A C D E G H I K M N P Q R S T U X

A

actionPerformed(ActionEvent) - Method in class ChannelDB.FileConnectAction

actionPerformed(ActionEvent) - Method in class ChannelDB.FileExitAction

actionPerformed(ActionEvent) - Method in class ChannelDB.HelpAboutAction

actionPerformed(ActionEvent) - Method in class ChannelDB.HelpUsingAction

actionPerformed(ActionEvent) - Method in class ConPanel.cancelListener

C

ChannelDB - class ChannelDB.

Main class for the Channel Database GUI

ChannelDB.FileConnectAction - class ChannelDB.FileConnectAction.

Inner class to define the menu "File/Connect" action

ChannelDB.FileConnectAction() - Constructor for class ChannelDB.FileConnectAction

ChannelDB.FileExitAction - class ChannelDB.FileExitAction.

Inner class to define the menu "File/Exit" action

ChannelDB.FileExitAction() - Constructor for class ChannelDB.FileExitAction

ChannelDB.HelpAboutAction - class ChannelDB.HelpAboutAction.

Inner class to define the menu "Help/About" action

ChannelDB.HelpAboutAction() - Constructor for class ChannelDB.HelpAboutAction

ChannelDB.HelpUsingAction - class ChannelDB.HelpUsingAction.

Inner class to define the menu "Help/Using" action

ChannelDB.HelpUsingAction() - Constructor for class ChannelDB.HelpUsingAction

ChannelDB() - Constructor for class ChannelDB

con - Variable in class ChannelDB

con - Variable in class ConPanel

connect() - Method in class ConPanel

Connect to the MySQL channel database using the MM.MySQL JDBC driver, obtained from http://mmmysql.sourceforge.net/

connectPane - Variable in class ChannelDB

ConPanel - class ConPanel.

A dialog window, brought up from the ChannelDB File/Connect menu.

ConPanel.cancelListener - class ConPanel.cancelListener.

ConPanel.cancelListener() - Constructor for class ConPanel.cancelListener

ConPanel(Frame) - Constructor for class ConPanel

convertConditional(String) - Static method in class Neuroml2GENESIS

D

db_field - Variable in class ConPanel

dbase - Variable in class ConPanel

descList - Variable in class SearchPanel

detailButton - Variable in class ParsePanel

displayResults(String[]) - Method in class ResultsPanel

E

equation2array(double, double, int, String) - Static method in class Neuroml2GENESIS

Given an equation that is a function of the variable x, parse it with the Java Expression Parser (JEP from http://jep.sourceforge.net/).

Erest - Static variable in class Neuroml2GENESIS

Optional parameter (default value = 0.0) for the resting potential of the cell containing the channel.

errorMsg - Variable in class ChannelDB

errorMsg - Static variable in class Neuroml2database

errorMsg - Static variable in class Neuroml2GENESIS

Exp - class Exp.

An extension to the Java Expression Parser (JEP) to allow an exponential function to be expressed as "exp(x)", rather than "e^x".

Exp() - Constructor for class Exp

G

generateText(String) - Method in class ChannelDB

This deals with generating the text (model description, xml source, or simulator (GENESIS) script), according to button press in ParsePanel

getConn() - Method in class ConPanel

getParamList(String, ParameterizedHHRate) - Static method in class Neuroml2GENESIS

Creates a space-separated list of parameters to be used by the GENESIS setupalpha or setuptau functions.

getRates(Object) - Static method in class Neuroml2GENESIS

Generate the code to fill the tabchannel rate tables

getResultList() - Method in class SearchPanel

getSelectionIndex() - Method in class ResultsPanel

getTable() - Method in class ConPanel

getUniqueIDs() - Method in class SearchPanel

getXML(String) - Static method in class Neuroml2database

H

host - Variable in class ConPanel

host_field - Variable in class ConPanel

I

IDList - Variable in class SearchPanel

insertDB(String, String, String, String, String, String) - Static method in class Neuroml2database

ionField - Variable in class SearchPanel

K

keyField - Variable in class SearchPanel

M

main(String[]) - Static method in class ChannelDB

Main method to instantiate ChannelDB and make it visible

main(String[]) - Static method in class Neuroml2database

N

Neuroml2database - class Neuroml2database.

Neuroml2database takes an XML (NeuroML) file name as an argument and stores the XML text along with descriptive information (name, uniqueID, description, keywords, and ion) in a MySQL database.

Neuroml2database() - Constructor for class Neuroml2database

neuroml2descrip(String) - Method in class ChannelDB

Parse the xml to get a model object, extract information about the model

Neuroml2GENESIS - class Neuroml2GENESIS.

Class to hold the method neuroml2genesis, used to convert a neuroml (xml) string into a string that holds a GENESIS script to create a channel.

Neuroml2GENESIS() - Constructor for class Neuroml2GENESIS

neuroml2genesis(String) - Static method in class Neuroml2GENESIS

Parse the xml to get a model object, convert to GENESIS script

P

panel2 - Variable in class ChannelDB

panel3 - Variable in class ChannelDB

panel4 - Variable in class ChannelDB

ParsePanel - class ParsePanel.

"panel4" of the ChannelDB GUI, used to show the results of parsing the xml from the database

ParsePanel() - Constructor for class ParsePanel

pass_field - Variable in class ConPanel

password - Variable in class ConPanel

Q

queryDB(Connection, String) - Method in class SearchPanel

R

readText(String) - Static method in class ChannelDB

resultbox - Variable in class ResultsPanel

ResultsPanel - class ResultsPanel.

"panel3" used to display the results of a database query

ResultsPanel() - Constructor for class ResultsPanel

resultText - Variable in class ParsePanel

run(Stack) - Method in class Exp

Applies the function to the parameters on the stack.

S

saveButton - Variable in class ParsePanel

saveField - Variable in class ParsePanel

scriptButton - Variable in class ParsePanel

searchButton - Variable in class SearchPanel

searchDB() - Method in class ChannelDB

SearchPanel - class SearchPanel.

"panel2" of the ChannelDB GUI, used to perform queries to the database

SearchPanel() - Constructor for class SearchPanel

T

tab4 - Variable in class ChannelDB

tab4 - Static variable in class Neuroml2database

tab4 - Static variable in class Neuroml2GENESIS

tab8 - Variable in class ChannelDB

tab8 - Static variable in class Neuroml2database

tab8 - Static variable in class Neuroml2GENESIS

table - Variable in class ChannelDB

table - Variable in class ConPanel

table_field - Variable in class ConPanel

U

user - Variable in class ConPanel

user_field - Variable in class ConPanel

X

xmlButton - Variable in class ParsePanel

A C D E G H I K M N P Q R S T U X