FORESTER 1.7

forester.atv
Class ATVgraphic_applet

java.lang.Object
  |
  +--java.awt.Component
        |
        +--java.awt.Container
              |
              +--javax.swing.JComponent
                    |
                    +--javax.swing.JPanel
                          |
                          +--forester.atv.ATVgraphic
                                |
                                +--forester.atv.ATVgraphic_applet
All Implemented Interfaces:
javax.accessibility.Accessible, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable

class ATVgraphic_applet
extends ATVgraphic

Version:
1.212 -- last modified: 12/05/00
Author:
Christian Zmasek
See Also:
Serialized Form

Inner classes inherited from class javax.swing.JPanel
javax.swing.JPanel.AccessibleJPanel
 
Inner classes inherited from class javax.swing.JComponent
javax.swing.JComponent.AccessibleJComponent, javax.swing.JComponent.ActionStandin, javax.swing.JComponent.IntVector, javax.swing.JComponent.KeyboardState
 
Inner classes inherited from class java.awt.Container
java.awt.Container.AccessibleAWTContainer
 
Inner classes inherited from class java.awt.Component
java.awt.Component.AccessibleAWTComponent, java.awt.Component.AWTTreeLock
 
Field Summary
(package private) static int GO_TO_SWISSPROT
           
(package private) static java.lang.String SWISSPROT_URL_AC
           
(package private) static java.lang.String SWISSPROT_URL_DE
           
 
Fields inherited from class forester.atv.ATVgraphic
action_when_node_clicked, atvnodeframes, atvpanel, background_color, bootstrap_color, box_color, BOX_SIZE, branch_color, branch_length_color, COLLAPSE, color_branches_acc_to_lnL, color_orthologous, color_scheme, color_super_orthologous, done, dub_spec_color, duplication_box_color, ec_color, ec_ext_nodes, ec_internal_nodes, editable, ext_node_seq_name_color, factor, fm_large, fm_large_italic, fm_small, fm_small_italic, green, HALF_BOX_SIZE, i, int_node_seq_name_color, j, large_font, large_italic_font, lnL_color, lnL_nf, longest_ext_node_info, MAX_NODEJFRAMES, max_ortho, MAX_SUBTREES, MOVE, red, REROOT, seq_name_ext_nodes, seq_name_internal_nodes, seq_x_color, SHOW_INFO, small_font, small_italic_font, small_maxAscent, small_maxDescent, species_color, species_ext_nodes, species_internal_nodes, SUBTREE, SWAP, tree, trees, use_real_br_lenghts, write_bootstrap_values, write_br_length_values, write_dup_spec, write_lnL_values, x, x_correction_factor, x_current, x_distance, x1, x2, xx, xxd, xxdd, y_current, y_distance, y1, y2, yyd
 
Fields inherited from class javax.swing.JComponent
_bounds, accessibleContext, listenerList, paintingChild, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW
 
Fields inherited from class java.awt.Container
component, containerListener, layoutMgr, listeningBoundsChildren, listeningChildren, ncomponents
 
Fields inherited from class java.awt.Component
actionListenerK, adjustmentListenerK, appContext, background, BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, componentListener, componentListenerK, componentOrientation, containerListenerK, cursor, dropTarget, enabled, eventMask, focusListener, focusListenerK, font, foreground, graphicsConfig, hasFocus, height, hierarchyBoundsListener, hierarchyBoundsListenerK, hierarchyListener, hierarchyListenerK, incRate, inputMethodListener, inputMethodListenerK, isInc, isPacked, itemListenerK, keyListener, keyListenerK, LEFT_ALIGNMENT, locale, LOCK, metrics, minSize, mouseListener, mouseListenerK, mouseMotionListener, mouseMotionListenerK, newEventsOnly, ownedWindowK, parent, peer, peerFont, popups, prefSize, RIGHT_ALIGNMENT, textListenerK, TOP_ALIGNMENT, valid, visible, width, windowClosingException, windowListenerK, y
 
Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
 
Constructor Summary
(package private) ATVgraphic_applet(Tree t, ATVpanel_applet ap)
          Constructor.
 
Method Summary
(package private)  void collapse(Node node)
           
(package private)  void goToSwissProt(Node node)
           
 void MouseClicked(int x, int y)
          Mouse clicked.
(package private)  void reRoot(Node node)
           
(package private)  void subTree(Node node)
           
 
Methods inherited from class forester.atv.ATVgraphic
calculateLongestExtNodeInfo, colorBranchesAccToLnL, colorOrthologous, colorSuperOrthologous, drawCollapsedNode, ECExtNodes, ECInternalNodes, findNode, getActionWhenNodeClicked, getATVpanel, getLengthOfRootSpecies, getLongestExtNodeInfo, getMaxOrtho, getTree, getXcorrectionFactor, getXdistance, getYdistance, isEditable, largeFonts, mediumFonts, paintComponent, removeAllNodeJFrames, removeNodeJFrame, removeRoot, removeRootTri, resetPreferredSize, seqNameExtNodes, seqNameInternalNodes, setActionWhenNodeClicked, setColorBranchesAccToLnL, setColorOrthologous, setColors1, setColors2, setColors3, setColors4, setColorSuperOrthologous, setECExtNodes, setECInternalNodes, setEditable, setLongestExtNodeInfo, setMaxOrtho, setParametersForPainting, setSeqNameExtNodes, setSeqNameInternalNodes, setSpeciesExtNodes, setSpeciesInternalNodes, setTree, setUseRealBranchLenghts, setWriteBootstrapValues, setWriteBranchLengthValues, setWriteDupSpec, setWriteLnLValues, setXcorrectionFactor, setXdistance, setYdistance, smallFonts, speciesExtNodes, speciesInternalNodes, swap, switchColors, tinyFonts, useRealBranchLenghts, writeBootstrapValues, writeBranchLengthValues, writeDupSpec, writeLnLValues
 
