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A

a - Variable in class mendel.util.Pair
 
absorbChildren() - Method in class mendel.vptree.VPNode
Recursively absorbs the elements contained in this node's children into this node, making this node a leaf node in the process.
accept(SelectionKey) - Method in class mendel.network.MessageRouter
Accepts new connections.
add(E) - Method in class mendel.vptree.BoundedPriorityQueue
Attempts to add an element to the bounded queue.
add(T) - Method in class mendel.vptree.VPNode
Adds a point to this node if it is a leaf node or one of its children if not.
add(T, boolean, Set<VPNode<T>>) - Method in class mendel.vptree.VPNode
Adds a point to this node if it is a leaf node or one of its children if not.
add(E) - Method in class mendel.vptree.VPTree
Adds a single point to this vp-tree.
addAll(Collection<? extends E>) - Method in class mendel.vptree.BoundedPriorityQueue
Attempts to add Collection of elements to the bounded queue.
addAll(Collection<? extends T>) - Method in class mendel.vptree.VPNode
Adds all of the elements in a collection to this node (if it is a leaf node) or its children.
addAll(Collection<? extends E>) - Method in class mendel.vptree.VPTree
Adds all of the points in the given collection to this vp-tree.
addData(Metadata, byte[]) - Method in class mendel.fs.Block
 
addException(Exception) - Method in class mendel.network.Transmission
Associates an Exception with this Tranmission to indicate errors or other information specific to the Tranmission.
addGroup(GroupInfo) - Method in class mendel.network.GroupInfo
 
addGroup(GroupInfo) - Method in class mendel.network.NetworkInfo
 
addListener(MessageListener) - Method in class mendel.network.MessageRouter
Adds a message listener (consumer) to this MessageRouter.
addListener(MessageListener) - Method in class mendel.network.ParallelMessageRouter
 
addMapping(int, Class<? extends Event>) - Method in class mendel.event.EventMap
Maps an event identifier to a particular Event class implementation.
addMapping(Class<? extends Event>) - Method in class mendel.event.EventMap
Maps an Event class implementation to an automatically-generated event identifier.
addNode(T) - Method in class mendel.dht.hash.BalancedHashRing
Add a node to the overlay network topology.
addNode(T) - Method in interface mendel.dht.hash.HashRing
Add a node to the overlay network topology.
addNode(NodeInfo) - Method in class mendel.network.GroupInfo
 
addPointsToArray(Object[]) - Method in class mendel.vptree.VPNode
Adds all of the elements from this node if it is a leaf node or its children if it is not to an array.
addPointsToArray(Object[], int) - Method in class mendel.vptree.VPNode
Adds all of the elements from this node and its children to the given array starting at the given offset.
addResults(List<QueryResult>) - Method in class mendel.dht.QueryTracker
 
appendSequence(String) - Method in class mendel.data.parse.FastaParser.FastaRecord
 

B

b - Variable in class mendel.util.Pair
 
BalancedHashRing<T> - Class in mendel.dht.hash
Creates an evenly-spaced hash ring network topology.
BalancedHashRing(HashFunction<T>) - Constructor for class mendel.dht.hash.BalancedHashRing
Creates a BalancedHashRing using the provided hash function.
BalancedHashRing(HashFunction<T>, boolean) - Constructor for class mendel.dht.hash.BalancedHashRing
Creates a BalancedHashRing using the provided hash function.
BasicEventWrapper - Class in mendel.event
Implements a basic EventWrapper that uses an EventMap to identify Events by their ID numbers.
BasicEventWrapper(EventMap) - Constructor for class mendel.event.BasicEventWrapper
 
binSize - Variable in class mendel.vptree.VPTree
 
BioJavaTest - Class in mendel.test
Created by ctolooee on 7/13/15.
BioJavaTest() - Constructor for class mendel.test.BioJavaTest
 
Block - Class in mendel.fs
The basic unit of storage in Mendel.
Block(byte[], String) - Constructor for class mendel.fs.Block
 
Block(Metadata, byte[]) - Constructor for class mendel.fs.Block
 
Block(List<Metadata>, List<byte[]>) - Constructor for class mendel.fs.Block
 
Block(SerializationInputStream) - Constructor for class mendel.fs.Block
 
BLOCK_EXTENSION - Static variable in interface mendel.fs.FileSystem
 
BoundedPriorityQueue<E extends VPPoint> - Class in mendel.vptree
 
BoundedPriorityQueue(VPPoint, int) - Constructor for class mendel.vptree.BoundedPriorityQueue
 
broadcastMessage(Iterable<NetworkDestination>, MendelMessage) - Method in class mendel.network.ClientMessageRouter
Sends a message to multiple network destinations.
ByteSerializable - Interface in mendel.serialize
Describes an interface for classes that can be serialized to portable byte form.
ByteSerializable.Deserialize - Annotation Type in mendel.serialize
Annotates constructors used for creating new object instances from a SerializationInputStream.

C

changeInterest - Variable in class mendel.network.MessageRouter
 
charMap - Static variable in class mendel.data.Nucleotide
Encoding Nucleotide characters: A = 00000000 C = 00000001 G = 00000010 N = 00000011 T = 00000100

Use this to bitwise OR individual nucleotides into a single byte.

