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

G

generateSeq(ArrayList<ArrayList<Integer>>) - Method in class BioinfoFieldExtractor.ConsensusSeq

Populates the consensus sequence from the multiple aligned sequences.

GenericSeqConstructor - Class in BioinfoFieldExtractor

This class provides functionality to extract primitive type from a sample of data values.

GenericSeqConstructor() - Constructor for class BioinfoFieldExtractor.GenericSeqConstructor

GenericSequence - Class in BioinfoFieldExtractor

This class is a replacement of ConsensusSeq class.

GenericSequence() - Constructor for class BioinfoFieldExtractor.GenericSequence

GenericSequence.MessageBlock - Class in BioinfoFieldExtractor

GenericSequence.MessageBlock() - Constructor for class BioinfoFieldExtractor.GenericSequence.MessageBlock

getAlignment1() - Method in class BioinfoFieldExtractor.NeedlemanWunschHolder

getAlignment2() - Method in class BioinfoFieldExtractor.NeedlemanWunschHolder

getAll() - Method in class socks.InetRange

Get all entries in the range as strings.

getAuthenticationMethod(int) - Method in class socks.Socks5Proxy

Get authentication method, which corresponds to given method id

getAutomaton() - Method in class FuzzingEngine.FuzzerMain

getChainProxy() - Method in class socks.Proxy

Get proxy which is used to connect to this proxy.

getClusters() - Method in class BioinfoFieldExtractor.UPGMA

Returns the clusters

getCompletionStatus() - Method in class ProxyServer.ProxyDataManipulator

Returns the completion %

getConsensusSeq() - Method in class BioinfoFieldExtractor.ConsensusSeq

getConsSeq() - Method in class BioinfoFieldExtractor.ConsensusSeq

Returns a consensus sequence with ? inserted whenever there is a mutation at a certain position in the consensus sequence

getConsSeqAsList() - Method in class BioinfoFieldExtractor.ConsensusSeq

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

getCurrentFuzzingLogFile() - Method in class AutoFuzzMain.ConfigVariables

getCurrentSystemLogFile() - Method in class AutoFuzzMain.ConfigVariables

getDefaultProxy() - Static method in class socks.Proxy

Get current default proxy.

getDirect() - Method in class socks.Proxy

Get the list of direct hosts.

getDistance() - Method in class BioinfoFieldExtractor.PhylogenTree

Returns the ditance score between the children

getErrorCode() - Method in exception socks.SocksException

Get the error code associated with this exception.

getFuzzer() - Method in class ProxyServer.ProxyDataManipulator

Returns the instance of the fuzzer object

getFuzzingData() - Method in class ProxyServer.ProxyDataManipulator

getFuzzingString() - Method in class ProtocolLearner.FSATransition

getGapsArrInA1() - Method in class BioinfoFieldExtractor.NeedlemanWunschHolder

getGapsArrInA2() - Method in class BioinfoFieldExtractor.NeedlemanWunschHolder

getGapsInAlignment1() - Method in class BioinfoFieldExtractor.NeedlemanWunschHolder

getGapsInAlignment2() - Method in class BioinfoFieldExtractor.NeedlemanWunschHolder

getGapsToBeInserted() - Method in class BioinfoFieldExtractor.PhylogenTree

Returns the array list of gaps

getGenericSequence() - Method in class BioinfoFieldExtractor.GenericSequence

getGenericSequence() - Method in class ProtocolLearner.FSATransition

getGenSequence() - Method in class FuzzingEngine.StringForFuzzing

getHeight() - Method in class BioinfoFieldExtractor.PhylogenTree

Returns the height of the tree

getHost() - Method in class socks.SocksServerSocket

Get the name of the host proxy is using to listen for incoming connection.

getHost() - Method in class socks.SocksSocket

Returns remote host name, it is usefull in cases when addresses are resolved by proxy, and we can't create InetAddress object.

getIndex() - Method in class BioinfoFieldExtractor.PhylogenTree

Returns the index

getInetAddress() - Method in class socks.Proxy

Get the ip address of the proxy server host.

getInetAddress() - Method in class socks.ProxyMessage

Get the Address field of this message as InetAddress object.

getInetAddress() - Method in class socks.SocksServerSocket

Get address assigned by proxy to listen for incomming connections, or the local machine address if doing direct connection.

