Serialized Form

Package org.bioquery.bqutils

Class org.bioquery.bqutils.BQUser implements Serializable

Serialized Fields

username

java.lang.String username

The stored username for this BQUser object.

password

char[] password

The stored password for this BQUser object.

Package org.bioquery.gui

Class org.bioquery.gui.BQFileChooser implements Serializable

Serialized Fields

dialogName

java.lang.String dialogName

filePath

java.lang.String filePath

fileName

java.lang.String fileName

dialogTree

javax.swing.JTree dialogTree

rootNode

BQTreeNode rootNode

myFrame

BQFrame myFrame

me

javax.swing.JDialog me

fileNameField

javax.swing.JTextField fileNameField

pathField

javax.swing.JTextField pathField

fileNamePanel

javax.swing.JPanel fileNamePanel

showDirOnly

boolean showDirOnly

chooseDirectory

boolean chooseDirectory

filenameListener

javax.swing.event.DocumentListener filenameListener

mouseClickListener

java.awt.event.MouseListener mouseClickListener

okButtonListener

java.awt.event.ActionListener okButtonListener

cancelButtonListener

java.awt.event.ActionListener cancelButtonListener

Class org.bioquery.gui.BQFileRenderer implements Serializable

Serialized Fields

directoryIcon

javax.swing.ImageIcon directoryIcon

textFileIcon

javax.swing.ImageIcon textFileIcon

queryFileIcon

javax.swing.ImageIcon queryFileIcon

Class org.bioquery.gui.BQFrame implements Serializable

Serialized Fields

iconpath

java.lang.String iconpath

myProgramManager

ProgramManager myProgramManager

myFileManager

BQFileManager myFileManager

myFileManagerView

FileManagerView myFileManagerView

myQueryManager

QueryManager myQueryManager

localFileChooser

javax.swing.JFileChooser localFileChooser

tabList

java.util.ArrayList tabList

Stores the path of each file displayed at a position in the ArrayList equivalent to it's tabIndex. i.e. Tab at index 3 displays the file saved at the path stored in tabList index 3.
Is null if the file has not been saved.

menuBar

javax.swing.JMenuBar menuBar

me

BQFrame me

this allows inner classes to access the frame by referring to 'me' rather than 'this'

newQuery

org.bioquery.gui.BQFrame.BQFrameAction newQuery

closeFile

org.bioquery.gui.BQFrame.BQFrameAction closeFile

saveFile

org.bioquery.gui.BQFrame.BQFrameAction saveFile

saveAsFile

org.bioquery.gui.BQFrame.BQFrameAction saveAsFile

openLocally

org.bioquery.gui.BQFrame.BQFrameAction openLocally

saveLocally

org.bioquery.gui.BQFrame.BQFrameAction saveLocally

print

org.bioquery.gui.BQFrame.BQFrameAction print

exit

org.bioquery.gui.BQFrame.BQFrameAction exit

openFile

org.bioquery.gui.BQFrame.BQFrameAction openFile

createDirectory

org.bioquery.gui.BQFrame.BQFrameAction createDirectory

renameFile

org.bioquery.gui.BQFrame.BQFrameAction renameFile

copyFile

org.bioquery.gui.BQFrame.BQFrameAction copyFile

moveFile

org.bioquery.gui.BQFrame.BQFrameAction moveFile

deleteFile

org.bioquery.gui.BQFrame.BQFrameAction deleteFile

undo

org.bioquery.gui.BQFrame.BQFrameAction undo

redo

org.bioquery.gui.BQFrame.BQFrameAction redo

cut

org.bioquery.gui.BQFrame.BQFrameAction cut

copy

org.bioquery.gui.BQFrame.BQFrameAction copy

paste

org.bioquery.gui.BQFrame.BQFrameAction paste

login

org.bioquery.gui.BQFrame.BQFrameAction login

accountOptions

org.bioquery.gui.BQFrame.BQFrameAction accountOptions

changePassword

org.bioquery.gui.BQFrame.BQFrameAction changePassword

createNewAccount

org.bioquery.gui.BQFrame.BQFrameAction createNewAccount

configureProxyServer

org.bioquery.gui.BQFrame.BQFrameAction configureProxyServer

logout

org.bioquery.gui.BQFrame.BQFrameAction logout

fileManager

org.bioquery.gui.BQFrame.BQFrameAction fileManager

refreshScreen

org.bioquery.gui.BQFrame.BQFrameAction refreshScreen

helpContents

org.bioquery.gui.BQFrame.BQFrameAction helpContents

viewTutorial

org.bioquery.gui.BQFrame.BQFrameAction viewTutorial

feedback

org.bioquery.gui.BQFrame.BQFrameAction feedback

aboutBioQuery

org.bioquery.gui.BQFrame.BQFrameAction aboutBioQuery

theSplitPane

javax.swing.JSplitPane theSplitPane

theSplitPane separates the FileManagerView (on the left) from theTabbedPane (on the right).

openDividerLocation

int openDividerLocation

closedDividerLocation

int closedDividerLocation

minimumDividerLocation

int minimumDividerLocation

theTabbedPane

javax.swing.JTabbedPane theTabbedPane

quickTipsLabel

javax.swing.JLabel quickTipsLabel

popup

javax.swing.JPopupMenu popup

welcomeDialog

javax.swing.JDialog welcomeDialog

popupListener

java.awt.event.MouseAdapter popupListener

tabListener

javax.swing.event.ChangeListener tabListener

The TabbedPane's listener that changes the enabled/disabled state of the actions (which control the buttons and menu items) depending on which type of view is in the currently selected tab.

