FORESTER 1.6

Serialized Form


Package forester.atv

Class forester.atv.ATVappletFrame implements Serializable

Serialized Fields

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

close_item

javax.swing.JMenuItem close_item

open_url_item

javax.swing.JMenuItem open_url_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

atvapplet

ATVjapplet atvapplet

atvpanel

ATVpanel_applet atvpanel

contentpane

java.awt.Container contentpane

atvtextframe

ATVtextframe atvtextframe

Class forester.atv.ATVcontrol implements Serializable

Serialized Fields

atvpanel

ATVpanel atvpanel

userealbl

javax.swing.JCheckBox userealbl

seqnameextnodes

javax.swing.JCheckBox seqnameextnodes

seqnameintnodes

javax.swing.JCheckBox seqnameintnodes

speciesextnodes

javax.swing.JCheckBox speciesextnodes

speciesintnodes

javax.swing.JCheckBox speciesintnodes

ecintnodes

javax.swing.JCheckBox ecintnodes

ecextnodes

javax.swing.JCheckBox ecextnodes

writelnl

javax.swing.JCheckBox writelnl

writebl

javax.swing.JCheckBox writebl

writebootstrap

javax.swing.JCheckBox writebootstrap

writed_s

javax.swing.JCheckBox writed_s

colorbranches

javax.swing.JCheckBox colorbranches

color_orthos

javax.swing.JCheckBox color_orthos

color_super_orthos

javax.swing.JCheckBox color_super_orthos

editable

javax.swing.JCheckBox editable

zoom_in_x

javax.swing.JButton zoom_in_x

zoom_in_y

javax.swing.JButton zoom_in_y

zoom_out_x

javax.swing.JButton zoom_out_x

zoom_out_y

javax.swing.JButton zoom_out_y

show_whole

javax.swing.JButton show_whole

display_info

javax.swing.JRadioButton display_info

collapse

javax.swing.JRadioButton collapse

reroot

javax.swing.JRadioButton reroot

swap

javax.swing.JRadioButton swap

subtree

javax.swing.JRadioButton subtree

group

javax.swing.ButtonGroup group

click_to

javax.swing.JLabel click_to

Class forester.atv.ATVcontrol_applet implements Serializable

Serialized Fields

go_to_swissprot

javax.swing.JRadioButton go_to_swissprot

Class forester.atv.ATVgraphic implements Serializable

Serialized Fields

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

trees

Tree[] trees

j

int j

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

MAX_NODEJFRAMES

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

Class forester.atv.ATVgraphic_applet implements Serializable

Serialized Fields

atvpanel

ATVpanel_applet atvpanel

Class forester.atv.ATVjapplet implements Serializable

Serialized Fields

atvappletframe

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

ATVpanel atvpanel

contentpane

java.awt.Container contentpane

atvtextframe

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

Class forester.atv.ATVnodeFrame implements Serializable

Serialized Fields

atvnodepanel

ATVnodePanel atvnodepanel

atvgraphic

ATVgraphic atvgraphic

i

int i

Class forester.atv.ATVnodePanel implements Serializable

Serialized Fields

node

Node node

atvnodeframe

ATVnodeFrame atvnodeframe

editable

boolean editable

title

javax.swing.JLabel title

seq_name_label

javax.swing.JLabel seq_name_label

Species_label

javax.swing.JLabel Species_label

EC_label

javax.swing.JLabel EC_label

Distance_parent_label

javax.swing.JLabel Distance_parent_label

Bootstrap_label

javax.swing.JLabel Bootstrap_label

LnL_label

javax.swing.JLabel LnL_label

Sum_ext_nodes_label

javax.swing.JLabel Sum_ext_nodes_label

taxo_id_label

javax.swing.JLabel taxo_id_label

orthologous_label

javax.swing.JLabel orthologous_label

super_orthologous_label

javax.swing.JLabel super_orthologous_label

message_label

javax.swing.JLabel message_label

Seq_name_tf

javax.swing.JTextField Seq_name_tf

Species_tf

javax.swing.JTextField Species_tf

EC_tf

javax.swing.JTextField EC_tf

Distance_parent_tf

javax.swing.JTextField Distance_parent_tf

taxo_id_tf

javax.swing.JTextField taxo_id_tf

Bootstrap_tf

javax.swing.JTextField Bootstrap_tf

LnL_tf

javax.swing.JTextField LnL_tf

Sum_ext_nodes_tf

javax.swing.JTextField Sum_ext_nodes_tf

orthologous_tf

javax.swing.JTextField orthologous_tf

super_orthologous_tf

javax.swing.JTextField super_orthologous_tf

Duplication_rb

javax.swing.JRadioButton Duplication_rb

Speciation_rb

javax.swing.JRadioButton Speciation_rb

NA_rb

