Serialized Form


Package core

Class core.CoreException extends java.lang.Exception implements Serializable

serialVersionUID: 1L


Package data

Class data.Configuration extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

ZeroSkipValue

float ZeroSkipValue
To avoid lose information, change 0.00f prob. for this value


minUnexpectedScore

float minUnexpectedScore
Minimum score to show the taxon at the unexpected results list


SignalScoreLimitUpp

float SignalScoreLimitUpp
When determining if a test is positive, negative or variable, there are two cut points. That point is the limit beetween Positive and Variable results.


SignalScoreLimitLow

float SignalScoreLimitLow
When determining if a test positive, negative or variable, there are two cut points. That point is the limit beetween Variable and Negative results.


foundValue

float foundValue
Minimum value to fire the Identified panel


bestScoredCount

int bestScoredCount
This number indicates the number of taxa that has to be considered on the best scored taxa list and unexpected list

Class data.DataException extends java.lang.Exception implements Serializable

serialVersionUID: 2L

Class data.Matrix extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

name

java.lang.String name
Matrix name (id of the Matrix)


info

java.lang.String info
General Text info about matrix entered by user


test_names

java.lang.String[] test_names
Names of the tests on the matrix


taxa_names

java.lang.String[] taxa_names
Names of the taxa on the matrix


importDate

java.util.Date importDate
Timestamp of the import moment


prob_test_taxa

float[][] prob_test_taxa
Matrix[x][y] with the probability (normalized from 0 to 1 about taxa "y" gives a positive on test "x"

Class data.Workspace extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

name

java.lang.String name
The name (identification) of the Workspace.


info

java.lang.String info
The information about the workspace.


dateCreated

java.util.Date dateCreated
Creation date


nameRefMatrix

java.lang.String nameRefMatrix
The name (identification) of the reference Matrix.


test_res

int[] test_res
Mantains at the pos "i" the results of the test "i"


config

Configuration config
The Workspace config


Package gui

Class gui.GuiException extends java.lang.Exception implements Serializable

serialVersionUID: 2L

Class gui.MainBar extends javax.swing.JMenuBar implements Serializable

serialVersionUID: 1L

Serialized Fields

ws

Workspace ws

pl

PanelLibrary pl

wsm

WorkspaceManager wsm

mFile

javax.swing.JMenu mFile

miNew

javax.swing.JMenuItem miNew

miLoad

javax.swing.JMenuItem miLoad

miSave

javax.swing.JMenuItem miSave

miImport

javax.swing.JMenuItem miImport

miLibrary

javax.swing.JMenuItem miLibrary

miViewLog

javax.swing.JMenuItem miViewLog

miExportLog

javax.swing.JMenuItem miExportLog

miClose

javax.swing.JMenuItem miClose

miExit

javax.swing.JMenuItem miExit

mHelp

javax.swing.JMenu mHelp

miGoWebsite

javax.swing.JMenuItem miGoWebsite

miCheckUpdates

javax.swing.JMenuItem miCheckUpdates

miAbout

javax.swing.JMenuItem miAbout

Class gui.MainFrame extends javax.swing.JFrame implements Serializable

serialVersionUID: 1L

Serialized Fields

mainBar

MainBar mainBar

panelWelcome

PanelWelcome panelWelcome

Class gui.PanelWelcome extends JPanelBackground implements Serializable

serialVersionUID: 1L

Serialized Fields

buttonRestore

javax.swing.JButton buttonRestore

buttonNew

javax.swing.JButton buttonNew

buttonLibrary

javax.swing.JButton buttonLibrary

labelTitle

javax.swing.JLabel labelTitle

labelIntro

javax.swing.JLabel labelIntro

Package gui.matrixLibrary

Class gui.matrixLibrary.DialogMatrixImport extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

ref_mat

Matrix ref_mat

exit_code

int exit_code

pmi

PanelMatrixInfo pmi

Class gui.matrixLibrary.DialogTree extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

treeComponent

javax.swing.JComponent treeComponent

treeView

TreeView treeView

idTree

Tree idTree

Class gui.matrixLibrary.PanelLibrary extends JPanelBackground implements Serializable

serialVersionUID: 1L

Serialized Fields

listMatrix

JListMatrix listMatrix

scrollMatrix

javax.swing.JScrollPane scrollMatrix

panelInfo

PanelMatrixInfo panelInfo

panelList

javax.swing.JPanel panelList

panelButtons

javax.swing.JPanel panelButtons

buttonReturn

javax.swing.JButton buttonReturn

buttonViewTree

javax.swing.JButton buttonViewTree

buttonImport

javax.swing.JButton buttonImport

buttonExport

javax.swing.JButton buttonExport

buttonDelete

javax.swing.JButton buttonDelete

currentIndex

int currentIndex

Class gui.matrixLibrary.PanelTree extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Class gui.matrixLibrary.TreeManager extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L


