FORESTER 1.7

forester.atv
Class ATVgraphic

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

class ATVgraphic
extends javax.swing.JPanel

Version:
1.221 -- last modified: 12/05/00
Author:
Christian M. 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)  int action_when_node_clicked
           
(package private)  ATVnodeFrame[] atvnodeframes
           
(package private)  ATVpanel atvpanel
           
(package private)  java.awt.Color background_color
           
(package private)  java.awt.Color bootstrap_color
           
(package private)  java.awt.Color box_color
           
(package private) static int BOX_SIZE
           
(package private)  java.awt.Color branch_color
           
(package private)  java.awt.Color branch_length_color
           
(package private) static int COLLAPSE
           
(package private)  boolean color_branches_acc_to_lnL
           
(package private)  boolean color_orthologous
           
(package private)  int color_scheme
           
(package private)  boolean color_super_orthologous
           
(package private)  boolean done
           
(package private)  java.awt.Color dub_spec_color
           
(package private)  java.awt.Color duplication_box_color
           
(package private)  java.awt.Color ec_color
           
(package private)  boolean ec_ext_nodes
           
(package private)  boolean ec_internal_nodes
           
(package private)  boolean editable
           
(package private)  java.awt.Color ext_node_seq_name_color
           
(package private)  int factor
           
(package private)  java.awt.FontMetrics fm_large
           
(package private)  java.awt.FontMetrics fm_large_italic
           
(package private)  java.awt.FontMetrics fm_small
           
(package private)  java.awt.FontMetrics fm_small_italic
           
(package private)  int green
           
(package private) static int HALF_BOX_SIZE
           
(package private)  int i
           
(package private)  java.awt.Color int_node_seq_name_color
           
(package private)  int j
           
(package private)  java.awt.Font large_font
           
(package private)  java.awt.Font large_italic_font
           
(package private)  java.awt.Color lnL_color
           
(package private)  java.text.NumberFormat lnL_nf
           
(package private)  int longest_ext_node_info
           
(package private)  int MAX_NODEJFRAMES
           
(package private)  int max_ortho
           
(package private) static int MAX_SUBTREES
           
(package private) static int MOVE
           
(package private)  int red
           
(package private) static int REROOT
           
(package private)  boolean seq_name_ext_nodes
           
(package private)  boolean seq_name_internal_nodes
           
(package private)  java.awt.Color seq_x_color
           
(package private) static int SHOW_INFO
           
(package private)  java.awt.Font small_font
           
(package private)  java.awt.Font small_italic_font
           
(package private)  int small_maxAscent
           
(package private)  int small_maxDescent
           
(package private)  java.awt.Color species_color
           
(package private)  boolean species_ext_nodes
           
(package private)  boolean species_internal_nodes
           
(package private) static int SUBTREE
           
(package private) static int SWAP
           
(package private)  Tree tree
           
(package private)  Tree[] trees
           
(package private)  boolean use_real_br_lenghts
           
(package private)  boolean write_bootstrap_values
           
(package private)  boolean write_br_length_values
           
(package private)  boolean write_dup_spec
           
(package private)  boolean write_lnL_values
           
(package private)  int x
           
(package private)  double x_correction_factor
           
(package private)  int x_current
           
(package private)  double x_distance
           
(package private)  int x1
           
(package private)  int x2
           
(package private)  int xx
           
(package private)  int xxd
           
(package private)  int xxdd
           
(package private)  int y_current
           
(package private)  double y_distance
           
(package private)  int y1
           
(package private)  int y2
           
(package private)  int 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()
          Default constructor.
(package private) ATVgraphic(Tree t, ATVpanel tjp)
          Constructor.
 
