Serialized Form

Package phenote.charactertemplate

Class phenote.charactertemplate.AbstractTemplateChooser extends org.bbop.framework.AbstractGUIComponent implements Serializable

Serialized Fields

charField

CharField charField

title

java.lang.String title

group

java.lang.String group

templateChoiceListeners

java.util.Set<E> templateChoiceListeners

Class phenote.charactertemplate.CharacterTemplateTable extends org.bbop.framework.AbstractGUIComponent implements Serializable

serialVersionUID: -3936482953613098775L

Serialized Fields

group

java.lang.String group

sortedCharacters

ca.odell.glazedlists.SortedList<E> sortedCharacters

filteredCharacters

ca.odell.glazedlists.FilterList<E> filteredCharacters

selectionModel

ca.odell.glazedlists.swing.EventSelectionModel<E> selectionModel

tableFormat

CharacterTemplateTableFormat tableFormat

loadSaveManager

LoadSaveManager loadSaveManager

filter

CharFieldMatcherEditor filter

sortChooser

ca.odell.glazedlists.swing.TableComparatorChooser<E> sortChooser

selectionListener

phenote.charactertemplate.CharacterTemplateTable.SelectionListener selectionListener

markedCharacters

java.util.Set<E> markedCharacters

tablePanel

javax.swing.JPanel tablePanel

characterTable

javax.swing.JTable characterTable

scrollPane

javax.swing.JScrollPane scrollPane

duplicateButton

javax.swing.JButton duplicateButton

deleteButton

javax.swing.JButton deleteButton

markButton

javax.swing.JButton markButton

unmarkButton

javax.swing.JButton unmarkButton

invertSelectionButton

javax.swing.JButton invertSelectionButton

generateButton

javax.swing.JButton generateButton

filterPanel

javax.swing.JPanel filterPanel

focusListener

phenote.charactertemplate.CharacterTemplateTable.ComponentLayoutListener focusListener

tableColumnSaver

TableColumnPrefsSaver tableColumnSaver

Class phenote.charactertemplate.TreeChooser extends AbstractTemplateChooser implements Serializable

serialVersionUID: 2683680201895012882L

Serialized Fields

window

javax.swing.JFrame window

treeViewer

jebl.gui.trees.treeviewer.TreeViewer treeViewer

newickField

javax.swing.JTextField newickField

newickFieldLabel

javax.swing.JLabel newickFieldLabel

treeViewerContainer

javax.swing.JPanel treeViewerContainer

applyButton

javax.swing.JButton applyButton

nexusButton

javax.swing.JButton nexusButton

Package phenote.config

Class phenote.config.ConfigException extends java.lang.Exception implements Serializable

Serialized Fields

wrappedEx

java.lang.Exception wrappedEx

Class phenote.config.ConfigFileQueryGui.CancelEx extends java.lang.Exception implements Serializable

Class phenote.config.ProxyDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

proxyHost

java.lang.String proxyHost

proxyPort

int proxyPort

userName

java.lang.String userName

userPassword

java.lang.String userPassword

hasAuthentication

boolean hasAuthentication

hasProxy

boolean hasProxy

server

javax.swing.JTextField server

port

javax.swing.JTextField port

name

javax.swing.JTextField name

password

javax.swing.JPasswordField password

authBox

javax.swing.JCheckBox authBox

proxyBox

javax.swing.JCheckBox proxyBox

authP

javax.swing.JPanel authP

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

buttonGroup

javax.swing.ButtonGroup buttonGroup

httpButton

javax.swing.JRadioButton httpButton

socksButton

javax.swing.JRadioButton socksButton

proxyProtocol

java.lang.String proxyProtocol

Package phenote.dataadapter

Class phenote.dataadapter.CharListChangeEvent extends java.util.EventObject implements Serializable

Serialized Fields

charList

CharacterListI charList

Class phenote.dataadapter.DataAdapterEx extends java.lang.Exception implements Serializable

Package phenote.datamodel

Class phenote.datamodel.CharacterEx extends java.lang.Exception implements Serializable

Class phenote.datamodel.CharFieldException extends java.lang.Exception implements Serializable

