forester.atv_awt
Class ATVgraphic
java.lang.Object
|
+--java.awt.Component
|
+--java.awt.Canvas
|
+--forester.atv_awt.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 java.awt.Canvas
- Version:
- AWT 1.110 -- last modified: 10/04/01
- Author:
- Christian M. Zmasek
- See Also:
- Serialized Form
Inner classes inherited from class java.awt.Canvas |
java.awt.Canvas.AccessibleAWTCanvas |
Inner classes inherited from class java.awt.Component |
java.awt.Component.AccessibleAWTComponent, java.awt.Component.AWTTreeLock |
Fields inherited from class java.awt.Component |
accessibleContext, 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 |
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,
boolean found)
|
(package private) void |
drawFoundNode(int x,
int y,
java.awt.Graphics g,
boolean duplication)
|
(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(java.awt.event.MouseEvent e)
Mouse clicked. |
void |
paint(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 |
setFoundNodes(java.util.Vector v)
|
(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 |
setPropertiesForPainting(Tree t)
|
(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 java.awt.Canvas |
, addNotify, constructComponentName, getAccessibleContext, postsOldMouseEvents |
Methods inherited from class java.awt.Component |
action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addPropertyChangeListener, addPropertyChangeListener, areInputMethodsEnabled, bounds, checkGD, checkImage, checkImage, checkWindowClosingException, coalesceEvents, contains, contains, createChildHierarchyEvents, createHierarchyEvents, createImage, createImage, deliverEvent, disable, disableEvents, dispatchEvent, dispatchEventImpl, doLayout, enable, enable, enableEvents, enableInputMethods, eventEnabled, firePropertyChange, getAccessibleIndexInParent, getAccessibleStateSet, getAlignmentX, getAlignmentY, getBackground, getBounds, getBounds, getColorModel, getComponentAt, getComponentAt, getComponentOrientation, getCursor, getDropTarget, getFont_NoClientCode, getFont, getFontMetrics, getForeground, getGraphics, getGraphicsConfiguration, getHeight, getInputContext, getInputMethodRequests, getListeners, getLocale, getLocation, getLocation, getLocationOnScreen_NoTreeLock, getLocationOnScreen, getMaximumSize, getMinimumSize, getName, getNativeContainer, getParent_NoClientCode, getParent, getPeer, getPreferredSize, getSize, getSize, getToolkit, getToolkitImpl, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, invalidate, isDisplayable, isDoubleBuffered, isEnabled, isEnabledImpl, isFocusTraversable, isLightweight, isOpaque, isRecursivelyVisible, isShowing, isValid, isVisible, keyDown, keyUp, layout, lightweightPaint, lightweightPrint, list, list, list, list, list, locate, location, lostFocus, minimumSize, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, numListening, paintAll, paintHeavyweightComponents, paramString, postEvent, preferredSize, prepareImage, prepareImage, print, printAll, printHeavyweightComponents, processComponentEvent, processEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeNotify, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, resetGC, reshape, resize, resize, setBackground, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setEnabled, setFont, setForeground, setLocale, setLocation, setLocation, setName, setSize, setSize, setVisible, show, show, size, toString, transferFocus, update, validate |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
BOX_SIZE
static final int BOX_SIZE
HALF_BOX_SIZE
static final int HALF_BOX_SIZE
MAX_SUBTREES
static final int MAX_SUBTREES
MAX_NODEJFRAMES
static final int MAX_NODEJFRAMES
MOVE
static final int MOVE
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
node
Node node
n
Node n
tree
Tree tree
trees
Tree[] trees
atvpanel
ATVpanel atvpanel
atvnodeframes
ATVnodeFrame[] atvnodeframes
found_nodes
java.util.Vector found_nodes
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
done
boolean done
longest_ext_node_info
int longest_ext_node_info
y_current
int y_current
x1
int x1
y1
int y1
x2
int x2
y2
int y2
factor
int factor
green
int green
red
int red
max_ortho
int max_ortho
j
int j
x
int x
action_when_node_clicked
int action_when_node_clicked
i
int i
color_scheme
int color_scheme
small_maxDescent
int small_maxDescent
small_maxAscent
int small_maxAscent
ext_nodes_x
int ext_nodes_x
x_current
double x_current
x2double
double x2double
x_correction_factor
double x_correction_factor
x_distance
double x_distance
y_distance
double y_distance
d
double d
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
collapesed_fill_color
java.awt.Color collapesed_fill_color
found_color
java.awt.Color found_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
lnL_nf
java.text.NumberFormat lnL_nf
dist_nf
java.text.NumberFormat dist_nf
ATVgraphic
ATVgraphic(Tree t,
ATVpanel tjp)
- Constructor.
ATVgraphic
ATVgraphic()
- Default constructor.
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)
setFoundNodes
void setFoundNodes(java.util.Vector v)
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(java.awt.event.MouseEvent e)
- Mouse clicked.
(Last modified: 10/04/01)
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)
paint
public void paint(java.awt.Graphics g)
- Paints the Tree.
- Overrides:
paint
in class java.awt.Canvas
drawFoundNode
void drawFoundNode(int x,
int y,
java.awt.Graphics g,
boolean duplication)
drawCollapsedNode
void drawCollapsedNode(int x,
int y,
java.awt.Graphics g,
Node node,
boolean found)
setPropertiesForPainting
void setPropertiesForPainting(Tree t)
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.