VARNAPanel

java.lang.Object
- java.awt.Component
- - java.awt.Container
  - - javax.swing.JComponent
    - - javax.swing.JPanel
      - fr.orsay.lri.varna.VARNAPanel

All Implemented Interfaces:

ImageObserver, MenuContainer, Serializable, Accessible
```
public class VARNAPanel
extends JPanel
```
The RNA 2D Panel is a lightweight component that allows for an automatic basic drawing of an RNA secondary structures. The drawing algorithms do not ensure a non-overlapping drawing of helices, thus it is possible to "spin the helices" through a click-and-drag approach. A typical usage of the class from within the constructor of a JFrame would be the following:
VARNAPanel _rna = new VARNAPanel("CCCCAUAUGGGGACC","((((....))))..."); this.getContentPane().add(_rna);

Version:

3.4

Author:

Yann Ponty & Kevin Darty

See Also:
Serialized Form

Nested Class Summary
- Nested classes/interfaces inherited from class javax.swing.JPanel
  JPanel.AccessibleJPanel
- Nested classes/interfaces inherited from class javax.swing.JComponent
  JComponent.AccessibleJComponent
- Nested classes/interfaces inherited from class java.awt.Container
  Container.AccessibleAWTContainer
- Nested classes/interfaces inherited from class java.awt.Component
  Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy

Field Summary

Fields
Modifier and Type	Field and Description
`fr.orsay.lri.varna.models.rna.ModeleBase`	`_hoveredBase`
`(package private) UndoManager`	`_manager`
`(package private) Point2D.Double`	`_target`
`(package private) Point2D.Double`	`_target2`
`static String`	`VARNA_SESSION_EXTENSION`
`static String`	`XML_ELEMENT_NAME`

Fields inherited from class javax.swing.JComponent
accessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW

Fields inherited from class java.awt.Component
BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

Constructors
Constructor and Description
`VARNAPanel()` Creates an RNA 2D panel with initially displays the empty structure.
`VARNAPanel(Reader r)`
`VARNAPanel(Reader r, int drawMode)`
`VARNAPanel(Reader r, int drawMode, String title)`
`VARNAPanel(fr.orsay.lri.varna.models.rna.RNA r)` Creates a VARNAPanel instance, and displays an RNA.
`VARNAPanel(String seq, String str)` 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 seq, String str, int drawMode)` 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 seq, String str, int drawMode, String title)` 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 seq1, String struct1, String seq2, String struct2, int drawMode, String title)`