getInetAddress() - Method in class socks.SocksSocket

Get remote host as InetAddress object, might return null if addresses are resolved by proxy, and it is not possible to resolve it locally

getInitStateIndex() - Method in class ProtocolLearner.FSAutomaton

Returns the index of the initial state

getInputStream() - Method in class ProxyServer.ProxyAuthenticator

Get input stream.

getInputStream() - Method in interface socks.server.ServerAuthenticator

This method should return input stream which should be used on the accepted socket.

getInputStream() - Method in class socks.server.ServerAuthenticatorNone

Get input stream.

getInputStream() - Method in class socks.SocksSocket

Same as Socket

getInputSymbol() - Method in class ProtocolLearner.FSATransition

Returns the input symbol of the transition

getIsLeaf() - Method in class BioinfoFieldExtractor.PhylogenTree

Check if the node is a leaf

getLeftChild() - Method in class BioinfoFieldExtractor.PhylogenTree

Returns the left child

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

getLocalAddress() - Method in class socks.Socks5DatagramSocket

Address assigned by the proxy, to which datagrams are send for relay.

getLocalAddress() - Method in class socks.SocksSocket

Get address assigned by proxy to make a remote connection, it might be different from the host specified for the proxy.

getLocalHost() - Method in class socks.SocksSocket

Get name of the host, proxy has assigned to make a remote connection for this socket.

getLocalPort() - Method in class socks.Socks5DatagramSocket

Returns port assigned by the proxy, to which datagrams are relayed.

getLocalPort() - Method in class socks.SocksServerSocket

Get port assigned by proxy to listen for incoming connections, or the port chosen by local system, if accepting directly.

getLocalPort() - Method in class socks.SocksSocket

Get the port assigned by the proxy for the socket, not the port on locall machine as in Socket.

getLoggingLevelCritical() - Method in class AutoFuzzMain.ConfigVariables

getLoggingLevelError() - Method in class AutoFuzzMain.ConfigVariables

getLoggingLevelInfo() - Method in class AutoFuzzMain.ConfigVariables

getLoggingLevelWarning() - Method in class AutoFuzzMain.ConfigVariables

getLoopLength() - Method in class ProtocolLearner.PassiveLearner.Loop

getLoops() - Method in class ProtocolLearner.MessageTrace

getModifiedMessage() - Method in class FuzzingFunctions.FuzzingFunctionReturnPair

getMsg(int) - Method in class ProtocolLearner.MessageTrace

getMsgTraces(String) - Method in class ProtocolLearner.AppDataParser

This function parses the traffic string (from the traffic text ares) and returns an array list of messages traces to be used for FSM construction

getNewState() - Method in class ProtocolLearner.FSATransition

Returns the next available index for a new state

getNewStateID() - Method in class FuzzingFunctions.FuzzingFunctionReturnPair

getNextFuzzingFuncIndex() - Method in class FuzzingEngine.StringForFuzzing

Returns the current index of the next fuzzing function

getNextFuzzingFuncIndex() - Method in class FuzzingEngine.StringFuzzerEngine

Returns the current index of the next fuzzing function

getNumOfLoops() - Method in class ProtocolLearner.PassiveLearner.Loop

getOutputMsgSeq() - Method in class ProtocolLearner.FSATransition

Returns the list of output symbol messages

getOutputStream() - Method in class ProxyServer.ProxyAuthenticator

Get output stream.

getOutputStream() - Method in interface socks.server.ServerAuthenticator

This method should return output stream to use to write to the accepted socket.

getOutputStream() - Method in class socks.server.ServerAuthenticatorNone

Get output stream.

getOutputStream() - Method in class socks.SocksSocket

Same as Socket

getParent() - Method in class BioinfoFieldExtractor.PhylogenTree

Returns the parent node

getPassword() - Method in class socks.UserPasswordAuthentication

Get password

getPort() - Method in class socks.Proxy

Get the port on which proxy server is running.

getPort() - Method in class socks.SocksSocket

Same as Socket

getProxy() - Static method in class socks.ProxyServer

Get proxy.

getProxy() - Method in class socks.SocksDialog

Displays SOCKS configuartion dialog.

getProxy(Proxy) - Method in class socks.SocksDialog

Initialises dialog to given proxy and displays SOCKS configuartion dialog.

