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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.
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.
getBPHeightIncrement()
- Method in class fr.orsay.lri.varna.
VARNAPanel
For the LINE_MODE drawing algorithm, sets the base pair height increment, i.e.
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
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.
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
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.
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
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
getRNAOffset()
- Method in class fr.orsay.lri.varna.
VARNAPanel
Returns the vector bringing the logical coordinate of left-top-most point in the panel to the left-top-most point of the RNA.
getScaleFactor()
- Method in class fr.orsay.lri.varna.
VARNAPanel
Gets the scale factor used by the autofitting function
getSelectedBase()
- Method in class fr.orsay.lri.varna.
VARNAPanel
Returns the currently selected base, obtained through a mouse-left click
getSelectedBaseIndex()
- Method in class fr.orsay.lri.varna.
VARNAPanel
Returns the currently selected base index, obtained through a mouse-left click
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
getZoom()
- Method in class fr.orsay.lri.varna.
VARNAPanel
Returns the current zoom factor
getZoomIncrement()
- Method in class fr.orsay.lri.varna.
VARNAPanel
Returns the atomic zoom factor step, or increment.
globalRotation(Double)
- Method in class fr.orsay.lri.varna.
VARNAPanel
Rotates the RNA coordinates by a certain angle
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