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`addAnnotation(fr.orsay.lri.varna.models.annotations.TextAnnotation textAnnotation)`
`void`	`addHighlightRegion(fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation n)`
`void`	`addHighlightRegion(int i, int j)`
`void`	`addHighlightRegion(int i, int j, Color fill, Color outline, double radius)`
`void`	`addRNAListener(fr.orsay.lri.varna.interfaces.InterfaceVARNARNAListener v)`
`void`	`addSelectionListener(fr.orsay.lri.varna.interfaces.InterfaceVARNASelectionListener v)`
`void`	`addToSelection(Collection<? extends Integer> indices)`
`void`	`addToSelection(int i)`
`void`	`addVARNABasesListener(fr.orsay.lri.varna.interfaces.InterfaceVARNABasesListener l)`
`void`	`addVARNAListener(fr.orsay.lri.varna.interfaces.InterfaceVARNAListener v)`
`(package private) Point2D.Double`	`buildCaptionPosition(fr.orsay.lri.varna.models.rna.ModeleBase mb, double scaleFactor, double heightEstimate)`
`void`	`centerViewOn(double x, double y)`
`void`	`checkTranslation()` Checks if the current translation doesn't "kick" the whole RNA out of the panel, and corrects the situation if necessary.
`void`	`clearSelection()` Stops highlighting bases
`void`	`drawBackbone(fr.orsay.lri.varna.models.export.VueVARNAGraphics g2D, Point2D.Double[] newCoords, double newRadius, double _scaleFactor)`
`void`	`drawBBox(boolean on)` Toggles on/off a rectangular outline of the bounding box.
`void`	`drawBorder(boolean on)` Toggles on/off a rectangular outline of the border.
`(package private) void`	`drawChemProbAnnotation(fr.orsay.lri.varna.models.export.VueVARNAGraphics g2D, fr.orsay.lri.varna.models.annotations.ChemProbAnnotation cpa, Point2D.Double anchor, double scaleFactor)`
`void`	`drawColorMap(boolean draw)`
`void`	`drawRegionHighlightsAnnotation(fr.orsay.lri.varna.models.export.VueVARNAGraphics g2D, Point2D.Double[] realCoords, Point2D.Double[] realCenters, double scaleFactor)`
`void`	`drawRNA()` Redraws the current RNA.
`void`	`drawRNA(Reader r, int drawMode)`
`void`	`drawRNA(fr.orsay.lri.varna.models.rna.RNA r)` Sets the RNA secondary structure to be drawn in this panel, using the current drawing algorithm.
`void`	`drawRNA(fr.orsay.lri.varna.models.rna.RNA r, int drawMode)` Sets the RNA secondary structure to be drawn in this panel, using a given layout algorithm.
`void`	`drawRNA(String seq, String str)` Sets the RNA secondary structure to be drawn in this panel, using the default layout algorithm.
`void`	`drawRNA(String seq, String str, int drawMode)` Sets the RNA secondary structure to be drawn in this panel, using a given layout algorithm.
`void`	`drawRNA(String firstSeq, String firstStruct, String secondSeq, String secondStruct, int drawMode)` When comparison mode is ON, sets the two RNA secondary structure to be drawn in this panel, using a given layout algorithm.
`void`	`drawRNAInterpolated(fr.orsay.lri.varna.models.rna.RNA target)` 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.
`void`	`drawRNAInterpolated(fr.orsay.lri.varna.models.rna.RNA target, int drawMode, fr.orsay.lri.varna.models.rna.Mapping m)` 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.
`void`	`drawRNAInterpolated(fr.orsay.lri.varna.models.rna.RNA target, fr.orsay.lri.varna.models.rna.Mapping m)` 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.
`void`	`drawRNAInterpolated(String seq, String str)` 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.
`void`	`drawRNAInterpolated(String seq, String str, int drawMode)` 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.
`void`	`drawRNAInterpolated(String seq, String str, int drawMode, fr.orsay.lri.varna.models.rna.Mapping m)` 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.
`void`	`drawRNAInterpolated(String seq, String str, fr.orsay.lri.varna.models.rna.Mapping m)` 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.
`void`	`emitWarning(String warning)` Displays a warning message through a modal dialog if warnings are set to be displayed.
`void`	`eraseSequence()`
`void`	`errorDialog(Exception error)` Pops up an error Dialog displaying an exception in an human-readable way.
`void`	`errorDialog(Exception error, Component c)` Pops up an error Dialog displaying an exception in an human-readable way if errors are set to be displayed.
`static void`	`errorDialogStatic(Exception error, Component c)` Pops up an error Dialog displaying an exception in an human-readable way.
`void`	`fireBaseClicked(fr.orsay.lri.varna.models.rna.ModeleBase mb, MouseEvent me)`
`void`	`fireHoverChanged(fr.orsay.lri.varna.models.rna.ModeleBase mold, fr.orsay.lri.varna.models.rna.ModeleBase mnew)`
`void`	`fireLayoutChanged()`
`void`	`fireLayoutChanged(Hashtable<Integer,Point2D.Double> movedPositions)`
`void`	`fireSelectionChanged(fr.orsay.lri.varna.models.BaseList mold, fr.orsay.lri.varna.models.BaseList mnew)`
`void`	`fireSequenceChanged(int index, String oldseq, String newseq)`
`void`	`fireStructureChanged(Set<fr.orsay.lri.varna.models.rna.ModeleBP> current, Set<fr.orsay.lri.varna.models.rna.ModeleBP> addedBasePairs, Set<fr.orsay.lri.varna.models.rna.ModeleBP> removedBasePairs)`
`void`	`fireTranslationChanged()`
`void`	`fireUINewStructure(fr.orsay.lri.varna.models.rna.RNA r)`
`void`	`fireZoomLevelChanged(double d)`
`fr.orsay.lri.varna.models.annotations.TextAnnotation`	`get_selectedAnnotation()`
`Color`	`getBackboneColor()` Returns the color used to draw backbone bounds.
`fr.orsay.lri.varna.models.rna.ModeleBase`	`getBaseAt(Point2D.Double po)`
`ArrayList<Integer>`	`getBasesInRectangle(Rectangle rec)`
`ArrayList<Integer>`	`getBasesInRectangleDiff(Rectangle recIn, Rectangle recOut)`
`Color`	`getBondColor()` Returns the color used to display hydrogen bonds (base pairings)
`Dimension`	`getBorderSize()` Returns the size of the border, i.e. the empty space between the end of the drawing area
`double`	`getBPHeightIncrement()` For the LINE_MODE drawing algorithm, sets the base pair height increment, i.e. the vertical distance between two nested arcs.
`fr.orsay.lri.varna.models.VARNAConfig.BP_STYLE`	`getBPStyle()` Returns the base-pair representation style
`boolean`	`getColorGapsBases()` Returns true if a special color is used for drawing "Gaps" bases in comparison mode
`fr.orsay.lri.varna.models.rna.ModeleColorMap`	`getColorMap()`
`String`	`getColorMapCaption()`
`boolean`	`getColorMapVisible()`
`boolean`	`getColorSpecialBases()` Returns true if a special color is used as inner color for non-standard base
`fr.orsay.lri.varna.models.VARNAConfig`	`getConfig()` Returns the current VARNA Panel configuration.
`boolean`	`getDrawBackbone()`
`int`	`getDrawMode()` Returns the current algorithm used for drawing the structure
`Rectangle2D.Double`	`getExtendedRNABBox()`
`boolean`	`getFlatExteriorLoop()`
`Color`	`getGapsBasesColor()` Returns the color used to draw 'Gaps' bases in comparison mode
`int`	`getInnerHeight()` Returns the "real pixels" height of the drawing surface for our RNA.
`int`	`getInnerWidth()` Returns the "real pixels" width of the drawing surface for our RNA.
`Point2D.Double`	`getLastSelectedPosition()`
`int`	`getLeftOffset()` Returns the "real pixels" x-coordinate of the RNA.
`ArrayList<fr.orsay.lri.varna.models.annotations.TextAnnotation>`	`getListeAnnotations()`
`fr.orsay.lri.varna.models.annotations.TextAnnotation`	`getNearestAnnotation(int x, int y)`
`Integer`	`getNearestBase()` Returns the index of the currently selected base, defaulting to the closest base to the last mouse-click.
`fr.orsay.lri.varna.models.rna.ModeleBase`	`getNearestBase(int x, int y)`
`fr.orsay.lri.varna.models.rna.ModeleBase`	`getNearestBase(int x, int y, boolean always, boolean onlyPaired)`
`int`	`getNearestBaseIndex(int x, int y, boolean always, boolean onlyPaired)`
`Color`	`getNonStandardBasesColor()` Returns the color used to draw non-standard bases
`int`	`getNumPeriod()` Returns the current numbering period.
`Point2D.Double`	`getOffsetPanel()` Returns the shifting of the origin of the Panel in zoom mode
`double`	`getOrientation()`
`fr.orsay.lri.varna.views.VueMenu`	`getPopup()` Returns the popup menu used for user mouse iteractions
`fr.orsay.lri.varna.views.VueMenu`	`getPopupMenu()` Returns this panel's UI menu
`Point2D.Double[]`	`getRealCoords()` Returns the coordinates of the currently displayed RNA
`fr.orsay.lri.varna.models.rna.RNA`	`getRNA()` Returns the current RNA model
`fr.orsay.lri.varna.models.BaseList`	`getSelection()`
`ArrayList<Integer>`	`getSelectionIndices()`
`boolean`	`getShowNonCanonicalBP()` Return the current display status for non-canonical base-pairs
`boolean`	`getShowNonPlanarBP()` Return the current display status for non-planar base-pairs
`boolean`	`getShowWarnings()` Get current warning display status
`String`	`getTitle()` Returns the title of this panel
`Color`	`getTitleColor()` Returns the color used to draw the title
`Font`	`getTitleFont()` Returns the font currently used for rendering the title.
`int`	`getTopOffset()` Returns the "real pixels" y-coordinate of the RNA.
`Point`	`getTranslation()` Returns the translation used for zooming in and out
`boolean`	`getUseBaseColorsForBPs()` Returns true if current base color is used as inner color for drawing base-pairs
`fr.orsay.lri.varna.views.VueUI`	`getVARNAUI()` Returns the view associated with user interactions
`Rectangle2D.Double`	`getViewClip()`
`double`	`getZoom()` Returns the current zoom factor
`Rectangle`	`getZoomedInTranslationBox()`
`double`	`getZoomIncrement()` Returns the atomic zoom factor step, or increment.
`void`	`globalRescale(double factor)`
`void`	`globalRotation(Double angleDegres)` Rotates the RNA coordinates by a certain angle
`void`	`highlightSelectedAnnotation()`
`void`	`highlightSelectedBase(fr.orsay.lri.varna.models.rna.ModeleBase m)` Starts highlighting the selected base.
`void`	`highlightSelectedStem(fr.orsay.lri.varna.models.rna.ModeleBase m)` Starts highlighting the selected base.
`static fr.orsay.lri.varna.models.FullBackup`	`importSession(InputStream fis, String path)`
`static fr.orsay.lri.varna.models.FullBackup`	`importSession(String path)`
`boolean`	`isAutoCentered()` Returns the current state of auto centering mode.
`boolean`	`isComparisonMode()` Checks if the current mode is the "comparison" mode
`boolean`	`isErrorsOn()` Checks whether errors are to be displayed
`boolean`	`isInSelection(int i)`
`boolean`	`isInterpolationInProgress()` Checks whether an interpolated transition bewteen two RNAs is occurring.
`boolean`	`isModifiable()` Returns current modification status
`boolean`	`isOutOfFrame()` Checks whether the drawn RNA is too large to be displayed, allowing for shifting mouse interactions.
`void`	`loadFile(String path)`
`void`	`loadFile(String path, boolean interpolate)`
`fr.orsay.lri.varna.models.FullBackup`	`loadSession(String path)`
`void`	`lockScrolling()`
`Point2D.Double`	`logicToPanel(Point2D.Double logicPoint)`
`void`	`paintComponent(Graphics g)`
`void`	`paintComponent(Graphics g, boolean transparentBackground)`
`Point2D.Double`	`panelToLogicPoint(Point2D.Double p)`
`void`	`readValues(Reader r)`
`void`	`redo()`
`boolean`	`removeAnnotation(fr.orsay.lri.varna.models.annotations.TextAnnotation textAnnotation)`
`void`	`removeColorMap()`
`void`	`removeFromSelection(int i)`
`void`	`removeHighlightRegion(fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation n)`
`void`	`removeLink()`
`void`	`removeSelectedAnnotation()`
`void`	`removeSelectionRectangle()`
`void`	`renderComponent(fr.orsay.lri.varna.models.export.VueVARNAGraphics g2D, boolean transparentBackground, double scaleFactor)` Draws current RNA structure in a given Graphics "device".
`Rectangle2D.Double`	`renderRNA(fr.orsay.lri.varna.models.export.VueVARNAGraphics g2D, Rectangle2D.Double bbox)`
`Rectangle2D.Double`	`renderRNA(fr.orsay.lri.varna.models.export.VueVARNAGraphics g2D, Rectangle2D.Double bbox, boolean localView, boolean autoCenter)`
`void`	`reset()` Resets the visual aspects (Zoom factor, shift) for the Panel.
`void`	`resetAnnotationHighlight()` Stops highlighting bases
`void`	`resetListeAnnotations()`
`void`	`restoreSelection()`
`void`	`saveSelection()`
`void`	`saveSession(String path)`
`void`	`set_selectedAnnotation(fr.orsay.lri.varna.models.annotations.TextAnnotation annotation)`
`void`	`setAutoCenter(boolean center)` Sets the current state of auto centering mode.
`void`	`setBackboneColor(Color backbone_color)` Sets the color to be used for drawing backbone interactions.
`void`	`setBackground(Color c)` Sets the background color
`void`	`setBaseFontSize(Float size)` Sets the font size for displaying bases
`void`	`setBaseFontStyle(int style)` Sets the font style for displaying bases
`void`	`setBaseInnerColor(Color c)`
`void`	`setBaseNameColor(Color c)`
`void`	`setBaseNumbersColor(Color c)`
`void`	`setBaseOutlineColor(Color c)`
`void`	`setBondColor(Color bond_color)` Sets the color used to display hydrogen bonds (base pairings)
`void`	`setBorderSize(Dimension b)` Sets the size of the border, i.e. the empty space between the end of the drawing area and the actual border.
`void`	`setBPHeightIncrement(double inc)` Sets the base pair height increment, i.e. the vertical distance between two arcs to be used in LINE_MODE.
`void`	`setBPStyle(fr.orsay.lri.varna.models.VARNAConfig.BP_STYLE st)` Sets the base-pair representation style
`void`	`setColorGapsBases(boolean on)` Toggles on/off using a special color used for drawing "Gaps" bases in comparison mode
`void`	`setColorMap(fr.orsay.lri.varna.models.rna.ModeleColorMap cm)`
`void`	`setColorMapCaption(String caption)`
`void`	`setColorMapMaxValue(double d)`
`void`	`setColorMapMinValue(double d)`
`void`	`setColorMapValues(Double[] values)`
`void`	`setColorMapVisible(boolean b)`
`void`	`setColorNonStandardBases(boolean on)` Toggles on/off using a special color used for drawing "non-standard" bases
`void`	`setConfig(fr.orsay.lri.varna.models.VARNAConfig cfg)`
`void`	`setDefaultBPColor(Color bond_color)` Sets the new color to be used for hydrogen bonds (base pairings)
`void`	`setDestinationLink(Point2D.Double p)`
`void`	`setDrawBackbone(boolean b)`
`void`	`setErrorsOn(boolean on)` Sets whether errors are to be displayed
`void`	`setFlatExteriorLoop(boolean on)`
`void`	`setGapsBasesColor(Color c)` Sets the color to use for 'Gaps' bases in comparison mode
`void`	`setHoverBase(fr.orsay.lri.varna.models.rna.ModeleBase m)`
`void`	`setLastSelectedPosition(Point2D.Double p)`
`void`	`setModifiable(boolean modifiable)` Toggles modifications on and off
`void`	`setNearestBase(Integer base)` Sets the index of the currently selected base.
`void`	`setNonStandardBasesColor(Color basesColor)` Sets the color used to draw non-standard bases
`void`	`setNumbersFontSize(Float size)` Sets the font size for displaying base numbers
`void`	`setNumPeriod(int n)` Sets the distance between consecutive base numbers.
`void`	`setOriginLink(Point2D.Double p)`
`void`	`setRealCoords(Point2D.Double[] coords)` Sets the coordinates of the currently displayed RNA
`void`	`setSelection(ArrayList<Integer> indices)`
`void`	`setSelection(Collection<? extends fr.orsay.lri.varna.models.rna.ModeleBase> mbs)`
`void`	`setSelectionRectangle(Rectangle rec)`
`void`	`setSequence(String s)`
`void`	`setShowNonCanonicalBP(boolean on)` Toggles on/off displaying non-canonical base-pairs
`void`	`setShowNonPlanarBP(boolean on)` Toggles on/off displaying "non-planar" base-pairs
`void`	`setShowWarnings(boolean on)` Toggles on/off displaying warnings
`void`	`setTitle(String title)` Sets the panel's title, giving a short description of the RNA secondary structure.
`void`	`setTitleColor(Color title_color)` Sets the color used to draw the title
`void`	`setTitleFont(Font font)` Sets the font used for rendering the title.
`void`	`setTitleFontColor(Color newColor)` Sets the color to be used for the title.
`void`	`setTitleFontFamily(String newFamily)` Sets the new font family to be used for the title.
`void`	`setTitleFontSize(float newSize)` Sets the new size of the title font.
`void`	`setTitleFontStyle(int newStyle)` Sets the new style of the title font.
`void`	`setTranslation(Point trans)` Sets the translation used for zooming in and out
`void`	`setUseBaseColorsForBPs(boolean on)` Toggles on/off using base inner color for drawing base-pairs
`void`	`setZoom(Object _zoom)` Sets the current zoom factor
`void`	`setZoomIncrement(double amount)` Sets the atomic zoom factor step, or increment.
`void`	`setZoomIncrement(Object amount)` Sets the atomic zoom factor step, or increment.
`void`	`showRNA(fr.orsay.lri.varna.models.rna.RNA r)` Sets the RNA to be displayed within this Panel.
`void`	`showRNA(fr.orsay.lri.varna.models.rna.RNA t, fr.orsay.lri.varna.models.VARNAConfig cfg)`
`void`	`showRNAInterpolated(fr.orsay.lri.varna.models.rna.RNA target)` Simply displays (does not redraw) a secondary structure , using an interpolated transition between the previous one and the new one.
`void`	`showRNAInterpolated(fr.orsay.lri.varna.models.rna.RNA target, fr.orsay.lri.varna.models.rna.Mapping m)` Simply displays (does not redraw) a secondary structure , using an interpolated transition between the previous one and the new one.
`void`	`showRNAInterpolated(fr.orsay.lri.varna.models.rna.RNA target, fr.orsay.lri.varna.models.VARNAConfig cfg, fr.orsay.lri.varna.models.rna.Mapping m)`
`void`	`toggleDrawOutlineBase()`
`void`	`toggleFillBase()`
`void`	`toggleSelection(Collection<? extends Integer> indices)`
`void`	`toggleSelection(int i)`
`void`	`toXML(PrintWriter out)`
`void`	`toXML(String path)`
`void`	`toXML(TransformerHandler hd)`
`Point2D.Double`	`transformCoord(Point2D.Double coordDebut)`
`Point2D.Double`	`transformCoord(Point2D.Double coordDebut, double offX, double offY, double rnaBBoxX, double rnaBBoxY, double scaleFactor)`
`void`	`undo()`
`void`	`unlockScrolling()`

