A B C D E F G H I J L M N O P Q R S T U V W

A

aboutBioQuery - Variable in class org.bioquery.gui.BQFrame

accept(File) - Method in class org.bioquery.gui.BQFileFilter

Accept directories and files that have any extension registered with the ProgramManager (that is, extensions listed in the bq.xml properties file).

accountOptions - Variable in class org.bioquery.gui.BQFrame

actionPerformed(ActionEvent) - Method in class org.bioquery.gui.DefaultQueryView

addBioQueryInfo(StringBuffer) - Method in class org.bioquery.query.NCBIQuerySubmitter

Courtesy to NCBI that lets them know who is using their utilites and how to contact us.

addField(String, String) - Method in class org.bioquery.query.Query

Add a field to the list of fields this query can search in it's database.

addFormat(String, String, int) - Method in class org.bioquery.query.Query

Adds a format to the list of formats that this query can return it's resultset in.

addParameter(String, String, String) - Static method in class org.bioquery.bqutils.UrlUtils

Takes the given url String and adds the given parameter to the querystring of that url.

addQueryLine() - Method in class org.bioquery.query.Query

Add a new blank QueryLine at the next available position.

addView(View) - Method in class org.bioquery.gui.BQFrame

AND - Static variable in class org.bioquery.query.Query

Represents the Boolean command AND.

autoSubmitOn() - Method in class org.bioquery.query.Query.QueryDescriptor

Returns whether the Query should automatically be submitted at some interval.

B

BEGIN_QUERYLINE_DATA - Static variable in class org.bioquery.bqutils.BQProtocol

Added to the server response to the client during a Query submission to indicate that the following lines contain a series of numbers, one per line, that indicate the result count for each QueryLine of the Query.

BEGIN_QUERYLINE_RESULTS - Static variable in class org.bioquery.bqutils.BQProtocol

Added to the server response to the client during a Query submission to indicate the end of the QueryLine Data, and the beginning of the resultset returned by the submission of the Query's submitLine to it's database.

BEGIN_RESULT_TEXT - Static variable in class org.bioquery.bqutils.BQProtocol

This String marks the end of the Header returned with Query Results.

BQFileChooser - class org.bioquery.gui.BQFileChooser.

A custom JDialog for that can be used to select directories or files and save files to the BioQuery file system.

BQFileChooser(BQFrame, BQTreeNode, String) - Constructor for class org.bioquery.gui.BQFileChooser

BQFileChooser(BQFrame, BQTreeNode, String, String) - Constructor for class org.bioquery.gui.BQFileChooser

BQFileChooser(BQFrame, BQTreeNode, String, String, TreePath) - Constructor for class org.bioquery.gui.BQFileChooser

BQFileChooser(BQFrame, BQTreeNode, String, String, TreePath, int) - Constructor for class org.bioquery.gui.BQFileChooser

BQFileFilter - class org.bioquery.gui.BQFileFilter.

BQFileFilter(ProgramManager) - Constructor for class org.bioquery.gui.BQFileFilter

Get the list of all acceptable file extensions from the ProgramManager.

BQFileManager - interface org.bioquery.gui.BQFileManager.

This interface defines the file operations required by the GUI.

BQFileRenderer - class org.bioquery.gui.BQFileRenderer.

Custom TreeCellRenderer displays filenames and the appropriate icons in the FileManagerView.

BQFileRenderer() - Constructor for class org.bioquery.gui.BQFileRenderer

BQFrame - class org.bioquery.gui.BQFrame.

The BQFrame class is the top-level container that holds the GUI, and thus runs the client-side portion of the BioQuery application.

BQFrame() - Constructor for class org.bioquery.gui.BQFrame

BQFrame(String) - Constructor for class org.bioquery.gui.BQFrame

BQGUI - interface org.bioquery.gui.BQGUI.

Interface that defines the basic operations of the GUI.

BQProtocol - class org.bioquery.bqutils.BQProtocol.

This class defines the constants used by the bioquery application.

BQProtocol() - Constructor for class org.bioquery.bqutils.BQProtocol

BQTreeNode - class org.bioquery.gui.BQTreeNode.

A MutableTreeNode customized to present files and directories.

BQTreeNode() - Constructor for class org.bioquery.gui.BQTreeNode

BQTreeNode(Object) - Constructor for class org.bioquery.gui.BQTreeNode

BQTreeNode(Object, boolean) - Constructor for class org.bioquery.gui.BQTreeNode

BQUser - class org.bioquery.bqutils.BQUser.

This class models the user and simply stores the username and password.

BQUser(String, char[]) - Constructor for class org.bioquery.bqutils.BQUser

Constructor accepts and sets the username and password for this account.

BrowserControl - class org.bioquery.gui.BrowserControl.

This class attempts to open the system default web browser and display a web page when a complete URL is passed to the displayURL method.

BrowserControl() - Constructor for class org.bioquery.gui.BrowserControl

C

changePassword - Variable in class org.bioquery.gui.BQFrame

checkPassword(char[]) - Method in class org.bioquery.bqutils.BQUser

Confirms whether the given password matches the password for this user.

checkUser(String, char[]) - Method in class org.bioquery.bqutils.BQUser

Checks whether the username and password given match the username and password of this user object.

CHOOSE_DIRECTORY - Static variable in class org.bioquery.gui.BQFileChooser

className - Variable in class org.bioquery.gui.ProgramManager.ClassInfo

close() - Method in class org.bioquery.gui.View

Blank implementation.

close() - Method in class org.bioquery.gui.DefaultQueryView

closeFile - Variable in class org.bioquery.gui.BQFrame

collapseFileManager() - Method in class org.bioquery.gui.FileManagerView

configureProxyServer - Variable in class org.bioquery.gui.BQFrame

configureProxyServer() - Method in class org.bioquery.gui.BQFrame

convertOperatorCase(String, boolean) - Static method in class org.bioquery.query.QuerySubmitter

Finds the textual Boolean operators AND, OR, NOT and NEAR surrounded by spaces and converts them to either uppercase or lowercase.

copy - Variable in class org.bioquery.gui.BQFrame

COPY_FILE - Static variable in class org.bioquery.bqutils.BQProtocol

A request by the client for the the server to copy one of the user's files, sent to the BQFileManagerServlet in the URL as the second half of the querystring.

copyFile - Variable in class org.bioquery.gui.BQFrame

copyFile(String, String) - Method in interface org.bioquery.gui.BQFileManager

copyFile(String, String) - Method in class org.bioquery.gui.ServerFileManager

CREATE_DIRECTORY - Static variable in class org.bioquery.bqutils.BQProtocol

A request by the client for the server to create a new subdirectory within the user's directory, sent to the BQFileManagerServlet in the URL as the second half of the querystring.

