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FORESTER 1.6 | |||||||
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SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object | +--java.awt.Component | +--java.awt.Canvas | +--forester.atv_awt.ATVgraphic
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 |
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) java.awt.Color |
branch_p_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 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 |
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 |
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 |
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 |
|
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 |
Field Detail |
Tree tree
ATVpanel atvpanel
boolean editable
boolean use_real_br_lenghts
boolean seq_name_internal_nodes
boolean species_internal_nodes
boolean ec_internal_nodes
boolean seq_name_ext_nodes
boolean species_ext_nodes
boolean ec_ext_nodes
boolean write_lnL_values
boolean write_br_length_values
boolean write_bootstrap_values
boolean write_dup_spec
boolean color_branches_acc_to_lnL
boolean color_orthologous
boolean color_super_orthologous
static final int MAX_SUBTREES
Tree[] trees
int j
static final int BOX_SIZE
static final int HALF_BOX_SIZE
static final int MOVE
int longest_ext_node_info
int x_current
int y_current
int x1
int y1
int x2
int y2
int factor
int xx
int xxd
int xxdd
int yyd
int green
int red
int max_ortho
int x
double x_correction_factor
double x_distance
double y_distance
int action_when_node_clicked
static final int SHOW_INFO
static final int COLLAPSE
static final int REROOT
static final int SUBTREE
static final int SWAP
final int MAX_NODEJFRAMES
int i
ATVnodeFrame[] atvnodeframes
boolean done
int color_scheme
java.awt.Color ext_node_seq_name_color
java.awt.Color int_node_seq_name_color
java.awt.Color species_color
java.awt.Color bootstrap_color
java.awt.Color ec_color
java.awt.Color dub_spec_color
java.awt.Color lnL_color
java.awt.Color branch_length_color
java.awt.Color branch_color
java.awt.Color box_color
java.awt.Color branch_p_color
java.awt.Color background_color
java.awt.Color duplication_box_color
java.awt.Color seq_x_color
java.awt.Font small_font
java.awt.Font large_font
java.awt.Font small_italic_font
java.awt.Font large_italic_font
java.awt.FontMetrics fm_small
java.awt.FontMetrics fm_large
java.awt.FontMetrics fm_small_italic
java.awt.FontMetrics fm_large_italic
int small_maxDescent
int small_maxAscent
java.text.NumberFormat lnL_nf
Constructor Detail |
ATVgraphic(Tree t, ATVpanel tjp)
ATVgraphic()
Method Detail |
void setMaxOrtho(int m)
int getMaxOrtho()
void setParametersForPainting(int x, int y)
void resetPreferredSize()
Tree getTree()
void setTree(Tree t)
ATVpanel getATVpanel()
int getLongestExtNodeInfo()
void setLongestExtNodeInfo(int i)
int getLengthOfRootSpecies()
void calculateLongestExtNodeInfo()
Node findNode(int x, int y)
void setActionWhenNodeClicked(int i)
int getActionWhenNodeClicked()
void collapse(Node node)
void reRoot(Node node)
void subTree(Node node)
void swap(Node node)
void removeRoot()
void removeRootTri()
public void MouseClicked(int x, int y)
void removeNodeJFrame(int i)
void removeAllNodeJFrames()
double getXdistance()
double getYdistance()
void setXdistance(double i)
void setYdistance(double i)
void setXcorrectionFactor(double i)
double getXcorrectionFactor()
boolean isEditable()
void setEditable(boolean b)
void setUseRealBranchLenghts(boolean b)
boolean useRealBranchLenghts()
void setSeqNameInternalNodes(boolean b)
boolean seqNameInternalNodes()
void setSpeciesInternalNodes(boolean b)
boolean speciesInternalNodes()
void setECInternalNodes(boolean b)
boolean ECInternalNodes()
void setSeqNameExtNodes(boolean b)
boolean seqNameExtNodes()
void setSpeciesExtNodes(boolean b)
boolean speciesExtNodes()
void setECExtNodes(boolean b)
boolean ECExtNodes()
void setWriteLnLValues(boolean b)
boolean writeLnLValues()
void setWriteBranchLengthValues(boolean b)
boolean writeBranchLengthValues()
void setWriteBootstrapValues(boolean b)
boolean writeBootstrapValues()
void setWriteDupSpec(boolean b)
boolean writeDupSpec()
void setColorBranchesAccToLnL(boolean b)
boolean colorBranchesAccToLnL()
boolean colorOrthologous()
void setColorOrthologous(boolean b)
boolean colorSuperOrthologous()
void setColorSuperOrthologous(boolean b)
public void paint(java.awt.Graphics g)
paint
in class java.awt.Canvas
void drawCollapsedNode(int x, int y, java.awt.Graphics g, Node node)
void setPropertiesForPainting(Tree t)
void switchColors()
void setColors1()
void setColors2()
void setColors3()
void setColors4()
void mediumFonts()
void largeFonts()
void smallFonts()
void tinyFonts()
|
FORESTER 1.6 | |||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||
SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |