A C D E F G H I L P R S T U V X _ 

A

addAnnotation(TextAnnotation) - Method in class fr.orsay.lri.varna.VARNAPanel
 
addHighlightRegion(HighlightRegionAnnotation) - Method in class fr.orsay.lri.varna.VARNAPanel
 
addHighlightRegion(int, int) - Method in class fr.orsay.lri.varna.VARNAPanel
 
addHighlightRegion(int, int, Color, Color, double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
addRNAListener(InterfaceVARNARNAListener) - Method in class fr.orsay.lri.varna.VARNAPanel
 
addSelectionListener(InterfaceVARNASelectionListener) - Method in class fr.orsay.lri.varna.VARNAPanel
 
addToSelection(Collection<? extends Integer>) - Method in class fr.orsay.lri.varna.VARNAPanel
 
addToSelection(int) - Method in class fr.orsay.lri.varna.VARNAPanel
 
addVARNABasesListener(InterfaceVARNABasesListener) - Method in class fr.orsay.lri.varna.VARNAPanel
 
addVARNAListener(InterfaceVARNAListener) - Method in class fr.orsay.lri.varna.VARNAPanel
 

C

centerViewOn(double, double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
checkTranslation() - Method in class fr.orsay.lri.varna.VARNAPanel
Checks if the current translation doesn't "kick" the whole RNA out of the panel, and corrects the situation if necessary.
clearSelection() - Method in class fr.orsay.lri.varna.VARNAPanel
Stops highlighting bases

D

DISTANCE_FACT - Static variable in class fr.orsay.lri.varna.VARNAPanel
 
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.

E

emitWarning(String) - Method in class fr.orsay.lri.varna.VARNAPanel
Displays a warning message through a modal dialog if warnings are set to be displayed.
emitWarningStatic(Exception, Component) - Static method in class fr.orsay.lri.varna.VARNAPanel
 
emitWarningStatic(String, Component) - Static method in class fr.orsay.lri.varna.VARNAPanel
 
eraseSequence() - Method in class fr.orsay.lri.varna.VARNAPanel
 
errorDialog(Exception) - Method in class fr.orsay.lri.varna.VARNAPanel
Pops up an error Dialog displaying an exception in an human-readable way.
errorDialog(Exception, Component) - Method in class fr.orsay.lri.varna.VARNAPanel
Pops up an error Dialog displaying an exception in an human-readable way if errors are set to be displayed.
errorDialogStatic(Exception, Component) - Static method in class fr.orsay.lri.varna.VARNAPanel
Pops up an error Dialog displaying an exception in an human-readable way.

F

fireBaseClicked(ModeleBase, MouseEvent) - Method in class fr.orsay.lri.varna.VARNAPanel
 
fireHoverChanged(ModeleBase, ModeleBase) - Method in class fr.orsay.lri.varna.VARNAPanel
 
fireLayoutChanged() - Method in class fr.orsay.lri.varna.VARNAPanel
 
fireLayoutChanged(Hashtable<Integer, Point2D.Double>) - Method in class fr.orsay.lri.varna.VARNAPanel
 
fireSelectionChanged(BaseList, BaseList) - Method in class fr.orsay.lri.varna.VARNAPanel
 
fireSequenceChanged(int, String, String) - Method in class fr.orsay.lri.varna.VARNAPanel
 
fireStructureChanged(Set<ModeleBP>, Set<ModeleBP>, Set<ModeleBP>) - Method in class fr.orsay.lri.varna.VARNAPanel
 
fireTranslationChanged() - Method in class fr.orsay.lri.varna.VARNAPanel
 
fireUINewStructure(RNA) - Method in class fr.orsay.lri.varna.VARNAPanel
 
fireZoomLevelChanged(double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
fr.orsay.lri.varna - package fr.orsay.lri.varna
 

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.
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
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

H

highlightSelectedAnnotation() - Method in class fr.orsay.lri.varna.VARNAPanel
 
highlightSelectedBase(ModeleBase) - Method in class fr.orsay.lri.varna.VARNAPanel
Starts highlighting the selected base.
highlightSelectedStem(ModeleBase) - Method in class fr.orsay.lri.varna.VARNAPanel
Starts highlighting the selected base.

I

importSession(String) - Static method in class fr.orsay.lri.varna.VARNAPanel
 
importSession(InputStream, String) - Static method in class fr.orsay.lri.varna.VARNAPanel
 
isAutoCentered() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns the current state of auto centering mode.
isComparisonMode() - Method in class fr.orsay.lri.varna.VARNAPanel
Checks if the current mode is the "comparison" mode
isErrorsOn() - Method in class fr.orsay.lri.varna.VARNAPanel
Checks whether errors are to be displayed
isInSelection(int) - Method in class fr.orsay.lri.varna.VARNAPanel
 
isInterpolationInProgress() - Method in class fr.orsay.lri.varna.VARNAPanel
Checks whether an interpolated transition bewteen two RNAs is occurring.
isModifiable() - Method in class fr.orsay.lri.varna.VARNAPanel
Returns current modification status
isOutOfFrame() - Method in class fr.orsay.lri.varna.VARNAPanel
Checks whether the drawn RNA is too large to be displayed, allowing for shifting mouse interactions.