Class org.bioquery.gui.BQTreeNode implements Serializable

Serialized Fields

fileSeparator

java.lang.String fileSeparator

the fileseparator returned in the path lists by the server. should be set after reading info returned by server.

fileName

java.lang.String fileName

isLoaded

boolean isLoaded

modifiable

boolean modifiable

filePath

java.lang.String filePath

Class org.bioquery.gui.DataView implements Serializable

Class org.bioquery.gui.DefaultQueryView implements Serializable

Serialized Fields

me

DefaultQueryView me

myFrame

BQFrame myFrame

myScrollPane

javax.swing.JScrollPane myScrollPane

databaseHelpButton

javax.swing.JButton databaseHelpButton

queryLineTable

com.synaptocode.swingtools.TablePane queryLineTable

addLineTable

com.synaptocode.swingtools.TablePane addLineTable

addLineTextArea

javax.swing.JTextArea addLineTextArea

searchButton

javax.swing.JButton searchButton

rollUp

com.synaptocode.swingtools.EmbeddedRollUpPane rollUp

controlPanel

com.synaptocode.swingtools.TablePane controlPanel

databaseLabel

javax.swing.JLabel databaseLabel

formatSelection

javax.swing.JComboBox formatSelection

numItemsToDisplay

javax.swing.JComboBox numItemsToDisplay

combineLabel

javax.swing.JLabel combineLabel

booleanOpCombo

javax.swing.JComboBox booleanOpCombo

combineButton

javax.swing.JButton combineButton

settingsLabel

javax.swing.JLabel settingsLabel

settingsButton

javax.swing.JButton settingsButton

clearResultsButton

javax.swing.JButton clearResultsButton

editResultsButton

javax.swing.JButton editResultsButton

saveResultsButton

javax.swing.JButton saveResultsButton

resultsPanel

javax.swing.JPanel resultsPanel

resultsPreview

View resultsPreview

settingsDialog

javax.swing.JDialog settingsDialog

buttonMap

java.util.HashMap buttonMap

textAreaMap

java.util.HashMap textAreaMap

labelMap

java.util.HashMap labelMap

popup

com.synaptocode.swingtools.MousePopup popup

toolsMenu

javax.swing.JMenu toolsMenu

insertLineBefore

org.bioquery.gui.DefaultQueryView.BuildingViewAction insertLineBefore

insertLineAfter

org.bioquery.gui.DefaultQueryView.BuildingViewAction insertLineAfter

deleteLine

org.bioquery.gui.DefaultQueryView.BuildingViewAction deleteLine

previewLine

org.bioquery.gui.DefaultQueryView.BuildingViewAction previewLine

column2Width

int column2Width

col1Width

int col1Width

col2Width

int col2Width

col3Width

int col3Width

col4Width

int col4Width

waitDialog

org.bioquery.gui.WaitDialog waitDialog

alwaysGetResults

boolean alwaysGetResults

previewButtonListener

java.awt.event.ActionListener previewButtonListener

fieldListener

java.awt.event.ActionListener fieldListener

traverseFocusAction

javax.swing.Action traverseFocusAction

focusLostListener

java.awt.event.FocusListener focusLostListener

searchAction

javax.swing.Action searchAction

Class org.bioquery.gui.DemoDialog implements Serializable

Serialized Fields

myFrame

BQFrame myFrame

demoLocation

java.lang.String demoLocation

iconpath

java.lang.String iconpath

demo

javax.swing.JEditorPane demo

linkClicked

javax.swing.event.HyperlinkListener linkClicked

Class org.bioquery.gui.FeedbackForm implements Serializable

Serialized Fields

myFrame

BQFrame myFrame

toAddress

java.lang.String toAddress

title

java.lang.String title

fromAddress

java.lang.String fromAddress

message

java.lang.String message

fromTextField

javax.swing.JTextField fromTextField

messageTextArea

javax.swing.JTextPane messageTextArea

sendButton

javax.swing.JButton sendButton

cancelButton

javax.swing.JButton cancelButton

Class org.bioquery.gui.FileManagerView implements Serializable

Serialized Fields

myFrame

BQFrame myFrame

myScrollPane

javax.swing.JScrollPane myScrollPane

tree

javax.swing.JTree tree

rootNode

BQTreeNode rootNode

me

FileManagerView me

filePopup

javax.swing.JPopupMenu filePopup

expandedPaths

java.util.ArrayList expandedPaths

A list of each TreePath that is expanded. Updated by the TreeExpansionListener and used to re-expand the same paths whenever the tree is redrawn.