Package gui.myClasses

Class gui.myClasses.CellEditorRadioButton extends javax.swing.DefaultCellEditor implements Serializable

serialVersionUID: 1L

Serialized Fields

button

javax.swing.JRadioButton button

Class gui.myClasses.EventDoneTest extends java.util.EventObject implements Serializable

serialVersionUID: 1L

Class gui.myClasses.EventTaxaFound extends java.util.EventObject implements Serializable

serialVersionUID: 1L

Class gui.myClasses.JListMatrix extends javax.swing.JList implements Serializable

serialVersionUID: 1L

Serialized Fields

rowColors

java.awt.Color[] rowColors

drawStripes

boolean drawStripes

wrapper

JListMatrix.RendererWrapper wrapper

Class gui.myClasses.JListWorkspace extends javax.swing.JList implements Serializable

serialVersionUID: 1L

Serialized Fields

rowColors

java.awt.Color[] rowColors

drawStripes

boolean drawStripes

wrapper

JListWorkspace.RendererWrapper wrapper

Class gui.myClasses.JPanelBackground extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

backgroundImage

java.awt.Image backgroundImage

Class gui.myClasses.JRadioButtonTest extends javax.swing.JRadioButton implements Serializable

serialVersionUID: 1L

Serialized Fields

testIndex

int testIndex

testResult

int testResult

Class gui.myClasses.JTableRadioButtons extends javax.swing.JTable implements Serializable

serialVersionUID: 1L

Serialized Fields

rowColors

java.awt.Color[] rowColors

drawStripes

boolean drawStripes

Class gui.myClasses.JTableTransparentBg extends javax.swing.JTable implements Serializable

serialVersionUID: 1L

Class gui.myClasses.NonEditTableModel extends javax.swing.table.DefaultTableModel implements Serializable

serialVersionUID: 1L

Serialized Fields

readOnly

boolean readOnly

nonEditRows

java.util.Vector<E> nonEditRows

Package gui.myWindows

Class gui.myWindows.DialogFirstRun extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

choosenDir

java.lang.String choosenDir

exit_code

int exit_code

textPath

javax.swing.JTextField textPath

buttonChoose

javax.swing.JButton buttonChoose

buttonOk

javax.swing.JButton buttonOk

buttonExit

javax.swing.JButton buttonExit

Class gui.myWindows.DialogMatrixInfo extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

refMat

Matrix refMat

pmi

PanelMatrixInfo pmi

Class gui.myWindows.DialogSetConfig extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

exit_code

int exit_code

config

Configuration config

pc

PanelConfig pc

buttonOk

javax.swing.JButton buttonOk

Class gui.myWindows.DialogTextArea extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

jta

javax.swing.JTextArea jta

jsp

javax.swing.JScrollPane jsp

buttonClose

javax.swing.JButton buttonClose

Class gui.myWindows.PanelConfig extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

config

Configuration config

labelVarRes1

javax.swing.JLabel labelVarRes1

formattedHigh

javax.swing.JFormattedTextField formattedHigh

labelVarRes2

javax.swing.JLabel labelVarRes2

formattedLow

javax.swing.JFormattedTextField formattedLow

labelFound

javax.swing.JLabel labelFound

formattedFound

javax.swing.JFormattedTextField formattedFound

Class gui.myWindows.PanelMatrixInfo extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