Checksum - Class in mendel.util
Provides convenience functions for dealing with MessageDigest algorithms.
Checksum() - Constructor for class mendel.util.Checksum
Initializes a new Checksum generator using the default SHA-1 algorithm.
Checksum(String) - Constructor for class mendel.util.Checksum
Initializes a new Checksum generator using the specified algorithm.
classToInt - Variable in class mendel.event.EventMap
 
clear() - Method in class mendel.vptree.VPTree
Removes all points from this vp-tree.
ClientConnectionPool - Class in mendel.network
Extends the standard ClientMessageRouter by aging out connections over time and caching frequently-used connections.
ClientConnectionPool() - Constructor for class mendel.network.ClientConnectionPool
 
ClientMessageRouter - Class in mendel.network
Provides client-side message routing capabilities.
ClientMessageRouter() - Constructor for class mendel.network.ClientMessageRouter
 
ClientMessageRouter(int, int) - Constructor for class mendel.network.ClientMessageRouter
 
ClientTest - Class in mendel.test
A simple client to test an query a running Mendel system.
ClientTest(String, int) - Constructor for class mendel.test.ClientTest
 
close() - Method in class mendel.data.parse.FastaParser
Closes the stream and releases any system resources associated with it.
close(int) - Method in class mendel.network.ServerMessageRouter
 
compare(VPPoint, VPPoint) - Method in class mendel.vptree.VPNodeComparator
 
compareTo(SmithWaterman) - Method in class mendel.util.SmithWaterman
 
compareTo(VPPoint) - Method in class mendel.vptree.types.Sequence
 
ConcurrentEventReactor - Class in mendel.event
Extends the single-threaded reactor implementation defined by EventReactor to enable multiple worker threads for processing events concurrently.
ConcurrentEventReactor(Object, EventMap, int) - Constructor for class mendel.event.ConcurrentEventReactor
Creates a ConcurrentEventReactor with the default BasicEventWrapper EventWrapper implementation.
ConcurrentEventReactor(Object, EventWrapper, int) - Constructor for class mendel.event.ConcurrentEventReactor
Creates a ConcurrentEventReactor with a custom EventWrapper implementation.
connect(SelectionKey) - Method in class mendel.network.MessageRouter
Finishes setting up a connection on a SocketChannel.
connectionAge - Variable in class mendel.network.ClientConnectionPool
 
contains(T) - Method in class mendel.vptree.VPNode
Tests whether this node or one of its children contains the given point.
contains(Object) - Method in class mendel.vptree.VPTree
Tests whether this vp-tree contains the given point.
containsAll(Collection<?>) - Method in class mendel.vptree.VPTree
Tests whether this vp-tree contains all of the points in the given collection.
count - Variable in class mendel.comm.QueryResponse
 
countBlocks() - Method in class mendel.fs.MendelFileSystem
 

D

decrementSendRecvCount() - Method in class mendel.dht.QueryTracker
 
DEFAULT_BIN_SIZE - Static variable in class mendel.vptree.VPTree
The default node capacity (32 points) for nodes in this vp-tree.
DEFAULT_PORT - Static variable in class mendel.config.NetworkConfig
 
DEFAULT_READ_BUFFER_SIZE - Static variable in class mendel.network.MessageRouter
The default read buffer size is 8 MB.
DEFAULT_WRITE_QUEUE_SIZE - Static variable in class mendel.network.MessageRouter
The default write queue allows 100 items to be inserted before it starts blocking.
deserialize(Class<T>, byte[]) - Static method in class mendel.serialize.Serializer
Loads a ByteSerializable object's binary form and then instantiates a new object using the SerializationInputStream constructor.
deserializeFromStream(Class<T>, SerializationInputStream) - Static method in class mendel.serialize.Serializer
Deserializes and instantiates a ByteSerializable class from a stream.
destinationToSocket - Variable in class mendel.network.ClientMessageRouter
 
disableCompression() - Method in class mendel.event.EventWithSynopsis
Disables compression when serializing this event.
disconnect(SelectionKey) - Method in class mendel.network.ClientMessageRouter
 
disconnect(SelectionKey) - Method in class mendel.network.MessageRouter
Handle termination of connections.
disconnect() - Method in class mendel.test.ClientTest
 
disconnect() - Method in class mendel.test.ExpectationCalc
 
disconnect() - Method in class mendel.test.FileUploadTest
 
disconnect() - Method in class mendel.test.ScalabilityBenchmark
 
dispatchConnect(NetworkDestination) - Method in class mendel.network.MessageRouter
Informs all listening consumers that a connection to a remote endpoint has been made.
dispatchDisconnect(NetworkDestination) - Method in class mendel.network.MessageRouter
Informs all listening consumers that a connection to a remote endpoint has been terminated.
dispatchMessage(MendelMessage) - Method in class mendel.network.MessageRouter
Dispatches a message to all listening consumers.
DNASequence - Class in mendel.data
Encapsulates a DNA sequence composed of one or more .Nucleotides as a operable unit in Mendel.
DNASequence() - Constructor for class mendel.data.DNASequence
 
DNASequence - Class in mendel.vptree.types
 
DNASequence(String) - Constructor for class mendel.vptree.types.DNASequence
 
DNASequence(Sequence) - Constructor for class mendel.vptree.types.DNASequence
 
DNASequence(VPPoint) - Constructor for class mendel.vptree.types.DNASequence
 
DNASequence(SerializationInputStream) - Constructor for class mendel.vptree.types.DNASequence
 

E

enableCompression() - Method in class mendel.event.EventWithSynopsis
Enables compression when serializing this event.
end - Variable in class mendel.util.PerformanceTimer.PerformanceSample
 
entryMap - Variable in class mendel.dht.hash.BalancedHashRing
Maps hash ring positions to ring entries
equals(Object) - Method in class mendel.network.NetworkDestination
 
equals(Object) - Method in class mendel.vptree.types.Sequence
 
erase() - Method in class mendel.fs.RecoveryManager
Removes the Index Journal.
Event - Interface in mendel.event
Defines an interface for events in the Mendel network.
EventContext - Class in mendel.event
Tracks the context of an event and allows retrieving event metadata.
EventContext(MendelMessage, EventWrapper) - Constructor for class mendel.event.EventContext
 