Method Summary
(package private)  void calculateLongestExtNodeInfo()
           
(package private)  void collapse(Node node)
           
(package private)  boolean colorBranchesAccToLnL()
           
(package private)  boolean colorOrthologous()
           
(package private)  boolean colorSuperOrthologous()
           
(package private)  void drawCollapsedNode(int x, int y, java.awt.Graphics g, Node node)
           
(package private)  boolean ECExtNodes()
           
(package private)  boolean ECInternalNodes()
           
(package private)  Node findNode(int x, int y)
           
(package private)  int getActionWhenNodeClicked()
           
(package private)  ATVpanel getATVpanel()
           
(package private)  int getLengthOfRootSpecies()
           
(package private)  int getLongestExtNodeInfo()
           
(package private)  int getMaxOrtho()
          Gets the maximal number a sequence is expected to be orthologous towards another, i.e.
(package private)  Tree getTree()
           
(package private)  double getXcorrectionFactor()
           
(package private)  double getXdistance()
           
(package private)  double getYdistance()
           
(package private)  boolean isEditable()
           
(package private)  void largeFonts()
          Large size.
(package private)  void mediumFonts()
          Medium size.
 void MouseClicked(int x, int y)
          Mouse clicked.
 void paintComponent(java.awt.Graphics g)
          Paints the Tree.
(package private)  void removeAllNodeJFrames()
           
(package private)  void removeNodeJFrame(int i)
           
(package private)  void removeRoot()
           
(package private)  void removeRootTri()
           
(package private)  void reRoot(Node node)
           
(package private)  void resetPreferredSize()
           
(package private)  boolean seqNameExtNodes()
           
(package private)  boolean seqNameInternalNodes()
           
(package private)  void setActionWhenNodeClicked(int i)
           
(package private)  void setColorBranchesAccToLnL(boolean b)
           
(package private)  void setColorOrthologous(boolean b)
           
(package private)  void setColors1()
          Sets the colors to the "original" scheme.
(package private)  void setColors2()
          Sets the colors to "grey".
(package private)  void setColors3()
          Sets the colors to "b/w".
(package private)  void setColors4()
          Sets the colors to "blue".
(package private)  void setColorSuperOrthologous(boolean b)
           
(package private)  void setECExtNodes(boolean b)
           
(package private)  void setECInternalNodes(boolean b)
           
(package private)  void setEditable(boolean b)
           
(package private)  void setLongestExtNodeInfo(int i)
           
(package private)  void setMaxOrtho(int m)
          Sets the maximal number a sequence is expected to be orthologous towards another, i.e.
(package private)  void setParametersForPainting(int x, int y)
           
(package private)  void setSeqNameExtNodes(boolean b)
           
(package private)  void setSeqNameInternalNodes(boolean b)
           
(package private)  void setSpeciesExtNodes(boolean b)
           
(package private)  void setSpeciesInternalNodes(boolean b)
           
(package private)  void setTree(Tree t)
           
(package private)  void setUseRealBranchLenghts(boolean b)
           
(package private)  void setWriteBootstrapValues(boolean b)
           
(package private)  void setWriteBranchLengthValues(boolean b)
           
(package private)  void setWriteDupSpec(boolean b)
           
(package private)  void setWriteLnLValues(boolean b)
           
(package private)  void setXcorrectionFactor(double i)
           
(package private)  void setXdistance(double i)
           
(package private)  void setYdistance(double i)
           
(package private)  void smallFonts()
          Small size.
(package private)  boolean speciesExtNodes()
           
(package private)  boolean speciesInternalNodes()
           
(package private)  void subTree(Node node)
           
(package private)  void swap(Node node)
           
(package private)  void switchColors()
          Switches colors between different schemes.
(package private)  void tinyFonts()
          Tiny size.
(package private)  boolean useRealBranchLenghts()
           
(package private)  boolean writeBootstrapValues()
           
(package private)  boolean writeBranchLengthValues()
           
(package private)  boolean writeDupSpec()
           