Methods inherited from class javax.swing.JPanel
, getAccessibleContext, getUIClassID, paramString, updateUI
 
Methods inherited from class javax.swing.JComponent
_paintImmediately, addAncestorListener, addNotify, addPropertyChangeListener, addPropertyChangeListener, addVetoableChangeListener, alwaysOnTop, checkIfChildObscuredBySibling, componentInputMapChanged, computeVisibleRect, computeVisibleRect, compWriteObjectNotify, contains, createToolTip, disable, enable, enableSerialization, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getActionMap, getAlignmentX, getAlignmentY, getAutoscrolls, getBorder, getBounds, getClientProperty, getComponentGraphics, getConditionForKeyStroke, getCreatedDoubleBuffer, getDebugGraphicsOptions, getGraphics, getHeight, getInputMap, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getVerifyInputWhenFocusTarget, getVisibleRect, getWidth, getX, getY, grabFocus, hasFocus, hide, isDoubleBuffered, isFocusCycleRoot, isFocusTraversable, isLightweightComponent, isManagingFocus, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isOptimizedDrawingEnabled, isPaintingTile, isPreferredSizeSet, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processFocusEvent, processKeyBinding, processKeyBindings, processKeyBindingsForAllComponents, processKeyEvent, processMouseMotionEvent, putClientProperty, rectangleIsObscured, rectangleIsObscuredBySibling, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removePropertyChangeListener, removePropertyChangeListener, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setCreatedDoubleBuffer, setDebugGraphicsOptions, setDoubleBuffered, setEnabled, setFont, setForeground, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPaintingChild, setPreferredSize, setRequestFocusEnabled, setToolTipText, setUI, setVerifyInputWhenFocusTarget, setVisible, shouldDebugGraphics, superProcessMouseMotionEvent, unregisterKeyboardAction, update
 
Methods inherited from class java.awt.Container
add, add, add, add, add, addContainerListener, addImpl, adjustListeningChildren, applyOrientation, checkGD, countComponents, createChildHierarchyEvents, createHierarchyEvents, deliverEvent, dispatchEventImpl, dispatchEventToSelf, doLayout, eventEnabled, findComponentAt, findComponentAt, findComponentAt, getAccessibleAt, getAccessibleChild, getAccessibleChildrenCount, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents_NoClientCode, getComponents, getLayout, getMouseEventTarget, getWindow, insets, invalidate, invalidateTree, isAncestorOf, layout, lightweightPaint, lightweightPrint, list, list, locate, minimumSize, nextFocus, numListening, paintComponents, paintHeavyweightComponents, postProcessKeyEvent, postsOldMouseEvents, preferredSize, preProcessKeyEvent, printComponents, printHeavyweightComponents, processContainerEvent, processEvent, proxyEnableEvents, proxyRequestFocus, remove, remove, removeAll, removeContainerListener, setFocusOwner, setLayout, transferFocus, validate, validateTree
 
Methods inherited from class java.awt.Component
action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, areInputMethodsEnabled, bounds, checkImage, checkImage, checkWindowClosingException, coalesceEvents, constructComponentName, contains, createImage, createImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, getAccessibleIndexInParent, getAccessibleStateSet, getBackground, getBounds, getColorModel, getComponentOrientation, getCursor, getDropTarget, getFont_NoClientCode, getFont, getFontMetrics, getForeground, getGraphicsConfiguration, getInputContext, getInputMethodRequests, getLocale, getLocation, getLocationOnScreen_NoTreeLock, getLocationOnScreen, getName, getNativeContainer, getParent_NoClientCode, getParent, getPeer, getSize, getToolkit, getToolkitImpl, getTreeLock, gotFocus, handleEvent, imageUpdate, inside, isDisplayable, isEnabled, isEnabledImpl, isLightweight, isRecursivelyVisible, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, repaint, repaint, repaint, resetGC, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

SWISSPROT_URL_DE

static final java.lang.String SWISSPROT_URL_DE

SWISSPROT_URL_AC

static final java.lang.String SWISSPROT_URL_AC

GO_TO_SWISSPROT

static final int GO_TO_SWISSPROT
Constructor Detail

ATVgraphic_applet

ATVgraphic_applet(Tree t,
                  ATVpanel_applet ap)
Constructor.
Method Detail

goToSwissProt

void goToSwissProt(Node node)

reRoot

void reRoot(Node node)
Overrides:
reRoot in class ATVgraphic

subTree

void subTree(Node node)
Overrides:
subTree in class ATVgraphic

collapse

void collapse(Node node)
Overrides:
collapse in class ATVgraphic

MouseClicked

public void MouseClicked(int x,
                         int y)
Mouse clicked.
Overrides:
MouseClicked in class ATVgraphic

FORESTER 1.7