CREATE_NEW_ACCOUNT - Static variable in class org.bioquery.bqutils.BQProtocol

A request by the client for the server create a new user account.

createDirectory - Variable in class org.bioquery.gui.BQFrame

createDirectory(String) - Method in interface org.bioquery.gui.BQFileManager

createDirectory(String) - Method in class org.bioquery.gui.ServerFileManager

createNewAccount - Variable in class org.bioquery.gui.BQFrame

createNewAccount() - Method in class org.bioquery.gui.BQFrame

createNewAccount(BQUser) - Method in interface org.bioquery.gui.BQFileManager

createNewAccount(BQUser) - Method in class org.bioquery.gui.ServerFileManager

createQuery(String) - Static method in class org.bioquery.query.QueryFactory

Returns a Query object configured to build and submit searches to the specific database passed as the parameter.

cut - Variable in class org.bioquery.gui.BQFrame

D

DataView - class org.bioquery.gui.DataView.

DataView() - Constructor for class org.bioquery.gui.DataView

DefaultQueryView - class org.bioquery.gui.DefaultQueryView.

This class represents a view and controller for manipulating Query objects.

DefaultQueryView() - Constructor for class org.bioquery.gui.DefaultQueryView

DELETE_FILE - Static variable in class org.bioquery.bqutils.BQProtocol

A request by the client for the the server to delete one of the user's files, sent to the BQFileManagerServlet in the URL as the second half of the querystring.

deleteFile - Variable in class org.bioquery.gui.BQFrame

deleteFile(String) - Method in interface org.bioquery.gui.BQFileManager

deleteFile(String) - Method in class org.bioquery.gui.ServerFileManager

deleteQueryLine(int) - Method in class org.bioquery.query.Query

Deletes the QueryLine at the designated line number.

DELIMITER - Static variable in class org.bioquery.bqutils.BQProtocol

The delimiter character, provided as a String, to aid parsing information coming from the server.

DemoDialog - class org.bioquery.gui.DemoDialog.

A JDialog used to display the BioQuery tutorial.

DemoDialog(BQFrame) - Constructor for class org.bioquery.gui.DemoDialog

DemoDialog(BQFrame, String) - Constructor for class org.bioquery.gui.DemoDialog

discardBetween(Reader, StringBuffer, String, String) - Static method in class org.bioquery.query.ReaderUtils

Convienence method simply calls saveUntil, then discardUntil, then saveToEnd
Puts everything EXCEPT what is in between the startTag and the endTag into the destination.

discardUntil(Reader, String) - Static method in class org.bioquery.query.ReaderUtils

Reads the passed Reader up until the first instance of tag is found, discarding the chars.

displayConnectError() - Method in class org.bioquery.gui.DemoDialog

displayConnectError() - Method in class org.bioquery.gui.HelpFrame

displayContent(Object) - Method in class org.bioquery.gui.View

displayContent(Object) - Method in class org.bioquery.gui.DefaultQueryView

displayContent(Object) - Method in class org.bioquery.gui.HtmlDataView

displayContent(Object) - Method in class org.bioquery.gui.TextDataView

displayError(Exception) - Method in interface org.bioquery.gui.BQGUI

displayError(Exception) - Method in class org.bioquery.gui.BQFrame

displayError(Exception, String) - Method in interface org.bioquery.gui.BQGUI

displayError(Exception, String) - Method in class org.bioquery.gui.BQFrame

displayError(String) - Method in interface org.bioquery.gui.BQGUI

displayError(String) - Method in class org.bioquery.gui.BQFrame

displayFileManager(List) - Method in interface org.bioquery.gui.BQGUI

displayFileManager(List) - Method in class org.bioquery.gui.BQFrame

displayMessage(String) - Method in interface org.bioquery.gui.BQGUI

displayMessage(String) - Method in class org.bioquery.gui.BQFrame

displayURL(String) - Static method in class org.bioquery.gui.BrowserControl

Display a file in the system browser.

displayView(Object, View, String, String) - Method in interface org.bioquery.gui.BQGUI

displayView(Object, View, String, String) - Method in class org.bioquery.gui.BQFrame

Displays theContent in an appropriate View.

dumpContentToStream(OutputStream) - Method in class org.bioquery.gui.View

dumpContentToStream(OutputStream) - Method in class org.bioquery.gui.DefaultQueryView

dumpContentToStream(OutputStream) - Method in class org.bioquery.gui.HtmlDataView

dumpContentToStream(OutputStream) - Method in class org.bioquery.gui.TextDataView

E

EFETCH_ADDRESS - Static variable in class org.bioquery.query.NCBIQuerySubmitter

Deprecated in favor of the RETRIEVE_ADDRESS and query.fcgi script.
Web address of the EFetch utility at NCBI/NIH Note: This is no longer used.

EFETCH_MODE - Static variable in class org.bioquery.query.NCBIQuerySubmitter

Deprecated in favor of the RETRIEVE_ADDRESS and query.fcgi script.
The mode is the file format of the results (html, file, text).

endDate - Variable in class org.bioquery.query.QuerySubmitter

ERROR_MESSAGE_HEADER - Static variable in class org.bioquery.bqutils.BQProtocol

Sent by the server to the client to indicate a server error while processing a request.

ESEARCH_ADDRESS - Static variable in class org.bioquery.query.NCBIQuerySubmitter

Web address of the ESearch utility at NCBI/NIH
ESearch retrieves the counts (when getQueryData is called) and a list of unique identifiers to pass to the retrieve scipt when getQueryResults is called.

exit - Variable in class org.bioquery.gui.BQFrame

extension - Variable in class org.bioquery.gui.ProgramManager.ClassInfo

F

FAILURE - Static variable in class org.bioquery.bqutils.BQProtocol

Added to the server response to the client during a Query submission to indicate that the requested operation failed.

feedback - Variable in class org.bioquery.gui.BQFrame

FeedbackForm - class org.bioquery.gui.FeedbackForm.

A JDialog that acts as a very simple Email client, allowing the user to compose and send a message.

FeedbackForm(BQFrame, String, String) - Constructor for class org.bioquery.gui.FeedbackForm

FeedbackForm(BQFrame, String, String, String) - Constructor for class org.bioquery.gui.FeedbackForm

FILE_METHOD - Static variable in class org.bioquery.bqutils.BQProtocol

This represents the first half of the querystring sent to the BQFileManagerServlet in the URL, indicating that the second half of this querystring will designate which file operation the client is requesting.

FILE_PATH - Static variable in class org.bioquery.bqutils.BQProtocol

This represents the first half of the querystring sent to the BQFileManagerServlet in the URL, indicating that the second half of this querystring contains the pathname of a file.

fileManager - Variable in class org.bioquery.gui.BQFrame

FileManagerView - class org.bioquery.gui.FileManagerView.

A JPanel that displays the users files in a TreeView.

FileManagerView(List, BQFrame) - Constructor for class org.bioquery.gui.FileManagerView

fileName - Variable in class org.bioquery.gui.View

filePath - Variable in class org.bioquery.gui.View

FileUtils - class org.bioquery.bqutils.FileUtils.