expandListener

javax.swing.event.TreeExpansionListener expandListener

clickListener

java.awt.event.MouseListener clickListener

treeSelectListener

javax.swing.event.TreeSelectionListener treeSelectListener

Class org.bioquery.gui.HelpFrame implements Serializable

Serialized Fields

myFrame

BQFrame myFrame

iconpath

java.lang.String iconpath

helpLocation

java.lang.String helpLocation

firstPage

java.lang.String firstPage

contentsPage

java.net.URL contentsPage

browser

com.synaptocode.swingtools.LightHtmlPane browser

backButton

javax.swing.JButton backButton

forwardButton

javax.swing.JButton forwardButton

contentsButton

javax.swing.JButton contentsButton

printButton

javax.swing.JButton printButton

Class org.bioquery.gui.HtmlDataView implements Serializable

Serialized Fields

myEditorPane

javax.swing.JEditorPane myEditorPane

myFrame

BQFrame myFrame

me

HtmlDataView me

Class org.bioquery.gui.QueryView implements Serializable

Serialized Fields

myQuery

Query myQuery

Class org.bioquery.gui.TextDataView implements Serializable

Serialized Fields

myTextPane

javax.swing.JTextPane myTextPane

myFrame

BQFrame myFrame

me

TextDataView me

editorKit

javax.swing.text.StyledEditorKit editorKit

Class org.bioquery.gui.UnknownFileTypeException implements Serializable

Class org.bioquery.gui.View implements Serializable

Serialized Fields

myGUI

BQGUI myGUI

fileName

java.lang.String fileName

filePath

java.lang.String filePath

modified

boolean modified

theBook

java.awt.print.Book theBook

Class org.bioquery.gui.ViewException implements Serializable

Serialized Fields

cause

java.lang.Throwable cause

Package org.bioquery.query

Class org.bioquery.query.InvalidQueryException implements Serializable

Class org.bioquery.query.InvalidQueryLineException implements Serializable

Class org.bioquery.query.Query implements Serializable

Serialized Fields

myQuerySubmitter

QuerySubmitter myQuerySubmitter

name

java.lang.String name

database

java.lang.String database

helpURL

java.lang.String helpURL

queryLines

java.util.ArrayList queryLines

fileExtension

java.lang.String fileExtension

formats

java.util.HashMap formats

Available formats for the results, along with a file extension that indicates how to display the results (txt, html). Format Name: File Extension

maxDisplayForFormat

java.util.HashMap maxDisplayForFormat

Sets the max number of results returned based on the format. Map items are: Format name : Integer

currentFormat

java.lang.String currentFormat

Format currently chosen for results. this is the key in the formats HashMap.

fields

java.util.HashMap fields

Searchable fields for this Query's database Human-readable name : field code

startDisplayNum

int startDisplayNum

Begin the range of refs to display.

endDisplayNum

int endDisplayNum

End of the range of refs to display. -1 indicates display all refs.

myDescriptor

Query.QueryDescriptor myDescriptor

Each Query possesses one and only one QueryDescriptor instantiated with the Query.

submitLine

int submitLine

QueryLine number to submit. 0 means submit nothing.

Class org.bioquery.query.Query.QueryDescriptor implements Serializable

Serialized Fields

this$0

Query this$0

filePath

java.lang.String filePath

created

java.util.Date created

lastSubmitted

java.util.Date lastSubmitted

lastModified

java.util.Date lastModified

autoSubmit

boolean autoSubmit

submitLineNumber

int submitLineNumber

submitReferencePoint

java.util.Date submitReferencePoint

submitIncrement

int submitIncrement

incrementNumber

int incrementNumber

nextSubmitDate

java.util.Date nextSubmitDate

sendEmail

boolean sendEmail

saveToFile

boolean saveToFile

emailAddress

java.lang.String emailAddress

saveDirectory

java.lang.String saveDirectory

timeIncrements

java.lang.String[][] timeIncrements

This array holds the pairings between human-readable time increment words, and the int constants in the Calendar class. This is used to provide the user with an intuitive way to set the time increment in the Query.QueryDescriptor object that determines how often they receive automated updates.

Class org.bioquery.query.QueryException implements Serializable

Serialized Fields

cause

java.lang.Throwable cause

Class org.bioquery.query.QueryLine implements Serializable

Serialized Fields

myQuery

Query myQuery

lineNumber

int lineNumber

queryText

javax.swing.text.PlainDocument queryText

numReturned

int numReturned

lastSubmitted

java.util.Date lastSubmitted

updateNeeded

boolean updateNeeded