(package private)  boolean 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

tree

Tree tree

atvpanel

ATVpanel atvpanel

editable

boolean editable

use_real_br_lenghts

boolean use_real_br_lenghts

seq_name_internal_nodes

boolean seq_name_internal_nodes

species_internal_nodes

boolean species_internal_nodes

ec_internal_nodes

boolean ec_internal_nodes

seq_name_ext_nodes

boolean seq_name_ext_nodes

species_ext_nodes

boolean species_ext_nodes

ec_ext_nodes

boolean ec_ext_nodes

write_lnL_values

boolean write_lnL_values

write_br_length_values

boolean write_br_length_values

write_bootstrap_values

boolean write_bootstrap_values

write_dup_spec

boolean write_dup_spec

color_branches_acc_to_lnL

boolean color_branches_acc_to_lnL

color_orthologous

boolean color_orthologous

color_super_orthologous

boolean color_super_orthologous

MAX_SUBTREES

static final int MAX_SUBTREES

trees

Tree[] trees

j

int j

BOX_SIZE

static final int BOX_SIZE

HALF_BOX_SIZE

static final int HALF_BOX_SIZE

MOVE

static final int MOVE

longest_ext_node_info

int longest_ext_node_info

x_current

int x_current

y_current

int y_current

x1

int x1

y1

int y1

x2

int x2

y2

int y2

factor

int factor

xx

int xx

xxd

int xxd

xxdd

int xxdd

yyd

int yyd

green

int green

red

int red

max_ortho

int max_ortho

x

int x

x_correction_factor

double x_correction_factor

x_distance

double x_distance

y_distance

double y_distance

action_when_node_clicked

int action_when_node_clicked

SHOW_INFO

static final int SHOW_INFO

COLLAPSE

static final int COLLAPSE

REROOT

static final int REROOT

SUBTREE

static final int SUBTREE

SWAP

static final int SWAP

MAX_NODEJFRAMES

final int MAX_NODEJFRAMES

i

int i

atvnodeframes

ATVnodeFrame[] atvnodeframes

done

boolean done

color_scheme

int color_scheme

ext_node_seq_name_color

java.awt.Color ext_node_seq_name_color

int_node_seq_name_color

java.awt.Color int_node_seq_name_color

species_color

java.awt.Color species_color

bootstrap_color

java.awt.Color bootstrap_color

ec_color

java.awt.Color ec_color

dub_spec_color

java.awt.Color dub_spec_color

lnL_color

java.awt.Color lnL_color

branch_length_color

java.awt.Color branch_length_color

branch_color

java.awt.Color branch_color

box_color

java.awt.Color box_color

background_color

java.awt.Color background_color

duplication_box_color

java.awt.Color duplication_box_color

seq_x_color

java.awt.Color seq_x_color

small_font

java.awt.Font small_font

large_font

java.awt.Font large_font

small_italic_font

java.awt.Font small_italic_font

large_italic_font

java.awt.Font large_italic_font

fm_small

java.awt.FontMetrics fm_small

fm_large

java.awt.FontMetrics fm_large

fm_small_italic

java.awt.FontMetrics fm_small_italic

fm_large_italic

java.awt.FontMetrics fm_large_italic

small_maxDescent

int small_maxDescent

small_maxAscent

int small_maxAscent

lnL_nf

java.text.NumberFormat lnL_nf
Constructor Detail

ATVgraphic

ATVgraphic(Tree t,
           ATVpanel tjp)
Constructor.

ATVgraphic

ATVgraphic()
Default constructor.
Method Detail

setMaxOrtho

void setMaxOrtho(int m)
Sets the maximal number a sequence is expected to be orthologous towards another, i.e. the number of resampling steps. (Last modified: 12/05/00)

getMaxOrtho

int getMaxOrtho()
Gets the maximal number a sequence is expected to be orthologous towards another, i.e. the number of resampling steps. (Last modified: 12/05/00)

setParametersForPainting

void setParametersForPainting(int x,
                              int y)

resetPreferredSize

void resetPreferredSize()

getTree

Tree getTree()

setTree

void setTree(Tree t)

getATVpanel

ATVpanel getATVpanel()

getLongestExtNodeInfo

int getLongestExtNodeInfo()