Class phenote.datamodel.OntologyException extends java.lang.Exception implements Serializable

Class phenote.datamodel.TermNotFoundException extends java.lang.Exception implements Serializable

Package phenote.edit

Class phenote.edit.CharChangeEvent extends java.util.EventObject implements Serializable

Serialized Fields

transaction

TransactionI transaction

Package phenote.error

Class phenote.error.ErrorEvent extends java.util.EventObject implements Serializable

Serialized Fields

message

java.lang.String message

Package phenote.gui

Class phenote.gui.BugWorkaroundTable extends javax.swing.JTable implements Serializable

Class phenote.gui.CharacterTable extends org.bbop.framework.AbstractGUIComponent implements Serializable

serialVersionUID: -3970995454868538116L

Serialized Fields

tableController

CharacterTableController tableController

focusListener

phenote.gui.CharacterTable.ComponentLayoutListener focusListener

addButton

javax.swing.JButton addButton

duplicateButton

javax.swing.JButton duplicateButton

deleteButton

javax.swing.JButton deleteButton

Class phenote.gui.CorrectLineBorderCellEditor extends javax.swing.DefaultCellEditor implements Serializable

Class phenote.gui.DelegatingTransferHandler extends javax.swing.TransferHandler implements Serializable

Serialized Fields

parent

javax.swing.TransferHandler parent

Class phenote.gui.FieldRightClickMenu extends javax.swing.JPopupMenu implements Serializable

Class phenote.gui.GetInfo extends javax.swing.JDialog implements Serializable

Serialized Fields

ontologyList

javax.swing.JList ontologyList

ontologyDetails

javax.swing.JEditorPane ontologyDetails

generalInfoPanel

javax.swing.JEditorPane generalInfoPanel

config

Config config

ontologyFiles

phenote.config.xml.OntologyFileDocument.OntologyFile[] ontologyFiles

termDefs

phenote.config.xml.TerminologyDefinitionsDocument.TerminologyDefinitions termDefs

ontologyConfig

java.util.List<E> ontologyConfig

ontologies

phenote.config.xml.OntologyFileDocument.OntologyFile[] ontologies

oboSession

org.obo.datamodel.OBOSession oboSession

selectedOntology

int selectedOntology

charFieldManager

CharFieldManager charFieldManager

charListManager

CharacterListManager charListManager

loadedOntologies

java.util.List<E> loadedOntologies

Class phenote.gui.LoadingScreen extends javax.swing.JFrame implements Serializable

Serialized Fields

startupProgressBar

javax.swing.JProgressBar startupProgressBar

Launch the application

message

javax.swing.JLabel message

Class phenote.gui.NcbiInfo extends org.bbop.framework.AbstractGUIComponent implements Serializable

Serialized Fields

selectionManager

SelectionManager selectionManager

omimAdapter

OMIMAdapter omimAdapter

pubmedAdapter

PubMedAdapter pubmedAdapter

ncbiInfoScroll

javax.swing.JScrollPane ncbiInfoScroll

ncbiTextArea

javax.swing.JEditorPane ncbiTextArea

actionListener

java.awt.event.ActionListener actionListener

Class phenote.gui.OldHelpMenu extends javax.swing.JMenu implements Serializable

Serialized Fields

help

javax.swing.JMenuItem help

splashScreen

SplashScreen splashScreen

termRequester

TermRequestGUI termRequester

logoFile

java.lang.String logoFile

Class phenote.gui.PhenoteMainFrame extends org.bbop.framework.MainFrame implements Serializable

Serialized Fields

menubar

org.bbop.swing.EnhancedMenuBar menubar

mainPanel

javax.swing.JPanel mainPanel

lockDoc

boolean lockDoc

mainToolBar

javax.swing.JToolBar mainToolBar

dimensionInfo

int[][] dimensionInfo

config size? 3 arrays of numbers to try for frame size - compare with screen size, first # in array is width, 2nd is height, the 3rd one doesnt seem to be used???

