forester v1.3

Serialized Form


Package forester.atv

Class forester.atv.ATVjapplet implements Serializable

Serialized Fields

atvappletframe

forester.atv.ATVappletFrame atvappletframe

url_string

java.lang.String url_string

message1

java.lang.String message1

message2

java.lang.String message2

exception

boolean exception

Class forester.atv.ATVjframe implements Serializable

Serialized Fields

treefile

java.io.File treefile

jmenubar

javax.swing.JMenuBar jmenubar

file_jmenu

javax.swing.JMenu file_jmenu

edit_jmenu

javax.swing.JMenu edit_jmenu

view_jmenu

javax.swing.JMenu view_jmenu

options_jmenu

javax.swing.JMenu options_jmenu

help_jmenu

javax.swing.JMenu help_jmenu

print_size_jmenu

javax.swing.JMenu print_size_jmenu

open_item

javax.swing.JMenuItem open_item

open_url_item

javax.swing.JMenuItem open_url_item

save_item

javax.swing.JMenuItem save_item

saveas_item

javax.swing.JMenuItem saveas_item

print_item

javax.swing.JMenuItem print_item

close_item

javax.swing.JMenuItem close_item

exit_item

javax.swing.JMenuItem exit_item

remove_root_item

javax.swing.JMenuItem remove_root_item

remove_root_tri_item

javax.swing.JMenuItem remove_root_tri_item

tiny_fonts_item

javax.swing.JMenuItem tiny_fonts_item

small_fonts_item

javax.swing.JMenuItem small_fonts_item

medium_fonts_item

javax.swing.JMenuItem medium_fonts_item

large_fonts_item

javax.swing.JMenuItem large_fonts_item

switch_colors_item

javax.swing.JMenuItem switch_colors_item

view_as_NH_item

javax.swing.JMenuItem view_as_NH_item

view_as_NHX_item

javax.swing.JMenuItem view_as_NHX_item

about_item

javax.swing.JMenuItem about_item

help_item

javax.swing.JMenuItem help_item

atvpanel

forester.atv.ATVpanel atvpanel

contentpane

java.awt.Container contentpane

atvtextframe

forester.atv.ATVtextframe atvtextframe

open_jfilechooser

javax.swing.JFileChooser open_jfilechooser

saveas_jfilechooser

javax.swing.JFileChooser saveas_jfilechooser

x_slider

javax.swing.JSlider x_slider

y_slider

javax.swing.JSlider y_slider

xs_label

javax.swing.JLabel xs_label

ys_label

javax.swing.JLabel ys_label

print_in_color

javax.swing.JCheckBox print_in_color


Package forester.atv_awt

Class forester.atv_awt.ATVapplet implements Serializable

Serialized Fields

atvappletframe

forester.atv_awt.ATVappletFrame atvappletframe

url_string

java.lang.String url_string

message1

java.lang.String message1

message2

java.lang.String message2

exception

boolean exception

Class forester.atv_awt.ATVappletWjs implements Serializable

Serialized Fields

atvappletWjsframe

forester.atv_awt.ATVappletWjsFrame atvappletWjsframe

js_getFileName

java.lang.String js_getFileName

js_setFileName

java.lang.String js_setFileName

js_printHook

java.lang.String js_printHook

js_saveFile

java.lang.String js_saveFile

Class forester.atv_awt.ATVframe implements Serializable

Serialized Fields

treefile

java.io.File treefile

menubar

java.awt.MenuBar menubar

file_jmenu

java.awt.Menu file_jmenu

edit_jmenu

java.awt.Menu edit_jmenu

view_jmenu

java.awt.Menu view_jmenu

options_jmenu

java.awt.Menu options_jmenu

help_jmenu

java.awt.Menu help_jmenu

open_item

java.awt.MenuItem open_item

open_url_item

java.awt.MenuItem open_url_item

save_item

java.awt.MenuItem save_item

saveas_item

java.awt.MenuItem saveas_item

print_item

java.awt.MenuItem print_item

close_item

java.awt.MenuItem close_item

exit_item