Simple file utilities for working with the bioquery file system.

FileUtils() - Constructor for class org.bioquery.bqutils.FileUtils

filterByDate(String) - Method in class org.bioquery.query.NCBIQuerySubmitter

Helper method adjusts the Query text to search for results added or modified between 2 specific dates: startDate and endDate.

findElement(Element, String) - Static method in class org.bioquery.query.JdomUtils

G

GET_QUERY_DATA - Static variable in class org.bioquery.bqutils.BQProtocol

This is the 2nd half of the querystring indicating that the QuerySubmitter method to call is getQueryData to only retrieve counts, not the full results.

GET_QUERY_RESULTS - Static variable in class org.bioquery.bqutils.BQProtocol

This is the 2nd half of the querystring indicating that the QuerySubmitter method to call is getQueryResults to retrieve the full results of the Query.

getAllFields() - Method in class org.bioquery.query.Query

Returns a Map containing the names of all available fields for this query.

getAllFileExtensions() - Method in class org.bioquery.gui.ProgramManager

getAllFormats() - Method in class org.bioquery.query.Query

Returns a Map containing all available result formats for this Query, and the file extension for each format.

getAllParameters(String) - Static method in class org.bioquery.bqutils.UrlUtils

Given a querystring from a URL, this method will extract all of the parameters and put them in a Hashtable in which the first part of the querystring is the key and the second part is the value.

getAllQueryLines() - Method in class org.bioquery.query.Query

Returns the entire query as an Array of QueryLine objects.

getAllValues() - Method in class org.bioquery.query.QueryLine

Returns an ArrayList of String objects that represent the 4 paramaters that define a QueryLine: Line number Query line text number of results date last submitted The List contains these 4 Strings in the order given above.

getAlwaysGetResults() - Method in class org.bioquery.gui.DefaultQueryView

getBook() - Method in class org.bioquery.gui.View

getBooleanOperators() - Static method in class org.bioquery.query.Query

Returns all available boolean operators as a String[].

getBQFileManager() - Method in class org.bioquery.gui.BQFrame

getCause() - Method in class org.bioquery.query.QueryException

Returns an embedded exception that may yield greater insight into why this exception was thrown.

getCause() - Method in class org.bioquery.gui.ViewException

Returns an embedded exception that may yield greater insight into why this exception was thrown.

getClassForExtension(String) - Method in class org.bioquery.gui.ProgramManager

getCount(Document) - Method in class org.bioquery.query.NCBIQuerySubmitter

Pulls the reference count out of the returned xml document when ESearch is asked to provide counts, such as when getQueryData is called.

getCreated() - Method in class org.bioquery.query.Query.QueryDescriptor

The Date the Query was created.

getCurrentFormat() - Method in class org.bioquery.query.Query

Returns the currently chosen format for the results of this query.

getDatabase() - Method in class org.bioquery.query.Query

Get the name of this query's database.

getDatabaseCode() - Method in class org.bioquery.query.NCBIQuerySubmitter

Returns a database code that can be added to the URLs to all NCBI scripts to tell it which database to search.

getDatabaseList() - Static method in class org.bioquery.query.QueryFactory

Returns a java.util.List containing the common name for each database available from this QueryFactory as Strings.

getDescription() - Method in class org.bioquery.gui.BQFileFilter

Return a simple String description of files that pass this filter "BioQuery files"

getEmailAddress() - Method in class org.bioquery.query.Query.QueryDescriptor

Returns the EMail address that the results of this Query should be sent to (if getSendEmail() == true).

getEndDisplayNum() - Method in class org.bioquery.query.Query

Get the end display number (the end number in the set of results to be returned).

getExtensionForFormat() - Method in class org.bioquery.query.Query

Returns the file extension of the results based on this Query's current format.

getExtensionForView(View) - Method in class org.bioquery.gui.ProgramManager

getFieldCode(String) - Method in class org.bioquery.query.Query

Returns the database-readable field code for the given human-readable field name.

getFileExtension() - Method in class org.bioquery.query.Query

The file extension used to save this Query as a file.

getFileExtension(String) - Static method in class org.bioquery.bqutils.FileUtils

Returns the file extension for the given filename or path.

getFileManagerServletAddress() - Method in class org.bioquery.gui.ProgramManager

getFileManagerView() - Method in class org.bioquery.gui.BQFrame

getFileName() - Method in class org.bioquery.gui.BQFileChooser

getFileName() - Method in class org.bioquery.gui.View

getFileName(String) - Static method in class org.bioquery.bqutils.FileUtils

Pulls the filename off the end of a full path and returns.

getFilePath() - Method in class org.bioquery.query.Query.QueryDescriptor

The path on the server this file is saved to.

getFilePath() - Method in class org.bioquery.gui.BQFileChooser

getFilePath() - Method in class org.bioquery.gui.View

getFilePath() - Method in class org.bioquery.gui.BQTreeNode

getFileSeparator() - Method in class org.bioquery.gui.BQTreeNode

getFileSeparator(String) - Static method in class org.bioquery.bqutils.FileUtils

Returns the file separator used by this path on this server.

getFormatCode(Query) - Method in class org.bioquery.query.NCBIQuerySubmitter

Deprecated in favor of the RETRIEVE_ADDRESS and query.fcgi script.

getHelpFilesLocation() - Method in class org.bioquery.gui.ProgramManager

getHelpURL() - Method in class org.bioquery.query.Query

Get the URL of the help file explaining the structure and use of this query's database.

getIconFilesLocation() - Method in class org.bioquery.gui.ProgramManager

getIDs(Document) - Method in class org.bioquery.query.NCBIQuerySubmitter

Takes the xml document returned by ESearch and pulls out all of the unique IDs and puts them into a List as Strings.

getIncrementNumber() - Method in class org.bioquery.query.Query.QueryDescriptor

Returns the number of time units in between each automatic submission of this Query.

getIsLoaded() - Method in class org.bioquery.gui.BQTreeNode

getLastModified() - Method in class org.bioquery.query.Query.QueryDescriptor

The date the Query was last modified.

getLastSubmitted() - Method in class org.bioquery.query.Query.QueryDescriptor

The Date of the last time the Query was submitted.

getLastSubmitted() - Method in class org.bioquery.query.QueryLine

Returns the time and date that this QueryLine was last submitted.

getLineNumber() - Method in class org.bioquery.query.QueryLine

Returns the line number associated with this QueryLine.

getMaxNumDisplayable() - Method in class org.bioquery.query.Query

Returns the maximum number of items that can be returned in the current format.

getModifiable() - Method in class org.bioquery.gui.BQTreeNode

getModified() - Method in class org.bioquery.gui.View

getMyGUI() - Method in class org.bioquery.gui.View

getMyGUI() - Method in class org.bioquery.gui.ServerFileManager

getName() - Method in class org.bioquery.query.Query

Get the name of this individual query.