Methods inherited from class javax.swing.JPanel
getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI

Methods inherited from class javax.swing.JComponent
addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update

Methods inherited from class java.awt.Container
add, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusDownCycle, validate, validateTree

Methods inherited from class java.awt.Component
action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - _manager
```
UndoManager _manager
```
  - _target
```
Point2D.Double _target
```
  - _target2
```
Point2D.Double _target2
```
  - VARNA_SESSION_EXTENSION
```
public static String VARNA_SESSION_EXTENSION
```
  - _hoveredBase
```
public fr.orsay.lri.varna.models.rna.ModeleBase _hoveredBase
```
  - XML_ELEMENT_NAME
```
public static String XML_ELEMENT_NAME
```
- Constructor Detail
  - VARNAPanel
```
public VARNAPanel()
```
    Creates an RNA 2D panel with initially displays the empty structure.
    
    Throws:
    
    fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength
  - VARNAPanel
```
public VARNAPanel(String seq,
          String str)
           throws fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength
```
    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).
    
    Parameters:
    seq - The raw nucleotide sequence
    str - The secondary structure in DBN format
    
    Throws:
    
    fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength
  - VARNAPanel
```
public VARNAPanel(String seq,
          String str,
          int drawMode)
           throws fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength
```
    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). Allows the user to choose the drawing algorithm to be used.
    
