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

A

AbstractionFuncs - package AbstractionFuncs

AbstractionFunct - Interface in AbstractionFuncs

An interface that defines an input/output abstraction functions on a message

abstractMsg(String) - Method in interface AbstractionFuncs.AbstractionFunct

abstractMsg(String) - Method in class AbstractionFuncs.FTPinputAbstraction

abstractMsg(String) - Method in class AbstractionFuncs.FTPoutputAbstraction

abstractMsg(String) - Method in class AbstractionFuncs.MSNinputAbstraction

abstractMsg(String) - Method in class AbstractionFuncs.MSNoutputAbstraction

abstractMsg(String) - Method in class AbstractionFuncs.SMTPinputAbstraction

abstractMsg(String) - Method in class AbstractionFuncs.SMTPoutputAbstraction

accept() - Method in class socks.SocksServerSocket

Accepts the incoming connection.

actionPerformed(ActionEvent) - Method in class socks.SocksDialog

add(String) - Method in class socks.InetRange

Adds another host or range to this range.

add(InetAddress) - Method in class socks.InetRange

Adds another ip for this range.

add(InetAddress, InetAddress) - Method in class socks.InetRange

Adds another range of ips for this range.Any host with ip address greater than or equal to the address of from and smaller than or equal to the address of to will be included in the range.

add(InetRange, Hashtable) - Method in class socks.server.IdentAuthenticator

Adds range of addresses from which connection is allowed.

addConstantDataMsgBlock(ArrayList<Integer>) - Method in class BioinfoFieldExtractor.GenericSequence

addDirect(InetAddress) - Method in class socks.Proxy

Adds given ip to the list of direct addresses.

addDirect(String) - Method in class socks.Proxy

Adds host to the list of direct addresses.

addDirect(InetAddress, InetAddress) - Method in class socks.Proxy

Adds given range of addresses to the lsit of direct addresses, machines within this range will be accessed without using proxy.

addIOPair(String, ArrayList<String>) - Method in class ProtocolLearner.MessageTrace

Adds a pair of input/output messages to the message trace

addLoop(PassiveLearner.Loop) - Method in class ProtocolLearner.MessageTrace

Identify a new loop in the trace

addMessageBlock(GenericSequence.MessageBlock) - Method in class BioinfoFieldExtractor.GenericSequence

addOuputSymbol(int, int, String, ArrayList<String>) - Method in class ProtocolLearner.FSAutomaton

Add an output message to an array of output message sequences for the particular input on a given state

addOutputSequence(ArrayList<String>) - Method in class ProtocolLearner.FSATransition

Adds an output message sequence to the list of output message sequences

addState() - Method in class ProtocolLearner.FSAutomaton

Adds a new state to the set of states

addTransition(int, String, int) - Method in class ProtocolLearner.FSAutomaton

Adds a next transition function to the automaton

addTransition(int, String, int, ArrayList<String>) - Method in class ProtocolLearner.FSAutomaton

Adds a next transition function to the automaton

addTransition(int, FSATransition) - Method in class ProtocolLearner.FSAutomaton

Add a transition object to the automaton

addValueDataMsgBlock(ArrayList<ArrayList<Integer>>, int, int) - Method in class BioinfoFieldExtractor.GenericSequence

alignGlobally(ArrayList<Integer>, ArrayList<Integer>) - Method in class BioinfoFieldExtractor.GlobalAlignment

alignGlobally(ArrayList<Integer>, ArrayList<Integer>, float[][]) - Method in class BioinfoFieldExtractor.GlobalAlignment

Converts the strings into a byte array and calls the main alignGlobaly method.

alignGlobally(int[], int[], float[][]) - Method in class BioinfoFieldExtractor.GlobalAlignment

Performs NeedlemanWunsch global alignment algorithm to calculate similarity between message sequences.

alignLocally(ArrayList<String>) - Method in class BioinfoFieldExtractor.LocalAlignment

alignLocally(ArrayList<String>, float[][]) - Method in class BioinfoFieldExtractor.LocalAlignment

Performs Smith Waterman local alignment algorithm to calculate similarity between message sequences.

alignMultipleSequences(ArrayList<ArrayList<Integer>>, ArrayList<ArrayList<Integer>>, PhylogenTree) - Method in class BioinfoFieldExtractor.MultiSequenceAligner

AppDataParser - Class in ProtocolLearner

AppDataParser() - Constructor for class ProtocolLearner.AppDataParser

ASCIIconverter - Class in BioinfoFieldExtractor

This class provides methods allowing to convert strings to decimal representation and vice-versa.

ASCIIconverter() - Constructor for class BioinfoFieldExtractor.ASCIIconverter

assignTreeAlignments(PhylogenTree) - Method in class BioinfoFieldExtractor.MultiSequenceAligner

Assigns the aligned messages sequences to the tree

Authentication - Interface in socks

The Authentication interface provides for performing method specific authentication for SOCKS5 connections.

AuthenticationNone - Class in socks

SOCKS5 none authentication.

AuthenticationNone() - Constructor for class socks.AuthenticationNone

AutoFuzzguiMain - Class in AutoFuzzMain

Summary description for AutoFuzzguiMain

AutoFuzzguiMain() - Constructor for class AutoFuzzMain.AutoFuzzguiMain

AutoFuzzMain - package AutoFuzzMain