getNextSubmitDate() - Method in class org.bioquery.query.Query.QueryDescriptor

Returns the Date at which the next automatic submission should occur.

getNumberOfPages() - Method in class org.bioquery.gui.View

getNumReturned() - Method in class org.bioquery.query.QueryLine

Returns the number of items in the result set of this QueryLine.

getPageFormat(int) - Method in class org.bioquery.gui.View

getPassword() - Method in class org.bioquery.bqutils.BQUser

Returns the password for this user.

getPath(String) - Method in class org.bioquery.gui.FileManagerView

Returns a TreePath object made up of the BQTreeNodes that comprise the given path.

getPath(String) - Static method in class org.bioquery.bqutils.FileUtils

This method takes a path String representing a file or directory and puts each file or directory name into a String array, discarding all of the File.separators.

getPathString(String) - Static method in class org.bioquery.bqutils.FileUtils

Strips the filename off the end of the path String and returns.

getPreferredScrollableViewportSize() - Method in class org.bioquery.gui.View

getPrintable(int) - Method in class org.bioquery.gui.View

getProgramManager() - Method in class org.bioquery.gui.BQFrame

getQuery() - Method in class org.bioquery.query.QueryLine

Returns the Query that this QueryLine is part of.

getQuery() - Method in class org.bioquery.gui.QueryView

getQueryData() - Method in class org.bioquery.query.QuerySubmitter

Finds the number of references returned by each line of the Query.

getQueryData() - Method in class org.bioquery.query.NCBIQuerySubmitter

Finds the number of references returned by each line of the Query.

getQueryData(Query) - Method in class org.bioquery.gui.ServerQueryManager

Deprecated.

getQueryData(Query) - Method in interface org.bioquery.gui.QueryManager

getQueryData(Query) - Method in class org.bioquery.gui.LocalQueryManager

getQueryDescriptor() - Method in class org.bioquery.query.Query

Returns the QueryDescriptor that holds information about the user, when to automatically submit the Query, and when it was last auto-submitted.

getQueryLine(int) - Method in class org.bioquery.query.Query

Returns a single QueryLine from the query.

getQueryLineDocument() - Method in class org.bioquery.query.QueryLine

Returns the underlying Document that holds the query Text.

getQueryManager() - Method in class org.bioquery.gui.BQFrame

getQueryResults() - Method in class org.bioquery.query.QuerySubmitter

Submits this QuerySubmitter's Query object to the appropriate database and returns a BufferedReader containing the text results.

getQueryResults() - Method in class org.bioquery.query.NCBIQuerySubmitter

Submits this QuerySubmitter's Query object to the appropriate database and returns a BufferedReader containing the text results.

getQueryResults(Query, View) - Method in class org.bioquery.gui.ServerQueryManager

Deprecated.

getQueryResults(Query, View) - Method in interface org.bioquery.gui.QueryManager

getQueryResults(Query, View) - Method in class org.bioquery.gui.LocalQueryManager

getQuerySubmitter() - Method in class org.bioquery.query.Query

Returns the QuerySubmitter that can submit this Query to it's database.

getQueryText() - Method in class org.bioquery.query.QueryLine

Returns the actual text of this QueryLine.

getReferencePoint() - Method in class org.bioquery.query.Query.QueryDescriptor

Returns the Reference Point: a Date that simply marks a point in time.

getResultsFooter() - Method in class org.bioquery.query.NCBIQuerySubmitter

Returns a footer String that simply ends the body and html tags.

getResultsHeader() - Method in class org.bioquery.query.NCBIQuerySubmitter

Returns a header containing details about the Query in HTML format.

getRootNode() - Method in class org.bioquery.gui.FileManagerView

getSaveDirectory() - Method in class org.bioquery.query.Query.QueryDescriptor

Returns the path to the Directory that the results of this Query should be saved to (if getSaveToFile() == true).

getSaveToFile() - Method in class org.bioquery.query.Query.QueryDescriptor

Returns whether the user wishes to have the results of this Query saved to a file.

getScrollableBlockIncrement(Rectangle, int, int) - Method in class org.bioquery.gui.View

getScrollableTracksViewportHeight() - Method in class org.bioquery.gui.View

getScrollableTracksViewportWidth() - Method in class org.bioquery.gui.View

getScrollableUnitIncrement(Rectangle, int, int) - Method in class org.bioquery.gui.View

getSelectedFileName() - Method in class org.bioquery.gui.FileManagerView

Note: this method does not guarentee that this is a file and not a directory.

getSelectedPath() - Method in class org.bioquery.gui.FileManagerView

getSendEmail() - Method in class org.bioquery.query.Query.QueryDescriptor

Returns whether the user wishes to have the results of this Query sent to them by Email.

getStartDisplayNum() - Method in class org.bioquery.query.Query

Get the start display number (the first number in the set of results to be returned).

getSubmitIncrement() - Method in class org.bioquery.query.Query.QueryDescriptor

Returns an int that is the unit of how often the Query is automatically submitted.

getSubmitIncrementText() - Method in class org.bioquery.query.Query.QueryDescriptor

Returns the auto-submit increment unit in textual format.

getSubmitLine() - Method in class org.bioquery.query.Query

returns the submitLine (the QueryLine designated as the one to be sent to the database).

getSubmitLineNumber() - Method in class org.bioquery.query.Query

returns the line number of the submitLine (the QueryLine designated as the one to be sent to the database).

getSubmitLineNumber() - Method in class org.bioquery.query.Query.QueryDescriptor

Returns the QueryLine line number that will be submitted to the database.

getSubmitQueryServletAddress() - Method in class org.bioquery.gui.ProgramManager

getSubmittableText() - Method in class org.bioquery.query.NCBIQuerySubmitter

Returns the text to be submitted of the Query.

getTimeIncrements() - Method in class org.bioquery.query.Query.QueryDescriptor

Gets an array of Strings representing the human-readable options for time increments (for example: 'Day', 'Week', or 'Month').

getTimeUnit(int) - Method in class org.bioquery.query.Query.QueryDescriptor

Converts the int constant time increment (from the Calendar class) to the human-readable time increment.

getTimeUnit(String) - Method in class org.bioquery.query.Query.QueryDescriptor

Converts a human-readable time increment into the int constant time increment (from the Calendar class).

getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class org.bioquery.gui.BQFileRenderer

getTutorialFilesLocation() - Method in class org.bioquery.gui.ProgramManager

getUpdate(int) - Method in class org.bioquery.query.Query

Indicates whether we need to update the ref count for the QueryLine the next time the Query is submitted.

getUpdateNeeded() - Method in class org.bioquery.query.QueryLine

Returns true if this QueryLine has been modified and needs to have it's data updated.

getUsername() - Method in class org.bioquery.bqutils.BQUser

Returns the username for this user.

getViewForExtension(String) - Method in class org.bioquery.gui.ProgramManager

guestDemo() - Method in class org.bioquery.gui.BQFrame

H

helpContents - Variable in class org.bioquery.gui.BQFrame

HelpFrame - class org.bioquery.gui.HelpFrame.