    Parameters:
    seq - The raw nucleotide sequence
    str - The secondary structure in DBN format
    drawMode - The drawing mode
    
    Throws:
    
    fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength
    See Also:
    RNA.DRAW_MODE_RADIATE, RNA.DRAW_MODE_CIRCULAR, RNA.DRAW_MODE_NAVIEW
  - VARNAPanel
```
public VARNAPanel(Reader r)
           throws fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength,
                  fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax
```
    Throws:
    
    fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength
    
    fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax
  - VARNAPanel
```
public VARNAPanel(Reader r,
          int drawMode)
           throws fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength,
                  fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax
```
    Throws:
    
    fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength
    
    fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax
  - VARNAPanel
```
public VARNAPanel(Reader r,
          int drawMode,
          String title)
           throws fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength,
                  fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax
```
    Throws:
    
    fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength
    
    fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax
  - VARNAPanel
```
public VARNAPanel(fr.orsay.lri.varna.models.rna.RNA r)
```
    Creates a VARNAPanel instance, and displays an RNA.
    
    Parameters:
    r - The RNA to be displayed within this panel
  - VARNAPanel
```
public VARNAPanel(String seq,
          String str,
          int drawMode,
          String title)
           throws fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength
```
    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). Allows the user to choose the drawing algorithm to be used. Additionally, sets the panel's title.
    
    Parameters:
    seq - The raw nucleotide sequence
    str - The secondary structure in DBN format
    drawMode - The drawing mode
    title - The panel title
    
    Throws:
    
    fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength
    See Also:
    RNA.DRAW_MODE_CIRCULAR, RNA.DRAW_MODE_RADIATE, RNA.DRAW_MODE_NAVIEW
  - VARNAPanel
```
public VARNAPanel(String seq1,
          String struct1,
          String seq2,
          String struct2,
          int drawMode,
          String title)
```
- Method Detail
  - setOriginLink
```
public void setOriginLink(Point2D.Double p)
```
  - setDestinationLink
```
public void setDestinationLink(Point2D.Double p)
```
  - removeLink
```
public void removeLink()
```
  - undo
```
public void undo()
```
  - redo
```
public void redo()
```
  - setTitleFontStyle
```
public void setTitleFontStyle(int newStyle)
```
    Sets the new style of the title font.
    
    Parameters:
    newStyle - An int that describes the new font style ("PLAIN","BOLD", "BOLDITALIC", or "ITALIC")
  - setTitleFontSize
```
public void setTitleFontSize(float newSize)
```
    Sets the new size of the title font.
    
    Parameters:
    newSize - The new size of the title font
  - setTitleFontFamily
```
public void setTitleFontFamily(String newFamily)
```
    Sets the new font family to be used for the title. Available fonts are system-specific, yet it seems that "Arial", "Dialog", and "MonoSpaced" are almost always available.
    
    Parameters:
    newFamily - New font family used for the title
  - setTitleFontColor
```
public void setTitleFontColor(Color newColor)
```
    Sets the color to be used for the title.
    
    Parameters:
    newColor - A color used to draw the title
  - setBaseFontSize
```
public void setBaseFontSize(Float size)
```
    Sets the font size for displaying bases
    
    Parameters:
    size - Font size for base caption
  - setNumbersFontSize
```
public void setNumbersFontSize(Float size)
```
    Sets the font size for displaying base numbers
    
    Parameters:
    size - Font size for base caption
  - setBaseFontStyle
```
public void setBaseFontStyle(int style)
```
    Sets the font style for displaying bases
    
    Parameters:
    style - An int that describes the new font style ("PLAIN","BOLD", "BOLDITALIC", or "ITALIC")
  - setTitle
```
public void setTitle(String title)
```
    Sets the panel's title, giving a short description of the RNA secondary structure.
    
    Parameters:
    title - The new title
  - setNumPeriod
```
public void setNumPeriod(int n)
```
    Sets the distance between consecutive base numbers. Please notice that :
    - The first and last base are always numbered
    - The numbering is based on the base numbers, not on the indices. So base numbers may appear more frequently than expected if bases are skipped
    - The periodicity is measured starting from 0. This means that for a period of 10 and bases numbered from 1 to 52, the base numbers [1,10,20,30,40,50,52] will be drawn.
    Parameters:
    n - New numbering period
  - getNumPeriod
```
public int getNumPeriod()
```
    Returns the current numbering period. Please notice that :
    - The first and last base are always numbered
    - The numbering is based on the base numbers, not on the indices. So base numbers may appear more frequently than expected if bases are skipped
    - The periodicity is measured starting from 0. This means that for a period of 10 and bases numbered from 1 to 52, the base numbers [1,10,20,30,40,50,52] will be drawn.
    Returns:
    Current numbering period
  - lockScrolling
```
public void lockScrolling()
```
  - unlockScrolling
```
public void unlockScrolling()
```
  - drawChemProbAnnotation
```
void drawChemProbAnnotation(fr.orsay.lri.varna.models.export.VueVARNAGraphics g2D,
                          fr.orsay.lri.varna.models.annotations.ChemProbAnnotation cpa,
                          Point2D.Double anchor,
                          double scaleFactor)
```
  - buildCaptionPosition
```
Point2D.Double buildCaptionPosition(fr.orsay.lri.varna.models.rna.ModeleBase mb,
                                  double scaleFactor,
                                  double heightEstimate)
```
  - getExtendedRNABBox
```
public Rectangle2D.Double getExtendedRNABBox()
```
  - drawBackbone
```
public void drawBackbone(fr.orsay.lri.varna.models.export.VueVARNAGraphics g2D,
                Point2D.Double[] newCoords,
                double newRadius,
                double _scaleFactor)
```
  - logicToPanel
```
public Point2D.Double logicToPanel(Point2D.Double logicPoint)
```
  - renderRNA
```
public Rectangle2D.Double renderRNA(fr.orsay.lri.varna.models.export.VueVARNAGraphics g2D,
                           Rectangle2D.Double bbox)
```
  - renderRNA
```
public Rectangle2D.Double renderRNA(fr.orsay.lri.varna.models.export.VueVARNAGraphics g2D,
                           Rectangle2D.Double bbox,
                           boolean localView,
                           boolean autoCenter)
```
  - centerViewOn
```
public void centerViewOn(double x,
                double y)
```
  - getBaseAt
```
public fr.orsay.lri.varna.models.rna.ModeleBase getBaseAt(Point2D.Double po)
```
  - setColorMapValues
```
public void setColorMapValues(Double[] values)
```
  - setColorMapMaxValue
```
public void setColorMapMaxValue(double d)
```
  - setColorMapMinValue
```
public void setColorMapMinValue(double d)
```
  - getColorMap
```
public fr.orsay.lri.varna.models.rna.ModeleColorMap getColorMap()
```
  - setColorMap
```
public void setColorMap(fr.orsay.lri.varna.models.rna.ModeleColorMap cm)
```
  - setColorMapCaption
```
public void setColorMapCaption(String caption)
```
  - getColorMapCaption
```
public String getColorMapCaption()
```
  - drawColorMap
```
public void drawColorMap(boolean draw)
```
  - panelToLogicPoint
```
public Point2D.Double panelToLogicPoint(Point2D.Double p)
```
  - transformCoord
```
public Point2D.Double transformCoord(Point2D.Double coordDebut,
                            double offX,
                            double offY,
                            double rnaBBoxX,
                            double rnaBBoxY,
                            double scaleFactor)
```
  - eraseSequence
```
public void eraseSequence()
```
  - transformCoord
```
public Point2D.Double transformCoord(Point2D.Double coordDebut)
```
  - paintComponent
```
public void paintComponent(Graphics g)
```
    Overrides:
    
    paintComponent in class JComponent
  - paintComponent
```
public void paintComponent(Graphics g,
                  boolean transparentBackground)
```
  - renderComponent
```
public void renderComponent(fr.orsay.lri.varna.models.export.VueVARNAGraphics g2D,
                   boolean transparentBackground,
                   double scaleFactor)
```
    Draws current RNA structure in a given Graphics "device".
    
    Parameters:
    g2D - A graphical device
    transparentBackground - Whether the background should be transparent, or drawn.
  - drawRegionHighlightsAnnotation
```
public void drawRegionHighlightsAnnotation(fr.orsay.lri.varna.models.export.VueVARNAGraphics g2D,
                                  Point2D.Double[] realCoords,
                                  Point2D.Double[] realCenters,
                                  double scaleFactor)
```
  - getViewClip
```
public Rectangle2D.Double getViewClip()
```
  - getBackboneColor
```
public Color getBackboneColor()
```
    Returns the color used to draw backbone bounds.
    