Class phenote.gui.ScratchGroupsView extends org.bbop.framework.AbstractGUIComponent implements Serializable

Serialized Fields

addButton

javax.swing.JButton addButton

deleteButton

javax.swing.JButton deleteButton

showTableButton

javax.swing.JButton showTableButton

selectionModel

ca.odell.glazedlists.swing.EventSelectionModel<E> selectionModel

Class phenote.gui.SplashScreen extends javax.swing.JWindow implements Serializable

Serialized Fields

borderLayout1

java.awt.BorderLayout borderLayout1

imageLabel

javax.swing.JLabel imageLabel

southPanel

javax.swing.JPanel southPanel

southPanelFlowLayout

java.awt.FlowLayout southPanelFlowLayout

progressBar

javax.swing.JProgressBar progressBar

imageIcon

javax.swing.ImageIcon imageIcon

enable

boolean enable

Class phenote.gui.StackedBox extends javax.swing.JPanel implements Serializable

Serialized Fields

titleBackgroundColor

java.awt.Color titleBackgroundColor

titleForegroundColor

java.awt.Color titleForegroundColor

separatorColor

java.awt.Color separatorColor

separatorBorder

javax.swing.border.Border separatorBorder

Class phenote.gui.StandardToolbar extends org.bbop.framework.AbstractGUIComponent implements Serializable

Serialized Fields

buttons

java.util.Vector<E> buttons

toolbar

javax.swing.JToolBar toolbar

Class phenote.gui.SynchOntologyDialog.CancelEx extends java.lang.Exception implements Serializable

Class phenote.gui.TermInfo2 extends org.bbop.framework.AbstractGUIComponent implements Serializable

Serialized Fields

cachedAnnotationInformationContentByClass

java.util.Map<K,V> cachedAnnotationInformationContentByClass

cachedAnnotationCountByClass

java.util.Map<K,V> cachedAnnotationCountByClass

includeImplicitAnnotations

boolean includeImplicitAnnotations

includeExternalDatabaseAnnotations

boolean includeExternalDatabaseAnnotations

currentOboClass

org.obo.datamodel.OBOObject currentOboClass

useTermListener

UseTermListener useTermListener

termHyperlinkListener

phenote.gui.TermInfo2.TermHyperlinkListener termHyperlinkListener

selectionManager

SelectionManager selectionManager

termInfoToolbar

TermInfoToolbar termInfoToolbar

termInfoScroll

javax.swing.JScrollPane termInfoScroll

termInfoPanel

StackedBox termInfoPanel

StackedBox is a class in the phenote.gui package, that nicole got from web & modified

basicInfoPanel

javax.swing.JPanel basicInfoPanel

termName

javax.swing.JEditorPane termName

termID

javax.swing.JTextField termID

ontologyName

javax.swing.JLabel ontologyName

annotationSummaryLabel

javax.swing.JLabel annotationSummaryLabel

definitionTextArea

javax.swing.JEditorPane definitionTextArea

annotationSummaryTextArea

org.bbop.swing.HyperlinkLabel annotationSummaryTextArea

considerReplacePanel

javax.swing.JPanel considerReplacePanel

considerTerms

javax.swing.JTextArea considerTerms

replacementTerms

javax.swing.JTextArea replacementTerms

synonymPanel

javax.swing.JPanel synonymPanel

annotationPanel

javax.swing.JPanel annotationPanel

dbxrefPanel

javax.swing.JPanel dbxrefPanel

dbxrefText

javax.swing.JTextArea dbxrefText

xpDefPanel

javax.swing.JPanel xpDefPanel

xpDefList

javax.swing.JTextArea xpDefList

propertyValuesPanel

javax.swing.JPanel propertyValuesPanel

ontologyLinksPanel

javax.swing.JPanel ontologyLinksPanel

parentsPanel

javax.swing.JPanel parentsPanel

parentsText

javax.swing.JTextArea parentsText

childrenPanel

javax.swing.JPanel childrenPanel

childrenText

javax.swing.JTextArea childrenText

commentsPanel

javax.swing.JPanel commentsPanel

commentsText

javax.swing.JTextArea commentsText

emptyPanel

javax.swing.JPanel emptyPanel

showEmptyPanelsFlag

boolean showEmptyPanelsFlag

useOBOSessionManager

boolean useOBOSessionManager

Class phenote.gui.TermInfoToolbar extends javax.swing.JToolBar implements Serializable