A JFrame used to display the help pages.

HelpFrame(String, BQFrame) - Constructor for class org.bioquery.gui.HelpFrame

HelpFrame(String, BQFrame, String) - Constructor for class org.bioquery.gui.HelpFrame

HtmlDataView - class org.bioquery.gui.HtmlDataView.

This DataView displays HTML files, but attempts to open an external web browser to display links.

HtmlDataView() - Constructor for class org.bioquery.gui.HtmlDataView

hyperlinkUpdate(HyperlinkEvent) - Method in class org.bioquery.gui.HtmlDataView

This HyperLinkListener opens all URLs in an external browser via the BrowserControl class.

I

idListURL - Variable in class org.bioquery.query.NCBIQuerySubmitter

URL to create the links in the id list format.

incrementNextSubmitDate() - Method in class org.bioquery.query.Query.QueryDescriptor

Resets the Next Submit Date.

initialize(Query, BQFrame) - Method in class org.bioquery.gui.DefaultQueryView

insertQueryLine(int) - Method in class org.bioquery.query.Query

Insert a blank QueryLine into the list of queryLines at the designated linenum.

INVALID_QUERY_OBJECT - Static variable in class org.bioquery.bqutils.BQProtocol

Sent by the server to the client to indicate the server was not able to read the Query object sent by the client.

InvalidQueryException - exception org.bioquery.query.InvalidQueryException.

Exception class thrown when data or methods within Query objects do not work as intended.

InvalidQueryException() - Constructor for class org.bioquery.query.InvalidQueryException

InvalidQueryException(String) - Constructor for class org.bioquery.query.InvalidQueryException

Constructor accepts a text message.

InvalidQueryException(String, Throwable) - Constructor for class org.bioquery.query.InvalidQueryException

Constructor accepts a text message and an embedded exception.

InvalidQueryException(Throwable) - Constructor for class org.bioquery.query.InvalidQueryException

Constructor accepts an embedded exception.

InvalidQueryLineException - exception org.bioquery.query.InvalidQueryLineException.

Exception class thrown when the query text of a QueryLine object is not valid or contains an invalid line number reference to another QueryLine.

InvalidQueryLineException() - Constructor for class org.bioquery.query.InvalidQueryLineException

InvalidQueryLineException(String) - Constructor for class org.bioquery.query.InvalidQueryLineException

Constructor accepts a text message.

InvalidQueryLineException(String, Throwable) - Constructor for class org.bioquery.query.InvalidQueryLineException

Constructor accepts a text message and an embedded exception.

InvalidQueryLineException(Throwable) - Constructor for class org.bioquery.query.InvalidQueryLineException

Constructor accepts an embedded exception.

isComplete() - Method in class org.bioquery.bqutils.BQUser

Checks whether this user object has a completed username and password of at least the minimum length.

isDirectory(String) - Static method in class org.bioquery.bqutils.FileUtils

Takes a path String representing a file on the server and determines whether it is a file or directory.

isExtensionValid(String, View) - Method in class org.bioquery.gui.ProgramManager

isLeaf() - Method in class org.bioquery.gui.BQTreeNode

Overrides parent method to link the isLeaf() designation with the getAllowsChildren() designation, which should ideally be explicitly set in the constructor.

isLoggedIn() - Method in class org.bioquery.gui.BQFrame

isMac() - Static method in class org.bioquery.gui.BrowserControl

Try to determine whether this application is running on a Macintosh OS or some other platform by examing the "os.name" property.

isWindows() - Static method in class org.bioquery.gui.BrowserControl

Try to determine whether this application is running under Windows or some other platform by examing the "os.name" property.

J

JdomUtils - class org.bioquery.query.JdomUtils.

Utilities that read and write JDOM Document objects to Streams and Files.

JdomUtils() - Constructor for class org.bioquery.query.JdomUtils

L

LocalQueryManager - class org.bioquery.gui.LocalQueryManager.

This class is responsible for retrieving Query data (the number of items returned by each line of the Query) and the Query results (the full resultset of the Query).

LocalQueryManager(BQFrame) - Constructor for class org.bioquery.gui.LocalQueryManager

login - Variable in class org.bioquery.gui.BQFrame

LOGIN - Static variable in class org.bioquery.bqutils.BQProtocol

A request by the client for the Login procedure, sent to the BQFileManagerServlet in the URL as the second half of the querystring.

login() - Method in class org.bioquery.gui.BQFrame

login(String, char[], boolean) - Method in interface org.bioquery.gui.BQFileManager

login(String, char[], boolean) - Method in class org.bioquery.gui.ServerFileManager

loginFailed() - Method in interface org.bioquery.gui.BQGUI

loginFailed() - Method in class org.bioquery.gui.BQFrame

loginSucceeded() - Method in interface org.bioquery.gui.BQGUI

loginSucceeded() - Method in class org.bioquery.gui.BQFrame

logout - Variable in class org.bioquery.gui.BQFrame

LOGOUT - Static variable in class org.bioquery.bqutils.BQProtocol

A request by the client for the server to log out this session.

logout() - Method in interface org.bioquery.gui.BQFileManager

logout() - Method in class org.bioquery.gui.ServerFileManager

logout() - Method in class org.bioquery.gui.BQFrame

M

main(String[]) - Static method in class org.bioquery.gui.StartBioQuery

MAX_NUM_DISPLAYED - Static variable in class org.bioquery.query.NCBIQuerySubmitter

The max number displayed is determined by how long the PMID-containing URL can be before it exceeds the URL size limit set by the NCBI Entrez server.

MIN_PASSWORD_LENGTH - Static variable in class org.bioquery.bqutils.BQUser

The minimum length for a valid password.

MIN_USERNAME_LENGTH - Static variable in class org.bioquery.bqutils.BQUser

The minimum length for a valid username.

modified - Variable in class org.bioquery.gui.View

MOVE_FILE - Static variable in class org.bioquery.bqutils.BQProtocol

A request by the client for the the server to move one of the user's files, sent to the BQFileManagerServlet in the URL as the second half of the querystring.

moveFile - Variable in class org.bioquery.gui.BQFrame

moveFile(String, String) - Method in interface org.bioquery.gui.BQFileManager

moveFile(String, String) - Method in class org.bioquery.gui.ServerFileManager

myGUI - Variable in class org.bioquery.gui.View

myQuery - Variable in class org.bioquery.query.QuerySubmitter

myQuery - Variable in class org.bioquery.gui.QueryView

N

name - Variable in class org.bioquery.gui.ProgramManager.ClassInfo

NCBIQuerySubmitter - class org.bioquery.query.NCBIQuerySubmitter.

The NCBIQuerySubmitter class handles the submission of 8 types of Querys associated with databases at the NCBI (National Center of Biotechnology Information) through their website at www.ncbi.nlm.nih.gov .
Like all QuerySubmitter subclasses, this class should not be instantiated directly, but instead is returned when the getQuerySubmitter method is called on a Query object.