ref_mat

Matrix ref_mat

overwriteRisk

boolean overwriteRisk

textName

javax.swing.JTextField textName

labelName

javax.swing.JLabel labelName

labelOverwite

javax.swing.JLabel labelOverwite

textareaDesc

javax.swing.JTextArea textareaDesc

labelDesc

javax.swing.JLabel labelDesc

scrollDesc

javax.swing.JScrollPane scrollDesc

panelData

javax.swing.JPanel panelData

listTest

javax.swing.JList listTest

scrollTest

javax.swing.JScrollPane scrollTest

listTaxa

javax.swing.JList listTaxa

scrollTaxa

javax.swing.JScrollPane scrollTaxa

labelTaxa

javax.swing.JLabel labelTaxa

labelTest

javax.swing.JLabel labelTest

labelImport

javax.swing.JLabel labelImport

buttonCancel

javax.swing.JButton buttonCancel

buttonConfirm

javax.swing.JButton buttonConfirm

textInspector

javax.swing.JTextField textInspector

labelInspector

javax.swing.JLabel labelInspector

Package gui.workSpace

Class gui.workSpace.DialogWSCreate extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

exit_code

int exit_code

choosenMatrix

java.lang.String choosenMatrix

config

Configuration config

pws

PanelWSCreate pws

Class gui.workSpace.PanelWSCreate extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

labelMatrix

javax.swing.JLabel labelMatrix

listMatrix

JListMatrix listMatrix

scrollMatrix

javax.swing.JScrollPane scrollMatrix

textId

javax.swing.JTextField textId

labelId

javax.swing.JLabel labelId

textareaDesc

javax.swing.JTextArea textareaDesc

labelDesc

javax.swing.JLabel labelDesc

scrollDesc

javax.swing.JScrollPane scrollDesc

buttonSettings

javax.swing.JButton buttonSettings

panelExtended

javax.swing.JPanel panelExtended

panelConfig

PanelConfig panelConfig

buttonMatrix

javax.swing.JButton buttonMatrix

buttonAccept

javax.swing.JButton buttonAccept

choosenMatrix

java.lang.String choosenMatrix

Class gui.workSpace.PanelWSEnterResults extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

parent

java.awt.Container parent

tableRes

JTableRadioButtons tableRes

scrollTable

javax.swing.JScrollPane scrollTable

rbt

JRadioButtonTest[][] rbt

btg

javax.swing.ButtonGroup[] btg

clearButton

javax.swing.JButton clearButton

Class gui.workSpace.PanelWSMain extends JPanelBackground implements Serializable

serialVersionUID: 1L

Serialized Fields

wsMan

WorkspaceManager wsMan

panelInfo

PanelWSShowInfo panelInfo

panelResults

PanelWSEnterResults panelResults

panelFound

PanelWSTaxaFound panelFound

isFoundOnce

boolean isFoundOnce

Class gui.workSpace.PanelWSShowInfo extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

listenerList

javax.swing.event.EventListenerList listenerList

tableTaxa

JTableTransparentBg tableTaxa

tableTest

JTableTransparentBg tableTest

separator

javax.swing.JSeparator separator

groupButton

javax.swing.ButtonGroup groupButton

rbAllVsAll

javax.swing.JRadioButton rbAllVsAll

rbBestVsAll

javax.swing.JRadioButton rbBestVsAll

buttonSummary

javax.swing.JButton buttonSummary

panelTaxa

javax.swing.JPanel panelTaxa

panelTest

javax.swing.JPanel panelTest

taxaColumnNames

java.lang.String[] taxaColumnNames

testColumnNames

java.lang.String[] testColumnNames

useAllVsAll

boolean useAllVsAll

Class gui.workSpace.PanelWSTaxaFound extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

parent

java.awt.Container parent

labelImg

javax.swing.JLabel labelImg

labelIntroName

javax.swing.JLabel labelIntroName

labelName

javax.swing.JLabel labelName

labelIntroProb

javax.swing.JLabel labelIntroProb

labelProb

javax.swing.JLabel labelProb

buttonExport

javax.swing.JButton buttonExport

buttonLog

javax.swing.JButton buttonLog

buttonBack

javax.swing.JButton buttonBack

buttonContinue

javax.swing.JButton buttonContinue

Class gui.workSpace.WorkspaceLoader extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

exit_code

int exit_code

listWS

JListWorkspace listWS

scrollList

javax.swing.JScrollPane scrollList

panelList

javax.swing.JPanel panelList

panelButtons

javax.swing.JPanel panelButtons

buttonLoad

javax.swing.JButton buttonLoad

buttonDelete

javax.swing.JButton buttonDelete

currentIndex

int currentIndex

wsName

java.lang.String wsName