Serialized Form

Class ColorQuestionCellRenderer implements Serializable


Class ColorTableCellRenderer implements Serializable


Class ComputedDistanceModel implements Serializable

Serialized Fields

distance

java.lang.Object[][] distance

count

int count

names

java.lang.String[] names


Class HTMLViewer implements Serializable

Serialized Fields

html

javax.swing.JEditorPane html

frame

javax.swing.JFrame frame

path

java.lang.String path


Class InputCharacterModel implements Serializable

Serialized Fields

characters

java.lang.Object[][] characters

numOfSites

int numOfSites


Class InputDistanceModel implements Serializable

Serialized Fields

distance

java.lang.Object[][] distance

dis

double[][] dis


Class InputModel implements Serializable

Serialized Fields

count

int count
The number of species


names

java.lang.String[] names
The names of the species


Class InterCharacterModel implements Serializable

Serialized Fields

numOfSubstitutions

int[][] numOfSubstitutions

infoSites

java.util.Vector infoSites

interNodes

java.util.Vector interNodes

random_site

int random_site

total

int total


Class InterDistanceModel implements Serializable

Serialized Fields

algorithm

Algorithm algorithm

nodes

Node[] nodes

numOfNodes

int numOfNodes

count

int count

colCount

int colCount

answer

double answer

answer_row

int answer_row

answer_col

int answer_col

random_i

int random_i

random_j

int random_j

distance

java.lang.Object[][] distance
The distance matrix in the distance based algorithms


names

java.lang.String[] names
The the names of the species


Class MyJTable implements Serializable


Class NumOfSubModel implements Serializable

Serialized Fields

allNumOfSubs

int[] allNumOfSubs


Class PreviousDistanceModel implements Serializable

Serialized Fields

dis

java.lang.Double[][] dis


Class PreviousFrame implements Serializable

Serialized Fields

pDistTable

MyJTable pDistTable

pTransDistTable

MyJTable pTransDistTable

treeDisplay

TreeDisplay treeDisplay


Class PTCControls implements Serializable

Serialized Fields

inputTable

MyJTable inputTable

interTable

MyJTable interTable

okButton

javax.swing.JButton okButton

settingButton

javax.swing.JButton settingButton

randomButton

javax.swing.JButton randomButton

resetButton

javax.swing.JButton resetButton

runButton

javax.swing.JButton runButton

traceButton

javax.swing.JButton traceButton

treeLabel

javax.swing.JLabel treeLabel

infoArea

javax.swing.JTextArea infoArea

hSB

javax.swing.JScrollBar hSB

vSB

javax.swing.JScrollBar vSB

leftPanel

javax.swing.JPanel leftPanel

algorithm

Algorithm algorithm

treeDisplay

TreeDisplay treeDisplay

algorithmType

int algorithmType

begin_name

char begin_name

count

int count

numOfSites

int numOfSites

names

java.lang.String[] names

first

boolean first

saveInput

boolean saveInput

popUpQues

boolean popUpQues

previousFrame

PreviousFrame previousFrame

settingDialog

javax.swing.JDialog settingDialog

countField

javax.swing.JTextField countField

sitesField

javax.swing.JTextField sitesField

namesArea

javax.swing.JTextField namesArea

acceptButton

javax.swing.JButton acceptButton


Class PTCFrame implements Serializable

Serialized Fields

file

javax.swing.JMenu file

open

javax.swing.JMenuItem open

exit

javax.swing.JMenuItem exit

algorithms

javax.swing.JMenu algorithms

menuItemsAlgorithms

java.lang.String[] menuItemsAlgorithms

algorithmTypes

int[] algorithmTypes

options

javax.swing.JMenu options

saveInput

javax.swing.JCheckBoxMenuItem saveInput

popUpQuestions

javax.swing.JCheckBoxMenuItem popUpQuestions

zoomIn

javax.swing.JMenu zoomIn

menuItemsIn

java.lang.String[] menuItemsIn

ratiosIn

double[] ratiosIn

zoomOut

javax.swing.JMenu zoomOut

menuItemsOut

java.lang.String[] menuItemsOut

ratiosOut

double[] ratiosOut

help

javax.swing.JMenu help

help_general

javax.swing.JMenuItem help_general

help_algorithms

javax.swing.JMenuItem help_algorithms

help_glossary

javax.swing.JMenuItem help_glossary

about

javax.swing.JMenuItem about

controls

PTCControls controls

algorithmType

int algorithmType

dir

java.lang.String dir

zoomInWarningFlag

boolean zoomInWarningFlag

zoomOutWarningFlag

boolean zoomOutWarningFlag


Class ResetModel implements Serializable


Class TransDistanceModel implements Serializable

Serialized Fields

count

int count

names

java.lang.String[] names

transDistance

java.lang.Object[][] transDistance

answer

double answer

answer_row

int answer_row

answer_col

int answer_col


Class TreeDisplay implements Serializable

Serialized Fields

begin

boolean begin

maxLength

double maxLength

minLength

double minLength

maxSeqWidth

int maxSeqWidth

unit_x

int unit_x

unit_y

int unit_y

init_x

int init_x

init_y

int init_y

radius

int radius

rect_width

int rect_width

size

int size

maxName

java.lang.String maxName

type

int type

numOfNodesLeft

int numOfNodesLeft

numOfLeaves

int numOfLeaves

height

double height

sumOfSquares

double sumOfSquares

flagString

java.lang.String flagString

numOfSubstitutions

int numOfSubstitutions

display

boolean display

roots

java.util.Vector roots

algorithm

Algorithm algorithm