NCBIQuerySubmitter() - Constructor for class org.bioquery.query.NCBIQuerySubmitter

Empty constructor is protected.

NEAR - Static variable in class org.bioquery.query.Query

Represents the Boolean command NEAR.

NEW_FILE - Static variable in class org.bioquery.bqutils.BQProtocol

This represents the first half of the querystring sent to the BQFileManagerServlet in the URL, indicating that the second half of this querystring contains a new path to move or copy a file to.

newQuery - Variable in class org.bioquery.gui.BQFrame

NO_CONSTRAINTS - Static variable in class org.bioquery.gui.BQFileChooser

NOT - Static variable in class org.bioquery.query.Query

Represents the Boolean command NOT.

O

OPEN_FILE - Static variable in class org.bioquery.bqutils.BQProtocol

A request by the client for the server to send back one of the user's saved files, sent to the BQFileManagerServlet in the URL as the second half of the querystring.

openFile - Variable in class org.bioquery.gui.BQFrame

openFile(String) - Method in interface org.bioquery.gui.BQFileManager

openFile(String) - Method in class org.bioquery.gui.ServerFileManager

openLocally - Variable in class org.bioquery.gui.BQFrame

OR - Static variable in class org.bioquery.query.Query

Represents the Boolean command OR.

org.bioquery.bqutils - package org.bioquery.bqutils

Contains several utility and helper classes for the BioQuery application, and contains the BQProtocol class that defines the communication protocol used to communicate between the client and the server.

org.bioquery.gui - package org.bioquery.gui

Contains the Graphical User Interface (GUI) for the BioQuery application

org.bioquery.query - package org.bioquery.query

A complete framework for modeling, storing, and submitting queries to mutliple different databases.

P

parseQueryLine(QueryLine) - Static method in class org.bioquery.query.QuerySubmitter

Takes a QueryLine object and returns the queryText for that object with any references to other QueryLines fully expanded into the raw fields and boolean commands that make up the Query.

parseQueryText(String) - Method in class org.bioquery.query.NCBIQuerySubmitter

Helper method takes the queryText and converts it to a String that can be directly submitted to NCBI.

parseWebPage(BufferedReader) - Method in class org.bioquery.query.NCBIQuerySubmitter

Parses the HTML query results returned by the query.fcgi script.

paste - Variable in class org.bioquery.gui.BQFrame

print - Variable in class org.bioquery.gui.BQFrame

ProgramManager - class org.bioquery.gui.ProgramManager.

This class holds system data, the location (URL) of the server, file type information, and class names for dynamically instantiating classes.

ProgramManager.ClassInfo - class org.bioquery.gui.ProgramManager.ClassInfo.

ProgramManager.ClassInfo(ProgramManager, String, String, String) - Constructor for class org.bioquery.gui.ProgramManager.ClassInfo

ProgramManager() - Constructor for class org.bioquery.gui.ProgramManager

Q

Query - class org.bioquery.query.Query.

Query encapsulates a user-created search to a particular database.

QUERY_ERROR - Static variable in class org.bioquery.bqutils.BQProtocol

Added to the server response to the client during a Query submission to indicate an error occured by submitting the Query.

QUERY_METHOD - Static variable in class org.bioquery.bqutils.BQProtocol

This represents the first half of the querystring sent to the SubmitQueryServlet in the URL, indicating that the second half of this querystring will designate which query operation the client is requesting.

QUERY_RETURNED_NULL - Static variable in class org.bioquery.bqutils.BQProtocol

Sent by the server to the client to indicate that the Query was submitted, but no there were no items in the resultset.

Query.QueryDescriptor - class org.bioquery.query.Query.QueryDescriptor.

Inner class holds data about the file this Query is saved in, and the details about automatic submission.

QueryException - exception org.bioquery.query.QueryException.

Exception class thrown when data or methods within Query objects do not work as intended.

QueryException() - Constructor for class org.bioquery.query.QueryException

QueryException(String) - Constructor for class org.bioquery.query.QueryException

Constructor accepts a text message.

QueryException(String, Throwable) - Constructor for class org.bioquery.query.QueryException

Constructor accepts a text message and an embedded exception.

QueryException(Throwable) - Constructor for class org.bioquery.query.QueryException

Constructor accepts an embedded exception.

QueryFactory - class org.bioquery.query.QueryFactory.

QueryFactory has the job of returning a list of available databases, and returning an instance of Query that handles any specific database on the list.

QueryFactory() - Constructor for class org.bioquery.query.QueryFactory

QueryLine - class org.bioquery.query.QueryLine.

This class models each individual line within a Query object.

QueryLine(Query) - Constructor for class org.bioquery.query.QueryLine

Creates a QueryLine object with the next available line number associated with the given Query.

QueryLine(Query, int) - Constructor for class org.bioquery.query.QueryLine

Creates a QueryLine object associated with the given Query at the given line number.

QueryLine(Query, int, String) - Constructor for class org.bioquery.query.QueryLine

Creates a QueryLine object associated with the given Query at the given line number and containing the given query text.

QueryLine(Query, String) - Constructor for class org.bioquery.query.QueryLine

Creates a QueryLine object with the next available line number associated with the given Query and containing the given query text.

QueryManager - interface org.bioquery.gui.QueryManager.

Interface that defines the parameters needed to submit a Query.

QUERYPROTOCOL_ERROR - Static variable in class org.bioquery.bqutils.BQProtocol

Sent by the server to the client to indicate that the server did not understand the protocol request made by the client.

QuerySubmitter - class org.bioquery.query.QuerySubmitter.

This is the abstract root class of the QuerySubmitter.

QuerySubmitter() - Constructor for class org.bioquery.query.QuerySubmitter

QueryView - class org.bioquery.gui.QueryView.

The abstract QueryView defines that a Query must be held as the model to child Views, and that the View is an Observer and must implement an update method to handle changes to the Query.

QueryView() - Constructor for class org.bioquery.gui.QueryView

QueryXmlConverter - class org.bioquery.query.QueryXmlConverter.

This class can write a Query object to XML and can read the XML and convert it back into a Query object.

QueryXmlConverter() - Constructor for class org.bioquery.query.QueryXmlConverter

R

readDocFromFile(String) - Static method in class org.bioquery.query.JdomUtils

readDocFromStream(InputStream) - Static method in class org.bioquery.query.JdomUtils

readDocFromStream(Reader) - Static method in class org.bioquery.query.JdomUtils

ReaderUtils - class org.bioquery.query.ReaderUtils.

ReaderUtils() - Constructor for class org.bioquery.query.ReaderUtils

readQuery(Object) - Static method in class org.bioquery.query.QueryXmlConverter

This method reads an XML representation of a Query from the given source and returns a new Query object.

redo - Variable in class org.bioquery.gui.BQFrame

refreshScreen - Variable in class org.bioquery.gui.BQFrame

removeSpaces(String) - Static method in class org.bioquery.bqutils.UrlUtils

Finds all spaces in the given String and replaces them with '+' chars.

