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G

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
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
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