EventException - Exception in mendel.event
 
EventException() - Constructor for exception mendel.event.EventException
 
EventException(String) - Constructor for exception mendel.event.EventException
 
EventException(String, Throwable) - Constructor for exception mendel.event.EventException
 
EventHandler - Annotation Type in mendel.event
Provides an annotation to be used to map EventTypes to methods or classes that handle them.
EventMap - Class in mendel.event
Provides a base implementation for mapping event identifiers to classes, and classes back to event identifiers.
EventMap() - Constructor for class mendel.event.EventMap
 
EventProducer - Class in mendel.event
This class makes it easy to publish events from a client to a server by linking a ClientMessageRouter instance to a EventReactor instance.
EventProducer(ClientMessageRouter, EventReactor) - Constructor for class mendel.event.EventProducer
 
EventPublisher - Class in mendel.client
Handles publishing events from a client to a server.
EventPublisher(ClientMessageRouter) - Constructor for class mendel.client.EventPublisher
Creates a new EventPublisher instance using the provided ClientMessageRouter instance for communications.
EventReactor - Class in mendel.event
Implements the reactor pattern for processing incoming events (MendelMessage instances).
EventReactor(Object, EventMap) - Constructor for class mendel.event.EventReactor
Creates an EventReactor with the default BasicEventWrapper EventWrapper implementation.
EventReactor(Object, EventWrapper) - Constructor for class mendel.event.EventReactor
Creates an EventReactor with a custom EventWrapper implementation.
EventWithSynopsis - Class in mendel.event
Encapsulates a raw (byte[] based) event that includes a String representing the event synopsis.
EventWithSynopsis(String, byte[]) - Constructor for class mendel.event.EventWithSynopsis
 
EventWithSynopsis(SerializationInputStream) - Constructor for class mendel.event.EventWithSynopsis
 
EventWrapper - Interface in mendel.event
Defines how Events are wrapped and unwrapped for serialization and transmission across the network.
ExpectationCalc - Class in mendel.test
The benchmarking code to time the same query over the same dataset on various cluster sizes.
ExpectationCalc(String, int) - Constructor for class mendel.test.ExpectationCalc
 

F

FastaParser - Class in mendel.data.parse
A parser for iterating over FASTA files.
FastaParser(InputStream, String) - Constructor for class mendel.data.parse.FastaParser
Constructs a FASTA file parser over the InputStream.
FastaParser(File) - Constructor for class mendel.data.parse.FastaParser
Constructs a FASTA file parser over the File.
FastaParser(String) - Constructor for class mendel.data.parse.FastaParser
Constructs a FASTA file parser over the FASTA file at the given absolute path.
FastaParser.FastaRecord - Class in mendel.data.parse
 
FastaParserTest - Class in mendel.test
 
FastaParserTest() - Constructor for class mendel.test.FastaParserTest
 
FastaRecord(String) - Constructor for class mendel.data.parse.FastaParser.FastaRecord
 
FastaRecord(FastaParser.FastaRecord) - Constructor for class mendel.data.parse.FastaParser.FastaRecord
 
FileNames - Class in mendel.util
Utility class for working with file names.
FileNames() - Constructor for class mendel.util.FileNames
 
FileSystem - Interface in mendel.fs
Defines the interface for on-disk storage.
FileSystemException - Exception in mendel.fs
 
FileSystemException() - Constructor for exception mendel.fs.FileSystemException
 
FileSystemException(String) - Constructor for exception mendel.fs.FileSystemException
 
FileSystemException(String, Throwable) - Constructor for exception mendel.fs.FileSystemException
 
FileUploadTest - Class in mendel.test
 
FileUploadTest(String, int) - Constructor for class mendel.test.FileUploadTest
 
findNodeContainingPoint(VPPoint, Deque<VPNode<T>>) - Method in class mendel.vptree.VPNode
Finds the node at or below this node that contains (or would contain) the given point.
finish() - Method in class mendel.network.Transmission
Causes the calling thread to wait until this transmission has completed.
finish() - Method in class mendel.util.ProgressBar
Display the completed progression bar.
forceShutdown() - Method in class mendel.network.ClientMessageRouter
Forcibly shuts down the message processor and disconnects from any connected server(s).
formatedOutput(Sequence) - Method in class mendel.vptree.types.DNASequence
 
formatedOutput(Sequence) - Method in class mendel.vptree.types.Sequence
 
fromSocketChannel(SocketChannel) - Static method in class mendel.network.NetworkDestination
Retrieves host:port information from a SocketChannel and instantiates a new NetworkDestination with the information.
fullRecovery() - Method in class mendel.fs.MendelFileSystem
Does a full recovery from disk; this scans every block in the system, reads metadata, and performs a checksum to verify integrity.
function - Variable in class mendel.dht.hash.BalancedHashRing
 

G

gatherLeafNodes(List<VPNode<T>>) - Method in class mendel.vptree.VPNode
Populates the given List with all of the leaf nodes that are descendants of this node.
generateDOT() - Method in class mendel.dht.partition.VPHashPartitioner
 
generateDot(int) - Method in class mendel.vptree.VPNode
 
generateDot() - Method in class mendel.vptree.VPTree
 
get(K) - Method in interface mendel.serialize.SimpleMap
Retrieves an item from this data structure.
getAlignment() - Method in class mendel.util.SmithWaterman
 
