statalign.postprocess.gui
Class StructureGUI

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  fr.orsay.lri.varna.VARNAPanel
                      statalign.postprocess.gui.StructureGUI

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible

public class StructureGUI
extends fr.orsay.lri.varna.VARNAPanel

See Also:

Serialized Form

Nested Class Summary

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

javax.swing.JComponent.AccessibleJComponent

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

java.awt.Component.BaselineResizeBehavior

Field Summary

boolean	probMode
java.lang.String	title

Fields inherited from class fr.orsay.lri.varna.VARNAPanel

_hoveredBase, VARNA_SESSION_EXTENSION

Fields inherited from class javax.swing.JComponent

TOOL_TIP_TEXT_KEY, 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

StructureGUI(java.lang.String title)

Method Summary

void	drawBasePair(fr.orsay.lri.varna.models.export.VueVARNAGraphics g2D, java.awt.geom.Point2D.Double orig, java.awt.geom.Point2D.Double dest, fr.orsay.lri.varna.models.rna.ModeleBP style, double newRadius)
void	drawSymbol(fr.orsay.lri.varna.models.export.VueVARNAGraphics g2D, double posx, double posy, double normx, double normy, double radius, boolean isCIS, fr.orsay.lri.varna.models.rna.ModeleBP.Edge e)
void	paintComponent(java.awt.Graphics g)
void	setMatrix(float[][] probMatrix)
void	updateAndDraw(java.lang.String seq, java.lang.String str)

Methods inherited from class fr.orsay.lri.varna.VARNAPanel

addAnnotation, addHighlightRegion, addHighlightRegion, addHighlightRegion, addRNAListener, addSelectionListener, addToSelection, addToSelection, addVARNAListener, checkTranslation, clearSelection, drawBackbone, drawBBox, drawBorder, drawColorMap, drawRegionHighlightsAnnotation, drawRNA, drawRNA, drawRNA, drawRNA, drawRNA, drawRNA, drawRNA, drawRNAInterpolated, drawRNAInterpolated, drawRNAInterpolated, drawRNAInterpolated, drawRNAInterpolated, drawRNAInterpolated, drawRNAInterpolated, emitWarning, eraseSequence, errorDialog, errorDialog, errorDialogStatic, fireHoverChanged, fireLayoutChanged, fireLayoutChanged, fireSelectionChanged, fireSequenceChanged, fireStructureChanged, fireUINewStructure, get_selectedAnnotation, getBackboneColor, getBaseAt, getBasesInRectangle, getBasesInRectangleDiff, getBondColor, getBorderSize, getBPHeightIncrement, getBPStyle, getColorGapsBases, getColorMap, getColorMapCaption, getColorMapVisible, getColorSpecialBases, getConfig, getDrawBackbone, getDrawMode, getExtendedRNABBox, getFlatExteriorLoop, getGapsBasesColor, getInnerHeight, getInnerWidth, getLastSelectedPosition, getLeftOffset, getListeAnnotations, getNearestBase, getNonStandardBasesColor, getNumPeriod, getOffsetPanel, getOrientation, getPopup, getPopupMenu, getRealCoords, getRNA, getRNAOffset, getScaleFactor, getSelection, getSelectionIndices, getShowNonCanonicalBP, getShowNonPlanarBP, getShowWarnings, getTitle, getTitleColor, getTitleFont, getTopOffset, getTranslation, getUseBaseColorsForBPs, getVARNAUI, getZoom, getZoomIncrement, globalRotation, highlightSelectedAnnotation, highlightSelectedBase, highlightSelectedStem, importSession, importSession, isAutoCentered, isComparisonMode, isErrorsOn, isInSelection, isInterpolationInProgress, isModifiable, isOutOfFrame, loadFile, loadFile, loadSession, lockScrolling, logicToPanel, paintComponent, panelToLogicPoint, readValues, redo, removeAnnotation, removeColorMap, removeFromSelection, removeHighlightRegion, removeLink, removeSelectedAnnotation, removeSelectionRectangle, renderComponent, reset, resetAnnotationHighlight, resetListeAnnotations, restoreSelection, saveSelection, saveSession, set_selectedAnnotation, setAutoCenter, setBackboneColor, setBackground, setBaseFontSize, setBaseFontStyle, setBaseInnerColor, setBaseNameColor, setBaseNumbersColor, setBaseOutlineColor, setBondColor, setBorderSize, setBPHeightIncrement, setBPStyle, setColorGapsBases, setColorMap, setColorMapCaption, setColorMapMaxValue, setColorMapMinValue, setColorMapValues, setColorMapVisible, setColorNonStandardBases, setConfig, setDefaultBPColor, setDestinationLink, setDrawBackbone, setErrorsOn, setFlatExteriorLoop, setGapsBasesColor, setHoverBase, setLastSelectedPosition, setModifiable, setNearestBase, setNonStandardBasesColor, setNumbersFontSize, setNumPeriod, setOriginLink, setRealCoords, setScaleFactor, setSelection, setSelection, setSelectionRectangle, setSequence, setShowNonCanonicalBP, setShowNonPlanarBP, setShowWarnings, setTitle, setTitleColor, setTitleFont, setTitleFontColor, setTitleFontFamily, setTitleFontSize, setTitleFontStyle, setTranslation, setUseBaseColorsForBPs, setZoom, setZoomIncrement, setZoomIncrement, showRNA, showRNA, showRNAInterpolated, showRNAInterpolated, showRNAInterpolated, toggleDrawOutlineBase, toggleFillBase, toggleSelection, toggleSelection, transformCoord, transformCoord, undo, unlockScrolling

Methods inherited from class javax.swing.JPanel

getAccessibleContext, getUI, getUIClassID, setUI, updateUI

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, 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, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintImmediately, paintImmediately, print, printAll, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, 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, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, 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, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusBackward, transferFocusDownCycle, validate

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, contains, createImage, createImage, createVolatileImage, createVolatileImage, dispatchEvent, enable, enableInputMethods, 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, 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, transferFocusUpCycle

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

title

public java.lang.String title

probMode

public boolean probMode

Constructor Detail

StructureGUI

public StructureGUI(java.lang.String title)
             throws fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength

Throws:

fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength

Method Detail

paintComponent

public void paintComponent(java.awt.Graphics g)

Overrides:

paintComponent in class fr.orsay.lri.varna.VARNAPanel

updateAndDraw

public void updateAndDraw(java.lang.String seq,
                          java.lang.String str)

drawSymbol

public void drawSymbol(fr.orsay.lri.varna.models.export.VueVARNAGraphics g2D,
                       double posx,
                       double posy,
                       double normx,
                       double normy,
                       double radius,
                       boolean isCIS,
                       fr.orsay.lri.varna.models.rna.ModeleBP.Edge e)

drawBasePair

public void drawBasePair(fr.orsay.lri.varna.models.export.VueVARNAGraphics g2D,
                         java.awt.geom.Point2D.Double orig,
                         java.awt.geom.Point2D.Double dest,
                         fr.orsay.lri.varna.models.rna.ModeleBP style,
                         double newRadius)

setMatrix

public void setMatrix(float[][] probMatrix)