    Returns:
    The color used to draw backbone bounds
  - setBackboneColor
```
public void setBackboneColor(Color backbone_color)
```
    Sets the color to be used for drawing backbone interactions.
    
    Parameters:
    backbone_color - The new color for the backbone bounds
  - getBondColor
```
public Color getBondColor()
```
    Returns the color used to display hydrogen bonds (base pairings)
    
    Returns:
    The color of hydrogen bonds
  - getTitle
```
public String getTitle()
```
    Returns the title of this panel
    
    Returns:
    The title
  - setDefaultBPColor
```
public void setDefaultBPColor(Color bond_color)
```
    Sets the new color to be used for hydrogen bonds (base pairings)
    
    Parameters:
    bond_color - The new color for hydrogen bonds
  - setBorderSize
```
public void setBorderSize(Dimension b)
```
    Sets the size of the border, i.e. the empty space between the end of the drawing area and the actual border.
    
    Parameters:
    b - The new border size
  - getBorderSize
```
public Dimension getBorderSize()
```
    Returns the size of the border, i.e. the empty space between the end of the drawing area
    
    Returns:
    The border size
  - showRNA
```
public void showRNA(fr.orsay.lri.varna.models.rna.RNA r)
```
    Sets the RNA to be displayed within this Panel. This method does not use a drawing algorithm to reassigns base coordinates, rather assuming that the RNA was previously drawn.
    
    Parameters:
    r - An already drawn RNA to display in this panel
  - drawRNA
```
public void drawRNA(String seq,
           String str)
             throws fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength
```
    Sets the RNA secondary structure to be drawn in this panel, using the default layout algorithm. In addition to the raw nucleotides sequence, the secondary structure is given in the so-called "Dot-bracket notation" (DBN) format. This format is a well-parenthesized word over the alphabet '(',')','.'.
    Ex:((((((((....))))..(((((...))).))))))
    Returns true if the sequence/structure couple could be parsed into a valid secondary structure, and false otherwise.
    
    Parameters:
    seq - The raw nucleotides sequence
    str - The secondary structure
    
    Throws:
    
    fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength
  - drawRNA
```
public void drawRNA(fr.orsay.lri.varna.models.rna.RNA r,
           int drawMode)
```
    Sets the RNA secondary structure to be drawn in this panel, using a given layout algorithm.
    
    Parameters:
    r - The new secondary structure
    drawMode - The drawing algorithm
  - drawRNA
```
public void drawRNA()
```
    Redraws the current RNA. This reassigns base coordinates to their default value using the current drawing algorithm.
  - drawRNA
```
public void drawRNA(fr.orsay.lri.varna.models.rna.RNA r)
```
    Sets the RNA secondary structure to be drawn in this panel, using the current drawing algorithm.
    
    Parameters:
    r - The new secondary structure
  - drawRNA
```
public void drawRNA(String seq,
           String str,
           int drawMode)
             throws fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength
```
    Sets the RNA secondary structure to be drawn in this panel, using a given layout algorithm. In addition to the raw nucleotides sequence, the secondary structure is given in the so-called "Dot-bracket notation" (DBN) format. This format is a well-parenthesized word over the alphabet '(',')','.'.
    Ex: ((((((((....))))..(((((...))).))))))
    Returns true if the sequence/structure couple could be parsed into a valid secondary structure, and false otherwise.
    
    Parameters:
    seq - The raw nucleotides sequence
    str - The secondary structure
    drawMode - The drawing algorithm
    
    Throws:
    
    fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength
  - drawRNA
```
public void drawRNA(Reader r,
           int drawMode)
             throws fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength,
                    fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax
```
    Throws:
    
    fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength
    
    fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax
  - drawRNAInterpolated
```
public void drawRNAInterpolated(String seq,
                       String str)
                         throws fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength
```
    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. Extra bases, resulting from a size difference between the two successive RNAs, are assumed to initiate from the middle of the sequence. In other words, both prefixes and suffixes of the RNAs are assumed to match, and what remains is an insertion.
    
    Parameters:
    seq - Sequence
    str - Structure in dot bracket notation
    
    Throws:
    
    fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength - If len(seq)!=len(str)
  - drawRNAInterpolated
```
public void drawRNAInterpolated(String seq,
                       String str,
                       int drawMode)
```
    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. Extra bases, resulting from a size difference between the two successive RNAs, are assumed to initiate from the middle of the sequence. In other words, both prefixes and suffixes of the RNAs are assumed to match, and what remains is an insertion.
    
    Parameters:
    seq - Sequence
    str - Structure in dot bracket notation
    drawMode - The drawing algorithm to be used for the initial placement
    
    Throws:
    
    fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength - If len(seq)!=len(str)
  - drawRNAInterpolated
```
public void drawRNAInterpolated(String seq,
                       String str,
                       fr.orsay.lri.varna.models.rna.Mapping m)
```
    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. Here, a mapping between those bases of the new structure and the previous one is explicitly provided.
    
    Parameters:
    seq - Sequence
    str - Structure in dot bracket notation
    m - A mapping between the currently rendered structure and its successor (seq,str)
    
    Throws:
    
    fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength - If len(seq)!=len(str)
  - drawRNAInterpolated
```
public void drawRNAInterpolated(String seq,
                       String str,
                       int drawMode,
                       fr.orsay.lri.varna.models.rna.Mapping m)
```
    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. Here, a mapping between those bases of the new structure and the previous one is provided.
    
    Parameters:
    seq - Sequence
    str - Structure in dot bracket notation
    drawMode - The drawing algorithm to be used for the initial placement
    m - A mapping between the currently rendered structure and its successor (seq,str)
  - drawRNAInterpolated
```
public void drawRNAInterpolated(fr.orsay.lri.varna.models.rna.RNA target)
```
    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. Here, a mapping between those bases of the new structure and the previous one is explicitly provided.
    
    Parameters:
    target - Secondary structure
  - drawRNAInterpolated
```
public void drawRNAInterpolated(fr.orsay.lri.varna.models.rna.RNA target,
                       fr.orsay.lri.varna.models.rna.Mapping m)
```
    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. Here, a mapping between those bases of the new structure and the previous one is explicitly provided.
    
    Parameters:
    target - Secondary structure
    m - A mapping between the currently rendered structure and its successor (seq,str)
  - drawRNAInterpolated
```
public void drawRNAInterpolated(fr.orsay.lri.varna.models.rna.RNA target,
                       int drawMode,
                       fr.orsay.lri.varna.models.rna.Mapping m)
```
    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. Here, a mapping between those bases of the new structure and the previous one is provided.
    
    Parameters:
    target - Secondary structure of RNA
    drawMode - The drawing algorithm to be used for the initial placement
    m - A mapping between the currently rendered structure and its successor (seq,str)
  - getDrawMode
```
public int getDrawMode()
```
    Returns the current algorithm used for drawing the structure
    
    Returns:
    The current drawing algorithm
  - showRNA
```
public void showRNA(fr.orsay.lri.varna.models.rna.RNA t,
           fr.orsay.lri.varna.models.VARNAConfig cfg)
```
  - isInterpolationInProgress
```
public boolean isInterpolationInProgress()
```
    Checks whether an interpolated transition bewteen two RNAs is occurring.
    
    Returns:
    True if an interpolated transition is occurring, false otherwise
  - showRNAInterpolated
```
public void showRNAInterpolated(fr.orsay.lri.varna.models.rna.RNA target)
```
    Simply displays (does not redraw) a secondary structure , using an interpolated transition between the previous one and the new one. A default mapping between those bases of the new structure and the previous one is used.
    
    Parameters:
    target - Secondary structure of RNA
  - showRNAInterpolated
```
public void showRNAInterpolated(fr.orsay.lri.varna.models.rna.RNA target,
                       fr.orsay.lri.varna.models.rna.Mapping m)
```
    Simply displays (does not redraw) a secondary structure , using an interpolated transition between the previous one and the new one. Here, a mapping between bases of the new structure and the previous one is given.
    