RENAME_FILE - Static variable in class org.bioquery.bqutils.BQProtocol

A request by the client for the the server to rename one of the user's files, sent to the BQFileManagerServlet in the URL as the second half of the querystring.

renameFile - Variable in class org.bioquery.gui.BQFrame

renameFile(String, String) - Method in interface org.bioquery.gui.BQFileManager

renameFile(String, String) - Method in class org.bioquery.gui.ServerFileManager

resetEndDate() - Method in class org.bioquery.query.QuerySubmitter

This method undoes the effects of calling setEndDate.

resetStartDate() - Method in class org.bioquery.query.QuerySubmitter

This method undoes the effects of calling setStartDate.

restoreSpaces(String) - Static method in class org.bioquery.bqutils.UrlUtils

Finds all '+' characters in the given String and replaces them with spaces.

RETRIEVE_ADDRESS - Static variable in class org.bioquery.query.NCBIQuerySubmitter

Web address of the query.fcgi script used to retrieve QueryResults from NCBI
This QuerySubmitter passes unique ids retrieved via ESearch to this script, though it is possible to directly pass the submittable Query text in the form of term=exampleterm[FIELD]

S

SAVE_FILE - Static variable in class org.bioquery.bqutils.BQProtocol

A request by the client for the server to save a file to the user's directory space on the bioquery server, sent to the BQFileManagerServlet in the URL as the second half of the querystring.

saveAsFile - Variable in class org.bioquery.gui.BQFrame

saveAsFile(View) - Method in class org.bioquery.gui.BQFrame

saveBetween(Reader, StringBuffer, String, String) - Static method in class org.bioquery.query.ReaderUtils

Convienence method simply calls discardUntil and then saveUntil
Puts the text from the source that is in between the 2 tags into the destination.
NOTE: Does not put the startTag into the destination, but DOES put the endTag in the destination.
If the startTag not found, will read the source to the end.
If the startTag found but no endTag, will read the source to the end, and return the destination with everything after the startTag inside it.

saveFile - Variable in class org.bioquery.gui.BQFrame

saveFile(String, View) - Method in interface org.bioquery.gui.BQFileManager

saveFile(String, View) - Method in class org.bioquery.gui.ServerFileManager

saveFile(View) - Method in class org.bioquery.gui.BQFrame

saveLocally - Variable in class org.bioquery.gui.BQFrame

saveLocally(View) - Method in class org.bioquery.gui.BQFrame

saveProxyInfo(String, String) - Method in class org.bioquery.gui.ProgramManager

saveToEnd(Reader, StringBuffer) - Static method in class org.bioquery.query.ReaderUtils

Simply dumps the source into the destination.

saveUntil(Reader, StringBuffer, String) - Static method in class org.bioquery.query.ReaderUtils

Reads the source and passes the contents into the destination until the tag is reached.

SEND_FEEDBACK - Static variable in class org.bioquery.bqutils.BQProtocol

A request by the client for the the server to receive a message and email back to bioquery support, sent to the BQFileManagerServlet in the URL as the second half of the querystring.

sendFeedback(String) - Method in interface org.bioquery.gui.BQFileManager

sendFeedback(String) - Method in class org.bioquery.gui.ServerFileManager

ServerFileManager - class org.bioquery.gui.ServerFileManager.

The ServerFileManager class implements BQFileManager and handles files operations for a remote file system located on a server.

ServerFileManager(BQGUI, ProgramManager) - Constructor for class org.bioquery.gui.ServerFileManager

ServerQueryManager - class org.bioquery.gui.ServerQueryManager.

Deprecated. This class is deprecated. It implements QueryManager but rather than directly submitting Querys from the client, it contacts the SubmitQueryServlet on the server and sends the Query across the network to be submitted from the server. This use of the bioquery server as a proxy for submitting Querys was originally used to bypass applet and java web start security restrictions, but is not required because BioQuery has evolved into a full application.

ServerQueryManager(BQGUI, ProgramManager) - Constructor for class org.bioquery.gui.ServerQueryManager

Deprecated.

setAllUpdates(boolean) - Method in class org.bioquery.query.Query

Sets the update needed value of every QueryLine in the Query to the given value.

setAlwaysGetResults(boolean) - Method in class org.bioquery.gui.DefaultQueryView

setAutoSubmit(boolean) - Method in class org.bioquery.query.Query.QueryDescriptor

Switch that determines whether the Query should automatically be submitted at some interval.

setBook(Book) - Method in class org.bioquery.gui.View

setChanged() - Method in class org.bioquery.query.Query

Notifies Observers that the Query has changed.

setCreated(Date) - Method in class org.bioquery.query.Query.QueryDescriptor

The Date the Query was created.

setCurrentFormat(String) - Method in class org.bioquery.query.Query

Designate the format for the results of this query.

setDatabase(String) - Method in class org.bioquery.query.Query

Set the name of this query's database.

setEmailAddress(String) - Method in class org.bioquery.query.Query.QueryDescriptor

Sets the EMail address that the results of this Query should be sent to (if getSendEmail() == true).

setEnabling() - Method in class org.bioquery.gui.BQFrame

setEndDate(Date) - Method in class org.bioquery.query.QuerySubmitter

Sets the ending date for the search.

setEndDisplayNum(int) - Method in class org.bioquery.query.Query

Set the end display number (the end number in the set of results to be returned).

setFileExtension(String) - Method in class org.bioquery.query.Query

The file extension used to save this Query as a file.

setFileName(String) - Method in class org.bioquery.gui.BQFileChooser

setFileName(String) - Method in class org.bioquery.gui.View

setFileName(String) - Method in class org.bioquery.gui.DefaultQueryView

setFilePath(String) - Method in class org.bioquery.query.Query.QueryDescriptor

The path on the server this file is saved to.

setFilePath(String) - Method in class org.bioquery.gui.View

setFilePath(String) - Method in class org.bioquery.gui.DefaultQueryView

setFileSeparator(String) - Method in class org.bioquery.gui.BQTreeNode

setHelpURL(String) - Method in class org.bioquery.query.Query

Set the URL of the help file explaining the structure and use of this query's database.

setIncrementNumber(int) - Method in class org.bioquery.query.Query.QueryDescriptor

Sets the number of time units in between each automatic submission of this Query.

setInitParams(HashMap) - Method in class org.bioquery.query.QuerySubmitter

Empty method should be overridden in subclasses if custom parameters are used.

setInitParams(HashMap) - Method in class org.bioquery.query.NCBIQuerySubmitter

Loads the idListUrl from the query.xml, which is only used by the ID List format.

setIsLoaded(boolean) - Method in class org.bioquery.gui.BQTreeNode

setLastModified(Date) - Method in class org.bioquery.query.Query.QueryDescriptor

The date the Query was last modified.