setLongestExtNodeInfo

void setLongestExtNodeInfo(int i)

getLengthOfRootSpecies

int getLengthOfRootSpecies()

calculateLongestExtNodeInfo

void calculateLongestExtNodeInfo()

findNode

Node findNode(int x,
              int y)

setActionWhenNodeClicked

void setActionWhenNodeClicked(int i)

getActionWhenNodeClicked

int getActionWhenNodeClicked()

collapse

void collapse(Node node)

reRoot

void reRoot(Node node)

subTree

void subTree(Node node)

swap

void swap(Node node)

removeRoot

void removeRoot()

removeRootTri

void removeRootTri()

MouseClicked

public void MouseClicked(int x,
                         int y)
Mouse clicked.

removeNodeJFrame

void removeNodeJFrame(int i)

removeAllNodeJFrames

void removeAllNodeJFrames()

getXdistance

double getXdistance()

getYdistance

double getYdistance()

setXdistance

void setXdistance(double i)

setYdistance

void setYdistance(double i)

setXcorrectionFactor

void setXcorrectionFactor(double i)

getXcorrectionFactor

double getXcorrectionFactor()

isEditable

boolean isEditable()

setEditable

void setEditable(boolean b)

setUseRealBranchLenghts

void setUseRealBranchLenghts(boolean b)

useRealBranchLenghts

boolean useRealBranchLenghts()

setSeqNameInternalNodes

void setSeqNameInternalNodes(boolean b)

seqNameInternalNodes

boolean seqNameInternalNodes()

setSpeciesInternalNodes

void setSpeciesInternalNodes(boolean b)

speciesInternalNodes

boolean speciesInternalNodes()

setECInternalNodes

void setECInternalNodes(boolean b)

ECInternalNodes

boolean ECInternalNodes()

setSeqNameExtNodes

void setSeqNameExtNodes(boolean b)

seqNameExtNodes

boolean seqNameExtNodes()

setSpeciesExtNodes

void setSpeciesExtNodes(boolean b)

speciesExtNodes

boolean speciesExtNodes()

setECExtNodes

void setECExtNodes(boolean b)

ECExtNodes

boolean ECExtNodes()

setWriteLnLValues

void setWriteLnLValues(boolean b)

writeLnLValues

boolean writeLnLValues()

setWriteBranchLengthValues

void setWriteBranchLengthValues(boolean b)

writeBranchLengthValues

boolean writeBranchLengthValues()

setWriteBootstrapValues

void setWriteBootstrapValues(boolean b)

writeBootstrapValues

boolean writeBootstrapValues()

setWriteDupSpec

void setWriteDupSpec(boolean b)

writeDupSpec

boolean writeDupSpec()

setColorBranchesAccToLnL

void setColorBranchesAccToLnL(boolean b)

colorBranchesAccToLnL

boolean colorBranchesAccToLnL()

colorOrthologous

boolean colorOrthologous()

setColorOrthologous

void setColorOrthologous(boolean b)

colorSuperOrthologous

boolean colorSuperOrthologous()

setColorSuperOrthologous

void setColorSuperOrthologous(boolean b)

paintComponent

public void paintComponent(java.awt.Graphics g)
Paints the Tree.
Overrides:
paintComponent in class javax.swing.JComponent

drawCollapsedNode

void drawCollapsedNode(int x,
                       int y,
                       java.awt.Graphics g,
                       Node node)

switchColors

void switchColors()
Switches colors between different schemes.

setColors1

void setColors1()
Sets the colors to the "original" scheme.

setColors2

void setColors2()
Sets the colors to "grey".

setColors3

void setColors3()
Sets the colors to "b/w".

setColors4

void setColors4()
Sets the colors to "blue".

mediumFonts

void mediumFonts()
Medium size.

largeFonts

void largeFonts()
Large size.

smallFonts

void smallFonts()
Small size.

tinyFonts

void tinyFonts()
Tiny size.

FORESTER 1.7