    Parameters:
    target - Secondary structure of RNA
    m - A mapping between the currently rendered structure and its successor (seq,str)
    
    Throws:
    
    fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength - If len(seq)!=len(str)
  - showRNAInterpolated
```
public void showRNAInterpolated(fr.orsay.lri.varna.models.rna.RNA target,
                       fr.orsay.lri.varna.models.VARNAConfig cfg,
                       fr.orsay.lri.varna.models.rna.Mapping m)
```
  - drawRNA
```
public void drawRNA(String firstSeq,
           String firstStruct,
           String secondSeq,
           String secondStruct,
           int drawMode)
```
    When comparison mode is ON, sets the two RNA secondary structure to be drawn in this panel, using a given layout algorithm. In addition to the raw nucleotides sequence, the secondary structure is given in the so-called "Dot-bracket notation" (DBN) format. This format is a well-parenthesized word over the alphabet '(',')','.'.
    Ex: ((((((((....))))..(((((...))).))))))
    
    Parameters:
    firstSeq - The first RNA raw nucleotides sequence
    firstStruct - The first RNA secondary structure
    secondSeq - The second RNA raw nucleotides sequence
    secondStruct - The second RNA secondary structure
    drawMode - The drawing algorithm
  - getRealCoords
```
public Point2D.Double[] getRealCoords()
```
    Returns the coordinates of the currently displayed RNA
    
    Returns:
    Coordinates array
  - setRealCoords
```
public void setRealCoords(Point2D.Double[] coords)
```
    Sets the coordinates of the currently displayed RNA
    
    Parameters:
    coords - New coordinates
  - getPopup
```
public fr.orsay.lri.varna.views.VueMenu getPopup()
```
    Returns the popup menu used for user mouse iteractions
    
    Returns:
    Popup menu
  - setBondColor
```
public void setBondColor(Color bond_color)
```
    Sets the color used to display hydrogen bonds (base pairings)
    
    Parameters:
    bond_color - The color of hydrogen bonds
  - getTitleColor
```
public Color getTitleColor()
```
    Returns the color used to draw the title
    
    Returns:
    The color used to draw the title
  - setTitleColor
```
public void setTitleColor(Color title_color)
```
    Sets the color used to draw the title
    
    Parameters:
    title_color - The new color used to draw the title
  - isAutoCentered
```
public boolean isAutoCentered()
```
    Returns the current state of auto centering mode.
    
    Returns:
    True if autocentered, false otherwise
  - setAutoCenter
```
public void setAutoCenter(boolean center)
```
    Sets the current state of auto centering mode.
    
    Parameters:
    center - New auto-centered state
  - getTitleFont
```
public Font getTitleFont()
```
    Returns the font currently used for rendering the title.
    
    Returns:
    Current title font
  - setTitleFont
```
public void setTitleFont(Font font)
```
    Sets the font used for rendering the title.
    
    Parameters:
    font - New title font
  - getBPHeightIncrement
```
public double getBPHeightIncrement()
```
    For the LINE_MODE drawing algorithm, sets the base pair height increment, i.e. the vertical distance between two nested arcs.
    
    Returns:
    The current base pair increment
  - setBPHeightIncrement
```
public void setBPHeightIncrement(double inc)
```
    Sets the base pair height increment, i.e. the vertical distance between two arcs to be used in LINE_MODE.
    
    Parameters:
    inc - New height increment
  - getOffsetPanel
```
public Point2D.Double getOffsetPanel()
```
    Returns the shifting of the origin of the Panel in zoom mode
    
    Returns:
    The logical coordinate of the top-left panel point
  - getPopupMenu
```
public fr.orsay.lri.varna.views.VueMenu getPopupMenu()
```
    Returns this panel's UI menu
    
    Returns:
    Applet's UI popupmenu
  - getZoomIncrement
```
public double getZoomIncrement()
```
    Returns the atomic zoom factor step, or increment.
    
    Returns:
    Atomic zoom factor increment
  - setZoomIncrement
```
public void setZoomIncrement(Object amount)
```
    Sets the atomic zoom factor step, or increment.
    
    Parameters:
    amount - Atomic zoom factor increment
  - setZoomIncrement
```
public void setZoomIncrement(double amount)
```
    Sets the atomic zoom factor step, or increment.
    
    Parameters:
    amount - Atomic zoom factor increment
  - getZoom
```
public double getZoom()
```
    Returns the current zoom factor
    
    Returns:
    Current zoom factor
  - setZoom
```
public void setZoom(Object _zoom)
```
    Sets the current zoom factor
    
    Parameters:
    _zoom - New zoom factor
  - getTranslation
```
public Point getTranslation()
```
    Returns the translation used for zooming in and out
    
    Returns:
    A vector describing the translation
  - setTranslation
```
public void setTranslation(Point trans)
```
    Sets the translation used for zooming in and out
    
    Parameters:
    trans - A vector describing the new translation
  - getRNA
```
public fr.orsay.lri.varna.models.rna.RNA getRNA()
```
    Returns the current RNA model
    
    Returns:
    Current RNA model
  - isOutOfFrame
```
public boolean isOutOfFrame()
```
    Checks whether the drawn RNA is too large to be displayed, allowing for shifting mouse interactions.
    
    Returns:
    true if the RNA is too large to be displayed, false otherwise
  - errorDialog
```
public void errorDialog(Exception error)
```
    Pops up an error Dialog displaying an exception in an human-readable way.
    
    Parameters:
    error - The exception to display within the Dialog
  - errorDialog
```
public void errorDialog(Exception error,
               Component c)
```
    Pops up an error Dialog displaying an exception in an human-readable way if errors are set to be displayed.
    
    Parameters:
    error - The exception to display within the Dialog
    c - Parent component for the dialog box
    See Also:
    setErrorsOn(boolean)
  - errorDialogStatic
```
public static void errorDialogStatic(Exception error,
                     Component c)
```
    Pops up an error Dialog displaying an exception in an human-readable way.
    
    Parameters:
    error - The exception to display within the Dialog
    c - Parent component for the dialog box
  - emitWarning
```
public void emitWarning(String warning)
```
    Displays a warning message through a modal dialog if warnings are set to be displayed.
    
    Parameters:
    warning - A message expliciting the warning
    See Also:
    setShowWarnings(boolean)
  - setModifiable
```
public void setModifiable(boolean modifiable)
```
    Toggles modifications on and off
    
    Parameters:
    modifiable - Modification status
  - isModifiable
```
public boolean isModifiable()
```
    Returns current modification status
    
    Returns:
    current modification status
  - reset
```
public void reset()
```
    Resets the visual aspects (Zoom factor, shift) for the Panel.
  - getNonStandardBasesColor
```
public Color getNonStandardBasesColor()
```
    Returns the color used to draw non-standard bases
    
    Returns:
    The color used to draw non-standard bases
  - setNonStandardBasesColor
```
public void setNonStandardBasesColor(Color basesColor)
```
    Sets the color used to draw non-standard bases
    
    Parameters:
    basesColor - The color used to draw non-standard bases
  - checkTranslation
```
public void checkTranslation()
```
    Checks if the current translation doesn't "kick" the whole RNA out of the panel, and corrects the situation if necessary.
  - getZoomedInTranslationBox
```
public Rectangle getZoomedInTranslationBox()
```
  - getLeftOffset
```
public int getLeftOffset()
```
    Returns the "real pixels" x-coordinate of the RNA.
    
    Returns:
    X-coordinate of the translation
  - getInnerWidth
```
public int getInnerWidth()
```
    Returns the "real pixels" width of the drawing surface for our RNA.
    
    Returns:
    Width of the drawing surface for our RNA
  - getTopOffset
```
public int getTopOffset()
```
    Returns the "real pixels" y-coordinate of the RNA.
    
    Returns:
    Y-coordinate of the translation
  - getInnerHeight
```
public int getInnerHeight()
```
    Returns the "real pixels" height of the drawing surface for our RNA.
    
    Returns:
    Height of the drawing surface for our RNA
  - isComparisonMode
```
public boolean isComparisonMode()
```
    Checks if the current mode is the "comparison" mode
    
    Returns:
    True if comparison, false otherwise
  - globalRotation
```
public void globalRotation(Double angleDegres)
```
    Rotates the RNA coordinates by a certain angle
    
    Parameters:
    angleDegres - Rotation angle, in degrees
  - getNearestBase
```
public Integer getNearestBase()
```
    Returns the index of the currently selected base, defaulting to the closest base to the last mouse-click.
    
    Returns:
    Index of the currently selected base
  - setNearestBase
```
public void setNearestBase(Integer base)
```
    Sets the index of the currently selected base.
    
    Parameters:
    base - Index of the new selected base
  - getGapsBasesColor
```
public Color getGapsBasesColor()
```
    Returns the color used to draw 'Gaps' bases in comparison mode
    
    Returns:
    Color used for 'Gaps'
  - setGapsBasesColor
```
public void setGapsBasesColor(Color c)
```
    Sets the color to use for 'Gaps' bases in comparison mode
    
    Parameters:
    c - Color used for 'Gaps'
  - isErrorsOn
```
public boolean isErrorsOn()
```
    Checks whether errors are to be displayed
    
    Returns:
    Error display status
  - setErrorsOn
```
public void setErrorsOn(boolean on)
```
    Sets whether errors are to be displayed
    
    Parameters:
    on - New error display status
  - getVARNAUI
```
public fr.orsay.lri.varna.views.VueUI getVARNAUI()
```
    Returns the view associated with user interactions
    
    Returns:
    A view associated with user interactions
  - setUseBaseColorsForBPs
```
public void setUseBaseColorsForBPs(boolean on)
```
    Toggles on/off using base inner color for drawing base-pairs
    
    Parameters:
    on - True for using base inner color for drawing base-pairs, false for classic mode
  - getUseBaseColorsForBPs
```
public boolean getUseBaseColorsForBPs()
```
    Returns true if current base color is used as inner color for drawing base-pairs
    
    Returns:
    True for using base inner color for drawing base-pairs, false for classic mode
  - setColorNonStandardBases
```
public void setColorNonStandardBases(boolean on)
```
    Toggles on/off using a special color used for drawing "non-standard" bases
    
    Parameters:
    on - True for using a special color used for drawing "non-standard" bases, false for classic mode
  - getColorSpecialBases
```
public boolean getColorSpecialBases()
```
    Returns true if a special color is used as inner color for non-standard base
    
    Returns:
    True for using a special color used for drawing "non-standard" bases, false for classic mode
  - setColorGapsBases
```
public void setColorGapsBases(boolean on)
```
    Toggles on/off using a special color used for drawing "Gaps" bases in comparison mode
    
    Parameters:
    on - True for using a special color used for drawing "Gaps" bases in comparison mode, false for classic mode
  - getColorGapsBases
```
public boolean getColorGapsBases()
```
    Returns true if a special color is used for drawing "Gaps" bases in comparison mode
    
    Returns:
    True for using a special color used for drawing "Gaps" bases in comparison mode, false for classic mode
  - setShowWarnings
```
public void setShowWarnings(boolean on)
```
    Toggles on/off displaying warnings
    
    Parameters:
    on - True to display warnings, false otherwise
  - getShowWarnings
```
public boolean getShowWarnings()
```
    Get current warning display status
    
    Returns:
    True to display warnings, false otherwise
  - setShowNonCanonicalBP
```
public void setShowNonCanonicalBP(boolean on)
```
    Toggles on/off displaying non-canonical base-pairs
    
    Parameters:
    on - True to display NC base-pairs, false otherwise
  - getShowNonCanonicalBP
```
public boolean getShowNonCanonicalBP()
```
    Return the current display status for non-canonical base-pairs
    
    Returns:
    True if NC base-pairs are displayed, false otherwise
  - setShowNonPlanarBP
```
public void setShowNonPlanarBP(boolean on)
```
    Toggles on/off displaying "non-planar" base-pairs
    
    Parameters:
    on - True to display "non-planar" base-pairs, false otherwise
  - getShowNonPlanarBP
```
public boolean getShowNonPlanarBP()
```
    Return the current display status for non-planar base-pairs
    
    Returns:
    True if non-planars base-pairs are displayed, false otherwise
  - setBPStyle
```
public void setBPStyle(fr.orsay.lri.varna.models.VARNAConfig.BP_STYLE st)
```
    Sets the base-pair representation style
    
    Parameters:
    st - The new base-pair style
  - getBPStyle
```
public fr.orsay.lri.varna.models.VARNAConfig.BP_STYLE getBPStyle()
```
    Returns the base-pair representation style
    
    Returns:
    The current base-pair style
  - getConfig
```
public fr.orsay.lri.varna.models.VARNAConfig getConfig()
```
    Returns the current VARNA Panel configuration. The returned instance should not be modified directly, but rather through the getters/setters from the VARNAPanel class.
    
    Returns:
    Current configuration
  - setBackground
```
public void setBackground(Color c)
```
    Sets the background color
    
    Overrides:
    
    setBackground in class JComponent
    
    Parameters:
    c - New background color
  - highlightSelectedBase
```
public void highlightSelectedBase(fr.orsay.lri.varna.models.rna.ModeleBase m)
```
    Starts highlighting the selected base.
  - highlightSelectedStem
```
public void highlightSelectedStem(fr.orsay.lri.varna.models.rna.ModeleBase m)
```
    Starts highlighting the selected base.
  - getSelection
```
public fr.orsay.lri.varna.models.BaseList getSelection()
```
  - getSelectionIndices
```
public ArrayList<Integer> getSelectionIndices()
```
  - setSelection
```
public void setSelection(ArrayList<Integer> indices)
```
  - setSelection
```
public void setSelection(Collection<? extends fr.orsay.lri.varna.models.rna.ModeleBase> mbs)
```
  - getBasesInRectangleDiff
```
public ArrayList<Integer> getBasesInRectangleDiff(Rectangle recIn,
                                         Rectangle recOut)
```
  - getBasesInRectangle
```
public ArrayList<Integer> getBasesInRectangle(Rectangle rec)
```
  - setSelectionRectangle
```
public void setSelectionRectangle(Rectangle rec)
```
  - removeSelectionRectangle
```
public void removeSelectionRectangle()
```
  - addToSelection
```
public void addToSelection(Collection<? extends Integer> indices)
```
  - addToSelection
```
public void addToSelection(int i)
```
  - removeFromSelection
```
public void removeFromSelection(int i)
```
  - isInSelection
```
public boolean isInSelection(int i)
```
  - toggleSelection
```
public void toggleSelection(int i)
```
  - toggleSelection
```
public void toggleSelection(Collection<? extends Integer> indices)
```
  - clearSelection
```
public void clearSelection()
```
    Stops highlighting bases
  - saveSelection
```
public void saveSelection()
```
  - restoreSelection
```
public void restoreSelection()
```
  - resetAnnotationHighlight
```
public void resetAnnotationHighlight()
```
    Stops highlighting bases
  - drawBBox
```
public void drawBBox(boolean on)
```
    Toggles on/off a rectangular outline of the bounding box.
    
    Parameters:
    on - True to draw the bounding box, false otherwise
  - drawBorder
```
public void drawBorder(boolean on)
```
    Toggles on/off a rectangular outline of the border.
    