javax.swing.JRadioButton NA_rb

sep

javax.swing.JSeparator sep

buttonjpanel

javax.swing.JPanel buttonjpanel

radiobuttonjpanel

javax.swing.JPanel radiobuttonjpanel

radiobuttongroup

javax.swing.ButtonGroup radiobuttongroup

close_button

javax.swing.JButton close_button

reset_button

javax.swing.JButton reset_button

write_button

javax.swing.JButton write_button

border

javax.swing.border.TitledBorder border

gbl

java.awt.GridBagLayout gbl

gbc

java.awt.GridBagConstraints gbc

message

java.lang.String message

Class forester.atv.ATVpanel implements Serializable

Serialized Fields

atvgraphic

ATVgraphic atvgraphic

atvcontrol

ATVcontrol atvcontrol

treegraphic_jsp

javax.swing.JScrollPane treegraphic_jsp

Class forester.atv.ATVpanel_applet implements Serializable

Serialized Fields

atvappletframe

ATVappletFrame atvappletframe

Class forester.atv.ATVprinter implements Serializable

Serialized Fields

tree

Tree tree

title

java.lang.String title

ag

ATVgraphic ag

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

x

int x

x_correction_factor

double x_correction_factor

x_distance

double x_distance

y_distance

double y_distance

done

boolean done

color

boolean color

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

Class forester.atv.ATVtextframe implements Serializable

Serialized Fields

text

java.lang.String text

jtextarea

javax.swing.JTextArea jtextarea

close_button

javax.swing.JButton close_button

copy_button

javax.swing.JButton copy_button

buttonjpanel

javax.swing.JPanel buttonjpanel

contentpane

java.awt.Container contentpane

Class forester.atv.DoubleDocument implements Serializable

Class forester.atv.IntegerDocument implements Serializable


Package forester.atv_awt

Class forester.atv_awt.ATVapplet implements Serializable

Serialized Fields

atvappletframe

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.ATVappletFrame implements Serializable

Serialized Fields

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

close_item

java.awt.MenuItem close_item

open_url_item

java.awt.MenuItem open_url_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

atvapplet

ATVapplet atvapplet

atvpanel

ATVpanel_applet atvpanel

d

java.awt.Dialog d

url_tf

java.awt.TextField url_tf

url_string

java.lang.String url_string

Class forester.atv_awt.ATVappletWjs implements Serializable

Serialized Fields

atvappletWjsframe

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.ATVappletWjsFrame implements Serializable

Serialized Fields

save_on_server_item

java.awt.MenuItem save_on_server_item

atv_applet_wjs

ATVappletWjs atv_applet_wjs

win

forester.atv_awt.JSObject win

Class forester.atv_awt.ATVcontrol implements Serializable

Serialized Fields

atvpanel

ATVpanel atvpanel

userealbl

java.awt.Checkbox userealbl

seqnameextnodes

java.awt.Checkbox seqnameextnodes

seqnameintnodes

java.awt.Checkbox seqnameintnodes

speciesextnodes

java.awt.Checkbox speciesextnodes

speciesintnodes

java.awt.Checkbox speciesintnodes

ecintnodes

java.awt.Checkbox ecintnodes

ecextnodes

java.awt.Checkbox ecextnodes

writelnl

java.awt.Checkbox writelnl

writebl

java.awt.Checkbox writebl

writebootstrap

java.awt.Checkbox writebootstrap

writed_s

java.awt.Checkbox writed_s

colorbranches

java.awt.Checkbox colorbranches

color_orthos

java.awt.Checkbox color_orthos

color_super_orthos

java.awt.Checkbox color_super_orthos

editable

java.awt.Checkbox editable

zoom_in_x

java.awt.Button zoom_in_x

zoom_in_y

java.awt.Button zoom_in_y

zoom_out_x

java.awt.Button zoom_out_x

zoom_out_y

java.awt.Button zoom_out_y

show_whole

java.awt.Button show_whole

display_info

java.awt.Checkbox display_info

collapse

java.awt.Checkbox collapse

reroot

java.awt.Checkbox reroot

swap

java.awt.Checkbox swap

subtree

java.awt.Checkbox subtree

group

java.awt.CheckboxGroup group

click_to

java.awt.Label click_to

Class forester.atv_awt.ATVcontrol_applet implements Serializable

Serialized Fields

go_to_swissprot

java.awt.Checkbox go_to_swissprot

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

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

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.ATVgraphic implements Serializable