java.awt.MenuItem exit_item

remove_root_item

java.awt.MenuItem remove_root_item

remove_root_tri_item

java.awt.MenuItem remove_root_tri_item

tiny_fonts_item

java.awt.MenuItem tiny_fonts_item

small_fonts_item

java.awt.MenuItem small_fonts_item

medium_fonts_item

java.awt.MenuItem medium_fonts_item

large_fonts_item

java.awt.MenuItem large_fonts_item

switch_colors_item

java.awt.MenuItem switch_colors_item

view_as_NH_item

java.awt.MenuItem view_as_NH_item

view_as_NHX_item

java.awt.MenuItem view_as_NHX_item

about_item

java.awt.MenuItem about_item

help_item

java.awt.MenuItem help_item

atvpanel

forester.atv_awt.ATVpanel atvpanel

contentpane

java.awt.Container contentpane

d

java.awt.Dialog d

url_tf

java.awt.TextField url_tf

url_string

java.lang.String url_string

Class forester.atv_awt.OutputFileRemotePopup implements Serializable

Serialized Fields

tf

java.awt.TextField tf

tfLabel

java.awt.Label tfLabel

win

netscape.javascript.JSObject win

setFile

java.lang.String setFile

saveFile

java.lang.String saveFile

Class forester.atv_awt.PopupProtected implements Serializable

Serialized Fields

parent

java.awt.Frame parent

apply

java.awt.Button apply

close

java.awt.Button close

status

java.awt.Label status

gb

java.awt.GridBagLayout gb

gbc

java.awt.GridBagConstraints gbc


Package forester.tree

Class forester.tree.Node implements Serializable

Serialized Fields

id

int id

taxo_id

int taxo_id

bootstrap

int bootstrap

sum_ext_nodes

int sum_ext_nodes

indicator

int indicator

x

int x

y

int y

duplication

boolean duplication

seq_name

java.lang.String seq_name

ec_number

java.lang.String ec_number

species

java.lang.String species

orig_seq_name

java.lang.String orig_seq_name

distance_parent

double distance_parent

lnL_on_parent_branch

double lnL_on_parent_branch

lnL_on_parent_branch_assigned

boolean lnL_on_parent_branch_assigned

significantly_worse

boolean significantly_worse

bl_of_seq_on_parent_branch

double bl_of_seq_on_parent_branch

duplication_or_spec_assigned

boolean duplication_or_spec_assigned

collapse

boolean collapse

next_ext_node

Node next_ext_node

prev_ext_node

Node prev_ext_node

child1

Node child1

child2

Node child2

parent

Node parent

link

Node link

vector

java.util.Vector vector

Class forester.tree.Tree implements Serializable

Serialized Fields

ext_node0

Node ext_node0

root

Node root

highest_lnL

double highest_lnL

lowest_lnL

double lowest_lnL

longest_distance

double longest_distance

number_of_branches

int number_of_branches

external_nodes

int external_nodes

number_of_duplications

int number_of_duplications

most_branches_per_ext_node

int most_branches_per_ext_node

rooted

boolean rooted

more_than_bin_nodes_in_NH

boolean more_than_bin_nodes_in_NH

name

java.lang.String name

idhash

java.util.Hashtable idhash

j

int j


Class forester.atv_awt.ATVapplet implements Serializable

Serialized Fields

atvappletframe

forester.atv_awt.ATVappletFrame atvappletframe

url_string

java.lang.String url_string

message1

java.lang.String message1

message2

java.lang.String message2

exception

boolean exception


Class forester.atv.ATVjapplet implements Serializable

Serialized Fields

atvappletframe

forester.atv.ATVappletFrame atvappletframe

url_string

java.lang.String url_string

message1

java.lang.String message1

message2

java.lang.String message2

exception

boolean exception


forester v1.3