getAllNodes() - Method in class mendel.network.GroupInfo
 
getAllNodes() - Method in class mendel.network.NetworkInfo
 
getBinSize() - Method in class mendel.vptree.VPTree
Returns the maximum number of points any leaf node of this vp-tree should contain.
getBlock() - Method in class mendel.comm.StorageEvent
Returns the block to be stored.
getBlock() - Method in class mendel.comm.StorageRequest
Returns the block to be stored.
getCenter() - Method in class mendel.vptree.VPNode
Returns a new point that is coincident with this node's center point.
getClass(int) - Method in class mendel.event.EventMap
Retrieves the class associated with the provided event identifier.
getClientString(SocketChannel) - Static method in class mendel.network.MessageRouter
Determines a connection's hostname and port, then concatenates the two values, separated by a colon (:).
getCloserNode() - Method in class mendel.vptree.VPNode
Returns a reference to this node's child that contains elements that are closer to this node's center than this node's distance threshold.
getConfDir() - Static method in class mendel.config.SystemConfig
Retrieves the system configuration directory, which contains all Mendel configuration directives.
getConsecScore() - Method in class mendel.query.QueryResult
 
getContext() - Method in class mendel.dht.QueryTracker
 
getContext() - Method in class mendel.network.MendelMessage
 
getContigName() - Method in class mendel.data.parse.FastaParser.FastaRecord
 
getData() - Method in class mendel.fs.Block
 
getDepth() - Method in class mendel.vptree.VPNode
 
getDestination(SocketChannel) - Static method in class mendel.network.MessageRouter
Determines a connection's endpoint information (hostname and port) and encapsulates them in a NetworkDestination.
getDistanceTo(VPPoint) - Method in class mendel.vptree.types.ProteinSequence
 
getDistanceTo(VPPoint) - Method in class mendel.vptree.types.Sequence
 
getDistanceTo(VPPoint) - Method in interface mendel.vptree.VPPoint
 
getElements() - Method in class mendel.vptree.VPNode
Returns a collection of all the elements stored directly in this node.
getExceptions() - Method in class mendel.network.Transmission
 
getFartherNode() - Method in class mendel.vptree.VPNode
Returns a reference to this node's child that contains elements that are farther away from this node's center than this node's distance threshold.
getFileName() - Method in class mendel.data.parse.FastaParser.FastaRecord
 
getFQDN() - Static method in class mendel.network.HostIdentifier
Retrieves the canonical (fully-qualified) hostname for the current host.
getFreeSpace() - Method in class mendel.fs.MendelFileSystem
Reports the amount of free space (in bytes) in the root storage directory.
getFurthestDistance() - Method in class mendel.vptree.BoundedPriorityQueue
Finds the distance of the element who is furthest from the center.
getGroups() - Method in class mendel.network.GroupInfo
 
getGroups() - Method in class mendel.network.NetworkInfo
 
getHashTreeDOT() - Method in class mendel.dht.hash.VPHashTree
 
getHostname() - Static method in class mendel.network.HostIdentifier
Retrieves the short host name of the current host.
getHostname() - Method in class mendel.network.NetworkDestination
 
getHostname() - Method in class mendel.network.NodeInfo
 
getIdentityScore() - Method in class mendel.query.QueryResult
 
getIdString(String) - Method in class mendel.dht.QueryTracker
 
getInstallDir() - Static method in class mendel.config.SystemConfig
Retrieves the Mendel installation directory, which contains the binaries, scripts, and libraries required to run Mendel.
getInt(Class<?>) - Method in class mendel.event.EventMap
Retrieves the event identifier associated with a given Event class.
getLastResult() - Method in class mendel.util.PerformanceTimer
Retrieves the last timing result, in miliseconds.
getLength() - Method in class mendel.vptree.types.Sequence
 
getMessageDigest() - Method in class mendel.util.Checksum
Retrieves the MessageDigest instance used by this Checksum generator.
getMessageRouter() - Method in class mendel.network.MessageContext
 
getMetadata() - Method in class mendel.fs.Block
 
getName() - Method in class mendel.data.Metadata
Returns the name of the sequence from which the segment originates.
getName() - Method in class mendel.network.GroupInfo
 
getNearestNeighbor(VPPoint) - Method in class mendel.vptree.VPTree
 
getNearestNeighbors(VPPoint, BoundedPriorityQueue<T>) - Method in class mendel.vptree.VPNode
Populates the given search result set with elements close to the query point.
getNearestNeighbors(VPPoint, int) - Method in class mendel.vptree.VPTree
 
getNetworkDestination() - Method in class mendel.network.MessageContext
Retrieves the originating endpoint that sent the message associated with this context.
getNodes() - Method in class mendel.network.GroupInfo
 
getPayload() - Method in class mendel.event.EventWithSynopsis
 
getPayload() - Method in class mendel.network.MendelMessage
Retrieves the payload for this MendelMessage.
getPayload() - Method in class mendel.network.Transmission
 
getPort() - Method in class mendel.network.NetworkDestination
 
getPort() - Method in class mendel.network.NodeInfo
 
getPrefix() - Method in class mendel.vptree.VPNode
Returns the prefix value of this node.
getPrefixOf(T) - Method in class mendel.vptree.VPNode
Deprecated.
getPrefixOf(T, int) - Method in class mendel.vptree.VPNode
 
getPrefixOf(E) - Method in class mendel.vptree.VPTree
Deprecated.
getPrefixOf(E, int) - Method in class mendel.vptree.VPTree
 
getPseudoFS() - Static method in class mendel.config.SystemConfig
Retrieves the flag that determines whether psuedoFS mode has been enabled.
getQuery() - Method in class mendel.comm.QueryEvent
Returns the SimilarityQuery that describes this Event.
getQuery() - Method in class mendel.comm.QueryRequest
Returns the SimilarityQuery that describes this Event.
getQuery() - Method in class mendel.comm.QueryResponse
Returns the base query.
getQuery() - Method in class mendel.query.QueryResult
 
getQueryID() - Method in class mendel.comm.QueryEvent
Returns the query's unique id string.
getQueryID() - Method in class mendel.comm.QueryRequest
Returns the query's unique id string.
getQueryID() - Method in class mendel.comm.QueryResponse
Returns the base query's unique ID
getQueryId() - Method in class mendel.dht.QueryTracker
 
getQuerySequence() - Method in class mendel.query.SimilarityQuery
Returns the whole base query of the SimilarityQuery.
getResponse() - Method in class mendel.comm.QueryResponse
Returns the list of QueryResults that were created during the processing of the base query.
getResults() - Method in class mendel.dht.QueryTracker
 
getRoot() - Method in class mendel.vptree.VPTree
Returns a reference to this vp-tree's root node.
getRootDir() - Static method in class mendel.config.SystemConfig
Retrieves the system root directory.
getSamples() - Method in class mendel.util.PerformanceTimer
Get all the samples recorded by this PerformanceTimer so far.
getScore() - Method in class mendel.util.SmithWaterman
 
getSegment() - Method in class mendel.data.Metadata
Returns the sequence segment.
getSelectionKey() - Method in class mendel.network.MessageContext
 
getSendRecvCount() - Method in class mendel.dht.QueryTracker
 
getSequence() - Method in class mendel.data.parse.FastaParser.FastaRecord
 
getSequenceID() - Method in class mendel.vptree.types.Sequence
 
getSequenceLength() - Method in class mendel.vptree.types.Sequence
 
getSequencePos() - Method in class mendel.vptree.types.Sequence
 
getSequenceSegments() - Method in class mendel.query.SimilarityQuery
Returns the list of a least one sequence segment for the query.
getServerPort() - Method in class mendel.event.EventContext
 
getServerPort() - Method in class mendel.network.MessageContext
 
getSessionID(int) - Static method in class mendel.network.HostIdentifier
Retrieve a Mendel session identifier.
getSocketChannel() - Method in class mendel.network.MessageContext
 
getSource() - Method in class mendel.event.EventContext
 
getSource() - Method in class mendel.network.MessageContext
 
getStagedDataDir() - Static method in class mendel.config.SystemConfig
Retrieves directory containing the fasta files used to populate the initial vantage point hashing tree.
getSubjectID() - Method in class mendel.util.SmithWaterman
 
getSynopsis() - Method in class mendel.event.EventWithSynopsis
 
getThreshold() - Method in class mendel.vptree.VPNode
Returns the distance threshold for this node if it is a non-leaf node.
getValue() - Method in class mendel.query.QueryResult
 
getVersion() - Static method in class mendel.util.Version
Gets the version number of the running version of Mendel
getWholeSequece() - Method in class mendel.vptree.types.Sequence
 
getWindowSize() - Static method in class mendel.config.SystemConfig
Retrieves the system-wide window size for indexing and querying data
getWord() - Method in class mendel.vptree.types.Sequence
 
GroupInfo - Class in mendel.network
Records network group information.
GroupInfo(String) - Constructor for class mendel.network.GroupInfo
 

H

handleQuery(QueryEvent, EventContext) - Method in class mendel.dht.StorageNode
Performs the query versus the data on this Node and replies the results back to the sender.
handleQueryRequest(QueryRequest, EventContext) - Method in class mendel.dht.StorageNode
Handles a query request from a client.
handleQueryResponse(QueryResponse, EventContext) - Method in class mendel.dht.StorageNode
Forwards all the queries responses from the initial query request back to the client.
handleStorage(StorageEvent, EventContext) - Method in class mendel.dht.StorageNode
 
handleStorageRequest(StorageRequest, EventContext) - Method in class mendel.dht.StorageNode
Handles a storage request from a client.
hasException() - Method in class mendel.network.Transmission
 
hash(T) - Method in interface mendel.dht.hash.HashFunction
Maps some given data to an integer location in the implemented hash space.
hash(Metadata) - Method in class mendel.dht.hash.SHA1
 
hash(long) - Method in class mendel.dht.hash.SHA1
 
hash(Metadata) - Method in class mendel.dht.hash.VPHashTree
Hashes the metadata in the tree.
hash(byte[]) - Method in class mendel.util.Checksum
Produce a checksum/hashsum of a given block of data.
hashCode() - Method in class mendel.network.NetworkDestination
 
hashCode() - Method in class mendel.vptree.types.Sequence
 
HashException - Exception in mendel.dht.hash
 
HashException() - Constructor for exception mendel.dht.hash.HashException
 
HashException(String) - Constructor for exception mendel.dht.hash.HashException
 
HashFunction<T> - Interface in mendel.dht.hash
Interface for mapping arbitrary data to a specific location in a hash space.
HashRing<T> - Interface in mendel.dht.hash
Provides a generic interface for representing a hash space.
HashRingEntry - Class in mendel.dht.hash
Represents a node entry in a hash ring.
HashRingEntry(BigInteger) - Constructor for class mendel.dht.hash.HashRingEntry
Creates the first entry in a hash ring (neighbor is self).
HashRingEntry(BigInteger, HashRingEntry) - Constructor for class mendel.dht.hash.HashRingEntry
Creates a hash ring entry with a provided position and neighbor.
hashToHexString(byte[]) - Method in class mendel.util.Checksum
Convert a hash to a hexidecimal String.
HashTopologyException - Exception in mendel.dht.hash
 
HashTopologyException() - Constructor for exception mendel.dht.hash.HashTopologyException
 
HashTopologyException(String) - Constructor for exception mendel.dht.hash.HashTopologyException
 
HostIdentifier - Class in mendel.network
Provides functionality for host identification.
HostIdentifier() - Constructor for class mendel.network.HostIdentifier
 
hostname - Variable in class mendel.network.NetworkDestination
 

I

incrementSendRecvCount() - Method in class mendel.dht.QueryTracker
 
init() - Method in interface mendel.dht.Node
 
init() - Method in class mendel.dht.StorageNode
Begins Server execution.
initialize(String) - Method in class mendel.fs.MendelFileSystem
 
intToClass - Variable in class mendel.event.EventMap
 
isAncestorOfNode(VPNode<T>) - Method in class mendel.vptree.VPNode
Tests whether this node is an ancestor of the given node.
isEmpty() - Method in class mendel.vptree.VPNode
Tests whether this node and all of its children are empty.
isEmpty() - Method in class mendel.vptree.VPTree
Tests whether this vp-tree is empty.
isLeafNode() - Method in class mendel.vptree.VPNode
Tests whether this is a leaf node.
isOnline() - Method in class mendel.network.MessageRouter
Determines whether or not this MessageRouter is online.
isOverloaded() - Method in class mendel.vptree.VPNode
Tests whether this node contains more elements than its maximum capacity.
isReadOnly() - Method in class mendel.fs.MendelFileSystem
Reports whether the Mendel filesystem is read-only.
iterator() - Method in class mendel.data.parse.FastaParser
 

L

length() - Method in class mendel.data.parse.FastaParser.FastaRecord
 
length - Variable in class mendel.vptree.types.Sequence
 
lineIterator() - Method in class mendel.data.parse.FastaParser
Returns a FastaParser.FastaLineIterator over the FASTA file.
linkEventHandlers() - Method in class mendel.event.EventReactor
This method links incoming event types to their relevant event handlers found in the handlerObject.
listen(int) - Method in class mendel.network.ParallelMessageRouter
 
listen(int) - Method in class mendel.network.ServerMessageRouter
Initializes the server socket channel for incoming client connections and begins listening for messages.
loadBlock(String) - Method in interface mendel.fs.FileSystem
Retrieves a Block instance, given its path on disk.
loadBlock(String) - Method in class mendel.fs.MendelFileSystem
 
loadMetadata(String) - Method in interface mendel.fs.FileSystem
Retrieves a Metadata instance, given a Block path on disk.
loadMetadata(String) - Method in class mendel.fs.MendelFileSystem
 
locate(T) - Method in class mendel.dht.hash.BalancedHashRing
 
locate(T) - Method in interface mendel.dht.hash.HashRing
Determine the node that is responsible for the given data.
locateData(T) - Method in class mendel.dht.partition.Partitioner
Determines where a file belongs in the system based on its properties.
locateData(Metadata) - Method in class mendel.dht.partition.SHA1Partitioner
 
locateData(Metadata) - Method in class mendel.dht.partition.VPHashPartitioner
 
logger - Static variable in class mendel.network.ClientMessageRouter
 
logger - Static variable in class mendel.network.MessageRouter
 
longToBytes(long) - Static method in class mendel.dht.hash.SHA1
 
lookup(VPPoint) - Method in class mendel.dht.hash.VPHashTree
Finds the prefix value in the hash tree of the specified @code{VPPoint}.

M

main(String[]) - Static method in class mendel.dht.hash.BalancedHashRing
 
main(String[]) - Static method in class mendel.dht.StorageNode
Executable to be run on each Mendel storage server.
main(String[]) - Static method in class mendel.test.BioJavaTest
 
main(String[]) - Static method in class mendel.test.ClientTest
 
main(String[]) - Static method in class mendel.test.ExpectationCalc
 
main(String[]) - Static method in class mendel.test.FastaParserTest
 
main(String[]) - Static method in class mendel.test.FileUploadTest
 
main(String[]) - Static method in class mendel.test.QueryTest
 
main(String[]) - Static method in class mendel.test.ScalabilityBenchmark
 
main(String[]) - Static method in class mendel.test.VPHashTreeTest
 
main(String[]) - Static method in class mendel.util.ProgressBar
 
main(String[]) - Static method in class mendel.util.ProteinAlignment
 
main(String[]) - Static method in class mendel.vptree.types.ProteinSequence
 
main(String[]) - Static method in class mendel.vptree.types.SubMatrix
 
maxHash - Variable in class mendel.dht.hash.BalancedHashRing
 
maxValue() - Method in interface mendel.dht.hash.HashFunction
Determines the maximum hash value that this hash function can produce.
maxValue() - Method in class mendel.dht.hash.SHA1
 
maxValue() - Method in class mendel.dht.hash.VPHashTree
 
mendel.client - package mendel.client
Provides client-side communication management.
mendel.comm - package mendel.comm
Contains communication structures to abstract away the networking implementation in the mendel.network package.
mendel.config - package mendel.config
 
mendel.data - package mendel.data
 
mendel.data.parse - package mendel.data.parse
Utility classes for parsing FASTA, SAM/BAM, GenBank, and other sequence data formats to be stored in Mendel.
mendel.dht - package mendel.dht
Implementation of the Mendel Distributed Hash Table.
mendel.dht.hash - package mendel.dht.hash
Implementations of various hash functions.
mendel.dht.partition - package mendel.dht.partition
Implementations of various DHT partitioners for both tiers of the Mendel DHT.
mendel.event - package mendel.event
Creation, management, and dispatch of events.
mendel.fs - package mendel.fs
Implementation of the Mendel file system on top of the platform OS.
mendel.log - package mendel.log
Handles configurations of log files.
mendel.network - package mendel.network
Handles network communication between Mendel entities.
mendel.query - package mendel.query
Contains the Mendel querying scheme and handles the construction, sending, and retrievals of all the supported queries.
mendel.serialize - package mendel.serialize
Handles serializing/deserializing data to/from the native Mendel binary format.
mendel.test - package mendel.test
Contains various tests for development.
mendel.util - package mendel.util
Various utility classes that help accomplish tasks.
mendel.vptree - package mendel.vptree
Implementation of the Vantage-point vptree used for content distribution; stolen from Jon Chambers from his Geospatial Point database, Jeospatial and heavily modified.
mendel.vptree.types - package mendel.vptree.types
 
MendelEventMap - Class in mendel.comm
Contains the mappings of Mendel event identifiers to the classes and vise versa.
MendelEventMap() - Constructor for class mendel.comm.MendelEventMap
 
MendelFileSystem - Class in mendel.fs
 
MendelFileSystem(String, boolean) - Constructor for class mendel.fs.MendelFileSystem
 
MendelFileSystem(String) - Constructor for class mendel.fs.MendelFileSystem
 
MendelMessage - Class in mendel.network
The unit of data transmission in the Mendel DHT.
MendelMessage(byte[]) - Constructor for class mendel.network.MendelMessage
Constructs a MendelMessage from an array of bytes.
MendelMessage(byte[], MessageContext) - Constructor for class mendel.network.MendelMessage
Constructs a MendelMessage from an array of bytes with an associated MessageContext representing the source of the message.
MessageContext - Class in mendel.network
Contains connection-specific information about the source of a MendelMessage.
MessageContext(MessageRouter, SelectionKey) - Constructor for class mendel.network.MessageContext
 
MessageListener - Interface in mendel.network
Interface for classes that will listen for incoming MendelMessage instances produced by a MessageRouter.
MessageRouter - Class in mendel.network
Provides an abstract implementation for consuming and publishing messages on both the server and client side.
MessageRouter() - Constructor for class mendel.network.MessageRouter
 
MessageRouter(int, int) - Constructor for class mendel.network.MessageRouter
 
Metadata - Class in mendel.data
Defines the metadata associated with a genomic segment segment.
Metadata(ProteinSequence, String) - Constructor for class mendel.data.Metadata
Constructs a Metadata item for the specified sequence segment.
Metadata(SerializationInputStream) - Constructor for class mendel.data.Metadata
 

N

name - Variable in class mendel.util.PerformanceTimer
The name of this PerformanceTimer
NAME - Static variable in class mendel.util.Version
 
nearestNeighboQuery(String) - Method in class mendel.fs.MendelFileSystem
 
nearestNeighborQuery(String) - Method in class mendel.fs.MendelFileSystem
 
neighbor - Variable in class mendel.dht.hash.HashRingEntry
Next neighboring node in the hash space
network - Variable in class mendel.dht.partition.Partitioner
 
NetworkConfig - Class in mendel.config
Reads and maintains Mendel network configuration from the installation on disk.
NetworkConfig() - Constructor for class mendel.config.NetworkConfig
 
NetworkDestination - Class in mendel.network
Represents a TCP network endpoint; a host/port pair.
NetworkDestination(String, int) - Constructor for class mendel.network.NetworkDestination
 
NetworkInfo - Class in mendel.network
Maintains information for all nodes within the Mendel cluster.
NetworkInfo() - Constructor for class mendel.network.NetworkInfo
 
Node - Interface in mendel.dht
 
NodeInfo - Class in mendel.network
Maintains a nodes information (i.e.
NodeInfo(String, int) - Constructor for class mendel.network.NodeInfo
 
NodeInfo(SerializationInputStream) - Constructor for class mendel.network.NodeInfo
 
NODES_FILE_NAME - Static variable in class mendel.config.NetworkConfig
 
nth_element(T[], int, int, int, VPPoint) - Method in class mendel.vptree.VPNode
Implementation of the selection algorithm.
Nucleotide - Class in mendel.data
Encapsulates a nucleotide base in a DNA sequence.
Nucleotide() - Constructor for class mendel.data.Nucleotide
 

O

onConnect(NetworkDestination) - Method in class mendel.event.EventReactor
 
onConnect(NetworkDestination) - Method in interface mendel.network.MessageListener
Called when a connection is established with a remote endpoint.
onConnect(NetworkDestination) - Method in class mendel.test.ClientTest
 
onConnect(NetworkDestination) - Method in class mendel.test.ExpectationCalc
 
onConnect(NetworkDestination) - Method in class mendel.test.FileUploadTest
 
onConnect(NetworkDestination) - Method in class mendel.test.ScalabilityBenchmark
 
onDisconnect(NetworkDestination) - Method in class mendel.event.EventReactor
 
onDisconnect(NetworkDestination) - Method in interface mendel.network.MessageListener
Called when the MessageListener has been disconnected from a remote endpoint.
onDisconnect(NetworkDestination) - Method in class mendel.test.ClientTest
 
onDisconnect(NetworkDestination) - Method in class mendel.test.ExpectationCalc
 
onDisconnect(NetworkDestination) - Method in class mendel.test.FileUploadTest
 
onDisconnect(NetworkDestination) - Method in class mendel.test.ScalabilityBenchmark
 
online - Variable in class mendel.network.MessageRouter
Flag used to determine whether the Selector thread should run
onMessage(MendelMessage) - Method in class mendel.event.EventReactor
 
onMessage(MendelMessage) - Method in interface mendel.network.MessageListener
Called when a message is ready to be processed.
onMessage(MendelMessage) - Method in class mendel.test.ClientTest
 
onMessage(MendelMessage) - Method in class mendel.test.ExpectationCalc
 
onMessage(MendelMessage) - Method in class mendel.test.FileUploadTest
 
onMessage(MendelMessage) - Method in class mendel.test.ScalabilityBenchmark
 

P

Pair<A,B> - Class in mendel.util
Simple tuple class for holding arbitrary value pairs.
Pair() - Constructor for class mendel.util.Pair
 
Pair(A, B) - Constructor for class mendel.util.Pair
 
ParallelMessageRouter - Class in mendel.network
A MessageRouter instance that can act as both a server and a client.
ParallelMessageRouter() - Constructor for class mendel.network.ParallelMessageRouter
 
