fr.orsay.lri.varna.VARNAPanel
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- getLeftOffset() - Method in class fr.orsay.lri.varna.VARNAPanel
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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
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- getNearestBase() - Method in class fr.orsay.lri.varna.VARNAPanel
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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
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- getNearestBase(int, int) - Method in class fr.orsay.lri.varna.VARNAPanel
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- getNearestBaseIndex(int, int, boolean, boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
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- getNonStandardBasesColor() - Method in class fr.orsay.lri.varna.VARNAPanel
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Returns the color used to draw non-standard bases
- getNumPeriod() - Method in class fr.orsay.lri.varna.VARNAPanel
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Returns the current numbering period.
- getOffsetPanel() - Method in class fr.orsay.lri.varna.VARNAPanel
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Returns the shifting of the origin of the Panel in zoom mode
- getOrientation() - Method in class fr.orsay.lri.varna.VARNAPanel
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- getPopup() - Method in class fr.orsay.lri.varna.VARNAPanel
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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
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- getSelectionIndices() - Method in class fr.orsay.lri.varna.VARNAPanel
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- getShowNonCanonicalBP() - Method in class fr.orsay.lri.varna.VARNAPanel
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Return the current display status for non-canonical base-pairs
- getShowNonPlanarBP() - Method in class fr.orsay.lri.varna.VARNAPanel
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Return the current display status for non-planar base-pairs
- getShowWarnings() - Method in class fr.orsay.lri.varna.VARNAPanel
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Get current warning display status
- 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
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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
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Returns the view associated with user interactions
- getViewClip() - Method in class fr.orsay.lri.varna.VARNAPanel
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- getZoom() - Method in class fr.orsay.lri.varna.VARNAPanel
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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
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Rotates the RNA coordinates by a certain angle