Serialized Fields

useTermListener

UseTermListener useTermListener

currentOboClass

org.obo.datamodel.OBOObject currentOboClass

BACKBUTTONINDEX

int BACKBUTTONINDEX

FORWARDBUTTONINDEX

int FORWARDBUTTONINDEX

FAVBUTTONINDEX

int FAVBUTTONINDEX

USETERMBUTTONINDEX

int USETERMBUTTONINDEX

GETANNOTATIONSBUTTONINDEX

int GETANNOTATIONSBUTTONINDEX

buttons

java.util.Vector<E> buttons

termField

javax.swing.JTextArea termField

Class phenote.gui.TermRequestGUI extends javax.swing.JFrame implements Serializable

Serialized Fields

buttonGroup

javax.swing.ButtonGroup buttonGroup

ontologyComboBox

javax.swing.JComboBox ontologyComboBox

newRadioButton

javax.swing.JRadioButton newRadioButton

newtermName

javax.swing.JTextField newtermName

newtermDef

javax.swing.JTextArea newtermDef

newtermComment

javax.swing.JTextArea newtermComment

thisframe

javax.swing.JFrame thisframe

Class phenote.gui.VerticalScrollingOnlyPanel extends javax.swing.JPanel implements Serializable

Package phenote.gui.actions

Class phenote.gui.actions.AboutAction extends javax.swing.AbstractAction implements Serializable

Class phenote.gui.actions.ActionManager.SaveAction extends javax.swing.AbstractAction implements Serializable

Class phenote.gui.actions.BackAction extends javax.swing.AbstractAction implements Serializable

Serialized Fields

textComponent

javax.swing.JComponent textComponent

Class phenote.gui.actions.CopyAction extends javax.swing.AbstractAction implements Serializable

Serialized Fields

textComponent

javax.swing.JComponent textComponent

Class phenote.gui.actions.DbCommitAction extends javax.swing.AbstractAction implements Serializable

Class phenote.gui.actions.DuplicateAnnotationAction extends javax.swing.AbstractAction implements Serializable

Class phenote.gui.actions.ForwardAction extends javax.swing.AbstractAction implements Serializable

Class phenote.gui.actions.MakeOntolAction extends javax.swing.AbstractAction implements Serializable

Serialized Fields

ontolMaker

OntologyMakerI ontolMaker

Class phenote.gui.actions.NCBIQueryAction extends javax.swing.AbstractAction implements Serializable

Serialized Fields

omimAdapter

OMIMAdapter omimAdapter

Class phenote.gui.actions.NewFileAction extends javax.swing.AbstractAction implements Serializable

Class phenote.gui.actions.OpenFileAction extends javax.swing.AbstractAction implements Serializable

Class phenote.gui.actions.RedoAction extends javax.swing.AbstractAction implements Serializable

Class phenote.gui.actions.ResponderChainAction extends javax.swing.AbstractAction implements Serializable

Serialized Fields

actionCommand

java.lang.String actionCommand

finalResponder

java.lang.Object finalResponder

Class phenote.gui.actions.SaveAsFileAction extends javax.swing.AbstractAction implements Serializable

Class phenote.gui.actions.SaveFileAction extends javax.swing.AbstractAction implements Serializable

Class phenote.gui.actions.TermRequestAction extends javax.swing.AbstractAction implements Serializable

Serialized Fields

termRequester

TermRequestGUI termRequester

Class phenote.gui.actions.UndoAction extends javax.swing.AbstractAction implements Serializable

Package phenote.gui.field

Class phenote.gui.field.CharFieldGuiEx extends java.lang.Exception implements Serializable

Class phenote.gui.field.FieldPanel extends org.bbop.framework.AbstractGUIComponent implements Serializable