setLastSubmitted(Date) - Method in class org.bioquery.query.Query.QueryDescriptor

The Date of the last time the Query was submitted.

setLastSubmitted(Date) - Method in class org.bioquery.query.QueryLine

Sets the time and date that this QueryLine was last submitted.

setLineNumber(int) - Method in class org.bioquery.query.QueryLine

Sets the line number associated with this QueryLine.

setModifiable(boolean) - Method in class org.bioquery.gui.BQTreeNode

setModified(boolean) - Method in class org.bioquery.gui.View

setModified(boolean) - Method in class org.bioquery.gui.DefaultQueryView

setModified(boolean) - Method in class org.bioquery.gui.HtmlDataView

setModified(boolean) - Method in class org.bioquery.gui.TextDataView

setMyGUI(BQGUI) - Method in class org.bioquery.gui.View

setMyGUI(BQGUI) - Method in class org.bioquery.gui.HtmlDataView

setMyGUI(BQGUI) - Method in class org.bioquery.gui.ServerFileManager

setMyGUI(BQGUI) - Method in class org.bioquery.gui.TextDataView

setName(String) - Method in class org.bioquery.query.Query

Designate the name of this individual query.

setNextSubmitDate() - Method in class org.bioquery.query.Query.QueryDescriptor

This calculates and sets the NextSubmitDate based on the interval between automatic submissions and the ReferencePoint Date.

setNextSubmitDate(Date) - Method in class org.bioquery.query.Query.QueryDescriptor

Explicitly sets the Next Submit Date to the given value.

setNumReturned(int) - Method in class org.bioquery.query.QueryLine

Sets the number of items in the result set of this QueryLine.

setPassword(char[]) - Method in class org.bioquery.bqutils.BQUser

Set the password.

setQuery(Query) - Method in class org.bioquery.query.QuerySubmitter

Sets the Query object for this QuerySubmitter.

setQueryLine(int, QueryLine) - Method in class org.bioquery.query.Query

Assigns a QueryLine object to the designed line number.

setQuerySubmitter(QuerySubmitter) - Method in class org.bioquery.query.Query

Sets the QuerySubmitter for this type of Query.

setQueryText(String) - Method in class org.bioquery.query.QueryLine

Sets the actual text of this QueryLine.

setReferencePoint(Date) - Method in class org.bioquery.query.Query.QueryDescriptor

Sets the Reference Point: a Date that simply marks a point in time.

setSaveDirectory(String) - Method in class org.bioquery.query.Query.QueryDescriptor

Sets the path to the Directory that the results of this Query should be saved to (if getSaveToFile() == true).

setSaveToFile(boolean) - Method in class org.bioquery.query.Query.QueryDescriptor

Sets whether the user wishes to have the results of this Query saved to a file.

setScreenSize(float) - Method in class org.bioquery.gui.HelpFrame

setScreenSize(float, float) - Method in class org.bioquery.gui.DemoDialog

setSendEmail(boolean) - Method in class org.bioquery.query.Query.QueryDescriptor

Sets whether the user wishes to have the results of this Query sent to them by Email.

setSession(String, String) - Static method in class org.bioquery.bqutils.UrlUtils

Takes the given url String and adds the given JSessionId.

setStartDate(Date) - Method in class org.bioquery.query.QuerySubmitter

Sets the starting date for the search.

setStartDisplayNum(int) - Method in class org.bioquery.query.Query

Set the start display number (the first number in the set of results to be returned).

setSubmitIncrement(int) - Method in class org.bioquery.query.Query.QueryDescriptor

Sets the units used to determine how often the Query is automatically submitted.

setSubmitIncrement(String) - Method in class org.bioquery.query.Query.QueryDescriptor

Sets the units used to determine how often the Query is automatically submitted.

setSubmitLine(int) - Method in class org.bioquery.query.Query

Sets which QueryLine should be submitted to the database.

setSubmitLineNumber(int) - Method in class org.bioquery.query.Query.QueryDescriptor

Sets which QueryLine will be submitted to the database.

setUpdate(int, boolean) - Method in class org.bioquery.query.Query

Set whether we need to update the ref count for the given QueryLine.

setUpdateNeeded(boolean) - Method in class org.bioquery.query.QueryLine

Sets the updateNeeded status of the QueryLine.

setUsername(String) - Method in class org.bioquery.bqutils.BQUser

Set the username.

SHOW_DIR_ONLY - Static variable in class org.bioquery.gui.BQFileChooser

showHelpDialog(String) - Method in class org.bioquery.gui.BQFrame

showWelcomeDialog() - Method in class org.bioquery.gui.BQFrame

size() - Method in class org.bioquery.query.Query

Returns the number of queryLines contained in this Query object.

StartBioQuery - class org.bioquery.gui.StartBioQuery.

This class starts the GUI by creating an instance of BQFrame from it's main method.

StartBioQuery() - Constructor for class org.bioquery.gui.StartBioQuery

startDate - Variable in class org.bioquery.query.QuerySubmitter

stripFileExtension(String) - Static method in class org.bioquery.bqutils.FileUtils

Removes the file extension from a filename or full path, including the final period (.).

stripFirstDirFromPath(String) - Static method in class org.bioquery.bqutils.FileUtils

Removes the first directory from the given path.

submitEFetch(List) - Method in class org.bioquery.query.NCBIQuerySubmitter

Deprecated in favor of the RETRIEVE_ADDRESS and query.fcgi script.
This helper method does the second of a 2-step process for submitting Querys to NCBI.

submitESearch(String, boolean) - Method in class org.bioquery.query.NCBIQuerySubmitter

This helper method does the first of a 2-step process for submitting Querys to NCBI.

submitESearch(String, int, int) - Method in class org.bioquery.query.NCBIQuerySubmitter

startNum less than 0 means we should just get the number of items, not the items themselves (getQueryData, not getQueryResults).

submitRetrieveUrl(List) - Method in class org.bioquery.query.NCBIQuerySubmitter

Returns the full results of the Query.

submitURL(StringBuffer) - Method in class org.bioquery.query.NCBIQuerySubmitter

Submits a URL and returns a BufferedReader containing the response.

SUCCESS - Static variable in class org.bioquery.bqutils.BQProtocol

Added to the server response to the client during a Query submission to indicate that the requested operation succeeded.

summateQueryLines(String) - Method in class org.bioquery.query.Query

Combines all of the QueryLines into a new QueryLine, separated by the bool text.

T

TextDataView - class org.bioquery.gui.TextDataView.

This DataView displays simple, editable text files, and is suitable for displaying resultsets that are returned in plain text.

TextDataView() - Constructor for class org.bioquery.gui.TextDataView

theBook - Variable in class org.bioquery.gui.View

toggleFileManager() - Method in class org.bioquery.gui.BQFrame

toString() - Method in class org.bioquery.query.Query

toString() - Method in class org.bioquery.query.QueryL