    Parameters:
    on - True to draw the bounding box, false otherwise
  - setBaseInnerColor
```
public void setBaseInnerColor(Color c)
```
  - setBaseNumbersColor
```
public void setBaseNumbersColor(Color c)
```
  - setBaseNameColor
```
public void setBaseNameColor(Color c)
```
  - setBaseOutlineColor
```
public void setBaseOutlineColor(Color c)
```
  - getListeAnnotations
```
public ArrayList<fr.orsay.lri.varna.models.annotations.TextAnnotation> getListeAnnotations()
```
  - resetListeAnnotations
```
public void resetListeAnnotations()
```
  - addAnnotation
```
public void addAnnotation(fr.orsay.lri.varna.models.annotations.TextAnnotation textAnnotation)
```
  - removeAnnotation
```
public boolean removeAnnotation(fr.orsay.lri.varna.models.annotations.TextAnnotation textAnnotation)
```
  - get_selectedAnnotation
```
public fr.orsay.lri.varna.models.annotations.TextAnnotation get_selectedAnnotation()
```
  - set_selectedAnnotation
```
public void set_selectedAnnotation(fr.orsay.lri.varna.models.annotations.TextAnnotation annotation)
```
  - removeSelectedAnnotation
```
public void removeSelectedAnnotation()
```
  - highlightSelectedAnnotation
```
public void highlightSelectedAnnotation()
```
  - getFlatExteriorLoop
```
public boolean getFlatExteriorLoop()
```
  - setFlatExteriorLoop
```
public void setFlatExteriorLoop(boolean on)
```
  - setLastSelectedPosition
```
public void setLastSelectedPosition(Point2D.Double p)
```
  - getLastSelectedPosition
```
public Point2D.Double getLastSelectedPosition()
```
  - setSequence
```
public void setSequence(String s)
```
  - setColorMapVisible
```
public void setColorMapVisible(boolean b)
```
  - getColorMapVisible
```
public boolean getColorMapVisible()
```
  - removeColorMap
```
public void removeColorMap()
```
  - saveSession
```
public void saveSession(String path)
```
  - loadSession
```
public fr.orsay.lri.varna.models.FullBackup loadSession(String path)
                                                 throws fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed
```
    Throws:
    
    fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed
  - importSession
```
public static fr.orsay.lri.varna.models.FullBackup importSession(String path)
                                                          throws fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed
```
    Throws:
    
    fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed
  - importSession
```
public static fr.orsay.lri.varna.models.FullBackup importSession(InputStream fis,
                                                 String path)
                                                          throws fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed
```
    Throws:
    
    fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed
  - loadFile
```
public void loadFile(String path)
```
  - getDrawBackbone
```
public boolean getDrawBackbone()
```
  - setDrawBackbone
```
public void setDrawBackbone(boolean b)
```
  - addHighlightRegion
```
public void addHighlightRegion(fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation n)
```
  - removeHighlightRegion
```
public void removeHighlightRegion(fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation n)
```
  - addHighlightRegion
```
public void addHighlightRegion(int i,
                      int j)
```
  - addHighlightRegion
```
public void addHighlightRegion(int i,
                      int j,
                      Color fill,
                      Color outline,
                      double radius)
```
  - loadFile
```
public void loadFile(String path,
            boolean interpolate)
```
  - setConfig
```
public void setConfig(fr.orsay.lri.varna.models.VARNAConfig cfg)
```
  - toggleDrawOutlineBase
```
public void toggleDrawOutlineBase()
```
  - toggleFillBase
```
public void toggleFillBase()
```
  - readValues
```
public void readValues(Reader r)
```
  - addVARNAListener
```
public void addVARNAListener(fr.orsay.lri.varna.interfaces.InterfaceVARNAListener v)
```
  - fireLayoutChanged
```
public void fireLayoutChanged()
```
  - fireUINewStructure
```
public void fireUINewStructure(fr.orsay.lri.varna.models.rna.RNA r)
```
  - fireZoomLevelChanged
```
public void fireZoomLevelChanged(double d)
```
  - fireTranslationChanged
```
public void fireTranslationChanged()
```
  - addSelectionListener
```
public void addSelectionListener(fr.orsay.lri.varna.interfaces.InterfaceVARNASelectionListener v)
```
  - fireSelectionChanged
```
public void fireSelectionChanged(fr.orsay.lri.varna.models.BaseList mold,
                        fr.orsay.lri.varna.models.BaseList mnew)
```
  - fireHoverChanged
```
public void fireHoverChanged(fr.orsay.lri.varna.models.rna.ModeleBase mold,
                    fr.orsay.lri.varna.models.rna.ModeleBase mnew)
```
  - addRNAListener
```
public void addRNAListener(fr.orsay.lri.varna.interfaces.InterfaceVARNARNAListener v)
```
  - addVARNABasesListener
```
public void addVARNABasesListener(fr.orsay.lri.varna.interfaces.InterfaceVARNABasesListener l)
```
  - fireSequenceChanged
```
public void fireSequenceChanged(int index,
                       String oldseq,
                       String newseq)
```
  - fireStructureChanged
```
public void fireStructureChanged(Set<fr.orsay.lri.varna.models.rna.ModeleBP> current,
                        Set<fr.orsay.lri.varna.models.rna.ModeleBP> addedBasePairs,
                        Set<fr.orsay.lri.varna.models.rna.ModeleBP> removedBasePairs)
```
  - fireLayoutChanged
```
public void fireLayoutChanged(Hashtable<Integer,Point2D.Double> movedPositions)
```
  - fireBaseClicked
```
public void fireBaseClicked(fr.orsay.lri.varna.models.rna.ModeleBase mb,
                   MouseEvent me)
```
  - getOrientation
```
public double getOrientation()
```
  - setHoverBase
```
public void setHoverBase(fr.orsay.lri.varna.models.rna.ModeleBase m)
```
  - toXML
```
public void toXML(String path)
```
  - toXML
```
public void toXML(PrintWriter out)
```
  - toXML
```
public void toXML(TransformerHandler hd)
           throws SAXException
```
    Throws:
    
    SAXException
  - getNearestAnnotation
```
public fr.orsay.lri.varna.models.annotations.TextAnnotation getNearestAnnotation(int x,
                                                                        int y)
```
  - getNearestBase
```
public fr.orsay.lri.varna.models.rna.ModeleBase getNearestBase(int x,
                                                      int y,
                                                      boolean always,
                                                      boolean onlyPaired)
```
  - getNearestBase
```
public fr.orsay.lri.varna.models.rna.ModeleBase getNearestBase(int x,
                                                      int y)
```
  - getNearestBaseIndex
```
public int getNearestBaseIndex(int x,
                      int y,
                      boolean always,
                      boolean onlyPaired)
```
  - globalRescale
```
public void globalRescale(double factor)
```

Class VARNAPanel

Nested Class Summary

Nested classes/interfaces inherited from class javax.swing.JPanel

Nested classes/interfaces inherited from class javax.swing.JComponent

Nested classes/interfaces inherited from class java.awt.Container

Nested classes/interfaces inherited from class java.awt.Component

Field Summary

Fields inherited from class javax.swing.JComponent

Fields inherited from class java.awt.Component

Fields inherited from interface java.awt.image.ImageObserver

Constructor Summary

Method Summary

Methods inherited from class javax.swing.JPanel

Methods inherited from class javax.swing.JComponent

Methods inherited from class java.awt.Container

Methods inherited from class java.awt.Component

Methods inherited from class java.lang.Object

Field Detail

_manager

_target

_target2

VARNA_SESSION_EXTENSION

_hoveredBase

XML_ELEMENT_NAME

Constructor Detail

VARNAPanel

VARNAPanel

VARNAPanel

VARNAPanel

VARNAPanel

VARNAPanel

VARNAPanel

VARNAPanel

VARNAPanel

Method Detail

setOriginLink

setDestinationLink

removeLink

undo

redo

setTitleFontStyle

setTitleFontSize

setTitleFontFamily

setTitleFontColor

setBaseFontSize

setNumbersFontSize

setBaseFontStyle

setTitle

setNumPeriod

getNumPeriod

lockScrolling

unlockScrolling

drawChemProbAnnotation

buildCaptionPosition

getExtendedRNABBox

drawBackbone

logicToPanel

renderRNA

renderRNA

centerViewOn

getBaseAt

setColorMapValues

setColorMapMaxValue

setColorMapMinValue

getColorMap

setColorMap

setColorMapCaption

getColorMapCaption

drawColorMap

panelToLogicPoint

transformCoord

eraseSequence

transformCoord

paintComponent

paintComponent

renderComponent

drawRegionHighlightsAnnotation

getViewClip

getBackboneColor

setBackboneColor