Serialized Fields

charFieldGuiList

java.util.List<E> charFieldGuiList

searchParamPanel

SearchParamPanel searchParamPanel

charFieldManager

CharFieldManager charFieldManager

fieldPanel

javax.swing.JPanel fieldPanel

jTabbedPane

javax.swing.JTabbedPane jTabbedPane

group

java.lang.String group

selectionManager

SelectionManager selectionManager

groupEditMan

EditManager groupEditMan

selectionModel

ca.odell.glazedlists.swing.EventSelectionModel<E> selectionModel

currentGridBagRow

int currentGridBagRow

Class phenote.gui.field.FieldPanelContainer extends org.bbop.framework.AbstractGUIComponent implements Serializable

serialVersionUID: 8979068659549011611L

Serialized Fields

panels

java.util.Map<K,V> panels

responderDelegate

java.lang.Object responderDelegate

Package phenote.gui.menu

Class phenote.gui.menu.EditMenu extends org.bbop.swing.DynamicMenu implements Serializable

Serialized Fields

editMenuItem

javax.swing.JMenuItem editMenuItem

Class phenote.gui.menu.FileMenu extends org.bbop.swing.DynamicMenu implements Serializable

Class phenote.gui.menu.PhenoteHelpMenu extends org.bbop.swing.DynamicMenu implements Serializable

Class phenote.gui.menu.SettingsMenu extends org.bbop.swing.DynamicMenu implements Serializable

Serialized Fields

ITEM_PLAIN

int ITEM_PLAIN

ITEM_CHECK

int ITEM_CHECK

ITEM_RADIO

int ITEM_RADIO

menuSearchFilterTerm

javax.swing.JMenuItem menuSearchFilterTerm

menuSearchFilterSynonym

javax.swing.JMenuItem menuSearchFilterSynonym

menuSearchFilterDefinition

javax.swing.JMenuItem menuSearchFilterDefinition

menuSearchFilterObsolete

javax.swing.JMenuItem menuSearchFilterObsolete

showHistory

javax.swing.JMenuItem showHistory

lockDoc

javax.swing.JMenuItem lockDoc

searchParams

SearchParams searchParams

selHist

SelectionHistory selHist

config

Config config

Package phenote.gui.selection

Class phenote.gui.selection.CharSelectionEvent extends java.util.EventObject implements Serializable

Serialized Fields

charList

java.util.List<E> charList

previouslySelectedChars

java.util.List<E> previouslySelectedChars

Class phenote.gui.selection.IDSelectionEvent extends java.util.EventObject implements Serializable

Serialized Fields

id

java.lang.String id

fieldType

java.lang.String fieldType

Class phenote.gui.selection.TermSelectionEvent extends java.util.EventObject implements Serializable

Serialized Fields

oboClass

org.obo.datamodel.OBOClass oboClass

useTermListener

UseTermListener useTermListener

isMouseOverEvent

boolean isMouseOverEvent

isHyperlinkEvent

boolean isHyperlinkEvent

Class phenote.gui.selection.UseTermEvent extends java.util.EventObject implements Serializable

Serialized Fields

oboObject

org.obo.datamodel.OBOObject oboObject

Package phenote.matrix.view

Class phenote.matrix.view.MatrixComponent extends org.bbop.framework.AbstractGUIComponent implements Serializable

Serialized Fields

controller

MatrixController controller

matrixTableModel

phenote.matrix.view.MatrixComponent.MatrixTableModel matrixTableModel

matrixTable

javax.swing.JTable matrixTable

matrixPane

javax.swing.JScrollPane matrixPane

Class phenote.matrix.view.MatrixTableRenderer extends javax.swing.table.DefaultTableCellRenderer implements Serializable

Package phenote.presentation.tags

Class phenote.presentation.tags.FileUtilTag extends javax.servlet.jsp.tagext.TagSupport implements Serializable

Serialized Fields

type

java.lang.String type

beanName

java.lang.String beanName

property

java.lang.String property

scope

java.lang.String scope

Class phenote.presentation.tags.RelationshipTag extends javax.servlet.jsp.tagext.TagSupport implements Serializable

Serialized Fields

type

java.lang.String type

beanName

java.lang.String beanName

property

java.lang.String property

scope

java.lang.String scope

Package phenote.servlet

Class phenote.servlet.DataInputServlet extends javax.servlet.http.HttpServlet implements Serializable

Class phenote.servlet.PhenoteServlet extends org.springframework.web.servlet.DispatcherServlet implements Serializable