L

loadFile(String) - Method in class fr.orsay.lri.varna.VARNAPanel
 
loadFile(String, boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
 
loadRNA(String) - Method in class fr.orsay.lri.varna.VARNAPanel
 
loadRNA(String, boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
 
loadSession(String) - Method in class fr.orsay.lri.varna.VARNAPanel
 
lockScrolling() - Method in class fr.orsay.lri.varna.VARNAPanel
 
logicToPanel(Point2D.Double) - Method in class fr.orsay.lri.varna.VARNAPanel
 

P

paintComponent(Graphics) - Method in class fr.orsay.lri.varna.VARNAPanel
 
paintComponent(Graphics, boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
 
panelToLogicPoint(Point2D.Double) - Method in class fr.orsay.lri.varna.VARNAPanel
 

R

readValues(Reader) - Method in class fr.orsay.lri.varna.VARNAPanel
 
redo() - Method in class fr.orsay.lri.varna.VARNAPanel
 
removeAnnotation(TextAnnotation) - Method in class fr.orsay.lri.varna.VARNAPanel
 
removeColorMap() - Method in class fr.orsay.lri.varna.VARNAPanel
 
removeFromSelection(int) - Method in class fr.orsay.lri.varna.VARNAPanel
 
removeHighlightRegion(HighlightRegionAnnotation) - Method in class fr.orsay.lri.varna.VARNAPanel
 
removeLink() - Method in class fr.orsay.lri.varna.VARNAPanel
 
removeSelectedAnnotation() - Method in class fr.orsay.lri.varna.VARNAPanel
 
removeSelectionRectangle() - Method in class fr.orsay.lri.varna.VARNAPanel
 
renderComponent(VueVARNAGraphics, boolean, double) - Method in class fr.orsay.lri.varna.VARNAPanel
Draws current RNA structure in a given Graphics "device".
renderRNA(VueVARNAGraphics, Rectangle2D.Double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
renderRNA(VueVARNAGraphics, Rectangle2D.Double, boolean, boolean) - Method in class fr.orsay.lri.varna.VARNAPanel
 
reset() - Method in class fr.orsay.lri.varna.VARNAPanel
Resets the visual aspects (Zoom factor, shift) for the Panel.
resetAnnotationHighlight() - Method in class fr.orsay.lri.varna.VARNAPanel
Stops highlighting bases
resetListeAnnotations() - Method in class fr.orsay.lri.varna.VARNAPanel
 
restoreSelection() - Method in class fr.orsay.lri.varna.VARNAPanel
 

S

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.
setBPHeightIncrement(double) - Method in class fr.orsay.lri.varna.VARNAPanel
Sets the base pair height increment, i.e.
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
 

T

toggleDrawOutlineBases() - Method in class fr.orsay.lri.varna.VARNAPanel
 
toggleFillBases() - Method in class fr.orsay.lri.varna.VARNAPanel
 
toggleSelection(int) - Method in class fr.orsay.lri.varna.VARNAPanel
 
toggleSelection(Collection<? extends Integer>) - Method in class fr.orsay.lri.varna.VARNAPanel
 
toXML(String) - Method in class fr.orsay.lri.varna.VARNAPanel
 
toXML(PrintWriter) - Method in class fr.orsay.lri.varna.VARNAPanel
 
toXML(TransformerHandler) - Method in class fr.orsay.lri.varna.VARNAPanel
 
transformCoord(Point2D.Double, double, double, double, double, double) - Method in class fr.orsay.lri.varna.VARNAPanel
 
transformCoord(Point2D.Double) - Method in class fr.orsay.lri.varna.VARNAPanel
 

U

undo() - Method in class fr.orsay.lri.varna.VARNAPanel
 
unlockScrolling() - Method in class fr.orsay.lri.varna.VARNAPanel
 

V

VARNA_SESSION_EXTENSION - Static variable in class fr.orsay.lri.varna.VARNAPanel
 
VARNAPanel - Class in fr.orsay.lri.varna
The RNA 2D Panel is a lightweight component that allows for an automatic basic drawing of an RNA secondary structures.
VARNAPanel() - Constructor for class fr.orsay.lri.varna.VARNAPanel
Creates an RNA 2D panel with initially displays the empty structure.
VARNAPanel(String, String) - Constructor for class fr.orsay.lri.varna.VARNAPanel
Creates an RNA 2D panel, and creates and displays an RNA coupled with its secondary structure formatted as a well-balanced parenthesis with dots word (DBN format).
VARNAPanel(String, String, int) - Constructor for class fr.orsay.lri.varna.VARNAPanel
Creates a VARNAPanel instance, and creates and displays an RNA coupled with its secondary structure formatted as a well-balanced parenthesis with dots word (DBN format).
VARNAPanel(Reader) - Constructor for class fr.orsay.lri.varna.VARNAPanel
 
VARNAPanel(Reader, int) - Constructor for class fr.orsay.lri.varna.VARNAPanel
 
VARNAPanel(Reader, int, String) - Constructor for class fr.orsay.lri.varna.VARNAPanel
 
VARNAPanel(RNA) - Constructor for class fr.orsay.lri.varna.VARNAPanel
Creates a VARNAPanel instance, and displays an RNA.
VARNAPanel(String, String, int, String) - Constructor for class fr.orsay.lri.varna.VARNAPanel
Creates a VARNAPanel instance, and creates and displays an RNA coupled with its secondary structure formatted as a well-balanced parenthesis with dots word (DBN format).
VARNAPanel(String, String, String, String, int, String) - Constructor for class fr.orsay.lri.varna.VARNAPanel
 

X

XML_ELEMENT_NAME - Static variable in class fr.orsay.lri.varna.VARNAPanel
 

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_hoveredBase - Variable in class fr.orsay.lri.varna.VARNAPanel
 
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