getRandomSessionsIndex() - Method in class AutoFuzzMain.ConfigVariables

getRightChild() - Method in class BioinfoFieldExtractor.PhylogenTree

Returns the right child

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

getSimilatiryScore() - Method in class BioinfoFieldExtractor.NeedlemanWunschHolder

getSkipMsgs() - Method in class ProtocolLearner.MessageTrace

getSkipString() - Method in interface AbstractionFuncs.AbstractionFunct

Every abstraction function (ie abstractMsg is allowed to have a skip string.

getSkipString() - Method in class AbstractionFuncs.FTPinputAbstraction

getSkipString() - Method in class AbstractionFuncs.FTPoutputAbstraction

getSkipString() - Method in class AbstractionFuncs.MSNinputAbstraction

getSkipString() - Method in class AbstractionFuncs.MSNoutputAbstraction

getSkipString() - Method in class AbstractionFuncs.SMTPinputAbstraction

getSkipString() - Method in class AbstractionFuncs.SMTPoutputAbstraction

getSoLinger(int) - Method in class socks.SocksSocket

Same as socket.

getSoTimeout(int) - Method in class socks.SocksSocket

Same as socket.

getStateColor(int) - Method in class ProtocolLearner.FSAutomaton

Returns the color of the state

getStateFuzzingData(FSAutomaton, int, ArrayList<ArrayList<Object>>, HashSet<Integer>) - Method in class ProxyServer.ProxyDataManipulator

getStateHeight(int) - Method in class ProtocolLearner.FSAutomaton

Returns the height of the state

getStates() - Method in class ProtocolLearner.FSAutomaton

Returns all states in the automaton

getStatesWithSpecHeight(int) - Method in class ProtocolLearner.FSAutomaton

Returns the array list of states with a particular height

getStatesWithTrans() - Method in class ProtocolLearner.FSAutomaton

Returns the list of states that have transitions

getStateTransition(int) - Method in class ProtocolLearner.FSAutomaton

Returns the set of transition functions for a state.

getStepsBeforeAdding() - Method in class ProtocolLearner.FSATransition

getSystemConfigPath() - Method in class AutoFuzzMain.ConfigVariables

getTcpNoDelay() - Method in class socks.SocksSocket

Same as socket.

getTotalGaps() - Method in class BioinfoFieldExtractor.NeedlemanWunschHolder

getTotalNumberOfFuzzingFuncs() - Method in class FuzzingEngine.StringForFuzzing

Returns the total number of available fuzzing functions

getTotalNumberOfFuzzingFuncs() - Method in class FuzzingEngine.StringFuzzerEngine

Returns the total number of available fuzzing functions

getTotalNumOfSamples() - Method in class BioinfoFieldExtractor.GenericSequence

getTrace() - Method in class ProtocolLearner.MessageTrace

Returns the whole message trace

getTraceId() - Method in class ProtocolLearner.MessageTrace

Returns the trace identifier

getTraceID() - Method in class ProtocolLearner.PassiveLearner.Loop

getTraceSize() - Method in class ProtocolLearner.MessageTrace

Returns the number of IO pais in the trace

getTrafficOrderIndex() - Method in class AutoFuzzMain.ConfigVariables

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

getUdpEncapsulation() - Method in class ProxyServer.ProxyAuthenticator

Allways returns null.

getUdpEncapsulation() - Method in interface socks.server.ServerAuthenticator

This method should return UDPEncapsulation, which should be used on the datagrams being send in/out.

getUdpEncapsulation() - Method in class socks.server.ServerAuthenticatorNone

Allways returns null.

getUser() - Method in class socks.UserPasswordAuthentication

Get the user name.

getValue() - Method in class BioinfoFieldExtractor.PhylogenTree

Returns the value

GlobalAlignment - Class in BioinfoFieldExtractor

This class provides functionality for global alignment for 2 messages sequences based on the NeedlemanWunsch algorithm.

GlobalAlignment() - Constructor for class BioinfoFieldExtractor.GlobalAlignment

GuiFASBuilder - Class in AutoFuzzMain

GuiFASBuilder() - Constructor for class AutoFuzzMain.GuiFASBuilder

GuiGraphBuilderFromFSA - Class in AutoFuzzMain

GuiGraphBuilderFromFSA() - Constructor for class AutoFuzzMain.GuiGraphBuilderFromFSA