Serialized Fields

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

trees

Tree[] trees

j

int j

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

MAX_NODEJFRAMES

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

branch_p_color

java.awt.Color branch_p_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

Class forester.atv_awt.ATVgraphic_applet implements Serializable

Serialized Fields

atvpanel

ATVpanel_applet atvpanel

Class forester.atv_awt.ATVnodeFrame implements Serializable

Serialized Fields

atvnodepanel

ATVnodePanel atvnodepanel

atvgraphic

ATVgraphic atvgraphic

i

int i

Class forester.atv_awt.ATVnodePanel implements Serializable

Serialized Fields

node

Node node

atvnodeframe

ATVnodeFrame atvnodeframe

editable

boolean editable

title

java.awt.Label title

seq_name_label

java.awt.Label seq_name_label

Species_label

java.awt.Label Species_label

EC_label

java.awt.Label EC_label

Distance_parent_label

java.awt.Label Distance_parent_label

Bootstrap_label

java.awt.Label Bootstrap_label

LnL_label

java.awt.Label LnL_label

Sum_ext_nodes_label

java.awt.Label Sum_ext_nodes_label

taxo_id_label

java.awt.Label taxo_id_label

orthologous_label

java.awt.Label orthologous_label

super_orthologous_label

java.awt.Label super_orthologous_label

message_label

java.awt.Label message_label

Seq_name_tf

java.awt.TextField Seq_name_tf

Species_tf

java.awt.TextField Species_tf

EC_tf

java.awt.TextField EC_tf

Distance_parent_tf

java.awt.TextField Distance_parent_tf

taxo_id_tf

java.awt.TextField taxo_id_tf

Bootstrap_tf

java.awt.TextField Bootstrap_tf

LnL_tf

java.awt.TextField LnL_tf

Sum_ext_nodes_tf

java.awt.TextField Sum_ext_nodes_tf

orthologous_tf

java.awt.TextField orthologous_tf

super_orthologous_tf

java.awt.TextField super_orthologous_tf

Duplication_rb

java.awt.Checkbox Duplication_rb

Speciation_rb

java.awt.Checkbox Speciation_rb

NA_rb

java.awt.Checkbox NA_rb

buttonjpanel

java.awt.Panel buttonjpanel

radiobuttonjpanel

java.awt.Panel radiobuttonjpanel

radiobuttongroup

java.awt.CheckboxGroup radiobuttongroup

close_button

java.awt.Button close_button

reset_button

java.awt.Button reset_button

write_button

java.awt.Button write_button

gbl

java.awt.GridBagLayout gbl

gbc

java.awt.GridBagConstraints gbc

message

java.lang.String message

Class forester.atv_awt.ATVpanel implements Serializable

Serialized Fields

atvgraphic

ATVgraphic atvgraphic

atvcontrol

ATVcontrol atvcontrol

treegraphic_jsp

java.awt.ScrollPane treegraphic_jsp

Class forester.atv_awt.ATVpanel_applet implements Serializable

Serialized Fields

atvappletframe

ATVappletFrame atvappletframe

Class forester.atv_awt.Message implements Serializable

Serialized Fields

SIZE_X

int SIZE_X

SIZE_Y

int SIZE_Y

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

indicator

int indicator

id

int id

taxo_id

int taxo_id

bootstrap

int bootstrap

sum_ext_nodes

int sum_ext_nodes

orthologous

int orthologous

super_orthologous

int super_orthologous

x

int x

y

int y

seq_name

java.lang.String seq_name

ec_number

java.lang.String ec_number

species

java.lang.String species

distance_parent

double distance_parent

lnL_on_parent_branch

float lnL_on_parent_branch

lnL_on_parent_branch_assigned

boolean lnL_on_parent_branch_assigned

significantly_worse

boolean significantly_worse

duplication_or_spec_assigned

boolean duplication_or_spec_assigned

duplication

boolean duplication

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

real_height

double real_height

external_nodes

int external_nodes

number_of_duplications

int number_of_duplications

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

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

ATVappletFrame atvappletframe

url_string

java.lang.String url_string

message1

java.lang.String message1

message2

java.lang.String message2

exception

boolean exception


FORESTER 1.6