ParallelMessageRouter(int, int) - Constructor for class mendel.network.ParallelMessageRouter
 
partition() - Method in class mendel.vptree.VPNode
Attempts to partition the elements contained in this node into two child nodes.
partition(T[], int, int) - Method in class mendel.vptree.VPNode
Attempts to partition the elements in a subset of the given array into two child nodes based on their distance from the center of this node.
Partitioner<T> - Class in mendel.dht.partition
This provides an abstract implementation of a Mendel Partitioner, which determines where all information is distributed in the system.
Partitioner(StorageNode, NetworkInfo) - Constructor for class mendel.dht.partition.Partitioner
 
partitioner - Variable in class mendel.test.VPHashTreeTest
 
PartitionerException - Exception in mendel.dht.partition
 
PartitionerException(String) - Constructor for exception mendel.dht.partition.PartitionerException
 
PartitionerException() - Constructor for exception mendel.dht.partition.PartitionerException
 
PartitionException - Class in mendel.dht.partition
 
PartitionException(String) - Constructor for class mendel.dht.partition.PartitionException
 
PartitionException - Exception in mendel.vptree
 
PartitionException() - Constructor for exception mendel.vptree.PartitionException
 
PartitionException(String) - Constructor for exception mendel.vptree.PartitionException
 
pendingRegistrations - Variable in class mendel.network.ClientMessageRouter
 
PerformanceSample() - Constructor for class mendel.util.PerformanceTimer.PerformanceSample
 
PerformanceTimer - Class in mendel.util
A very simple performance timer implementation using System.nanoTime().
PerformanceTimer() - Constructor for class mendel.util.PerformanceTimer
Create a new nameless PerformanceTimer.
PerformanceTimer(String) - Constructor for class mendel.util.PerformanceTimer
Create a named PerformanceTimer.
PerformanceTimer.PerformanceSample - Class in mendel.util
Records information about an interval of time as a performance sample.
persist(ByteSerializable, File) - Static method in class mendel.serialize.Serializer
Dumps a ByteSerializable object to a portable byte array and stores it on disk.
persist(ByteSerializable, String) - Static method in class mendel.serialize.Serializer
Dumps a ByteSerializable object to a portable byte array and stores it on disk.
port - Variable in class mendel.network.NetworkDestination
 
portAvailable(int) - Static method in class mendel.network.PortTester
Determines if the given port can be bound to on this machine.
PortTester - Class in mendel.network
Provides utility functions for testing ports on the local machine.
PortTester() - Constructor for class mendel.network.PortTester
 
position - Variable in class mendel.dht.hash.HashRingEntry
Position in the hash space
PREFIX_SZ - Static variable in class mendel.network.MessageRouter
The size (in bytes) of the message prefix used in the system.
printSplash() - Static method in class mendel.util.Version
Print the Mendel splash art and version information.
printVersionInformation() - Method in class mendel.util.Version
Print Mendel version information.
processIncomingMessage(SelectionKey) - Method in class mendel.network.MessageRouter
Process data received from a client SocketChannel.
processNextEvent() - Method in class mendel.event.EventReactor
Retrieves the next message from the queue, and calls the appropriate event handler method to process the message.
processSelectionKeys() - Method in class mendel.network.MessageRouter
Performs a select operation, and then processes the resulting SelectionKey set based on interest ops.
ProgressBar - Class in mendel.util
A tool to show progression of a task with a graphical bar and estimated time remaining.
ProgressBar(int, String) - Constructor for class mendel.util.ProgressBar
Create a progression bar with the specified name and max value.
ProteinAlignment - Class in mendel.util
 
ProteinAlignment() - Constructor for class mendel.util.ProteinAlignment
 
ProteinSequence - Class in mendel.vptree.types
 
ProteinSequence(String) - Constructor for class mendel.vptree.types.ProteinSequence
 
ProteinSequence(Sequence) - Constructor for class mendel.vptree.types.ProteinSequence
 
ProteinSequence(VPPoint) - Constructor for class mendel.vptree.types.ProteinSequence
 
ProteinSequence(SerializationInputStream) - Constructor for class mendel.vptree.types.ProteinSequence
 
pruneEmptyNode(VPNode<E>) - Method in class mendel.vptree.VPTree
"Prunes" an empty leaf node from the vp-tree.
publish(NetworkDestination, Event) - Method in class mendel.client.EventPublisher
Publishes a Event via the client's ClientMessageRouter.
publishEvent(NetworkDestination, Event) - Method in class mendel.event.EventProducer
 
put(V) - Method in interface mendel.serialize.SimpleMap
Places an item in this data structure.

Q

query(String) - Method in class mendel.test.ClientTest
 
query(String) - Method in class mendel.test.ExpectationCalc
 
query(String) - Method in class mendel.test.FileUploadTest
 
query(String) - Method in class mendel.test.ScalabilityBenchmark
 
QueryEvent - Class in mendel.comm
Defines an internal SimilarityQuery between .StorageNodes.
QueryEvent(SimilarityQuery, String) - Constructor for class mendel.comm.QueryEvent
Constructs a QueryEvent with the given SimilarityQuery and ID.
QueryEvent(SerializationInputStream) - Constructor for class mendel.comm.QueryEvent
 
queryLock - Static variable in class mendel.test.ExpectationCalc
 
queryLock - Static variable in class mendel.test.ScalabilityBenchmark
 
QueryRequest - Class in mendel.comm
Defines an internal event to signal to forward queries to the correct StorageNodes for processing.
QueryRequest(SimilarityQuery, String) - Constructor for class mendel.comm.QueryRequest
Constructs a QueryRequest with the given SimilarityQuery and ID.
QueryRequest(SerializationInputStream) - Constructor for class mendel.comm.QueryRequest
 
QueryResponse - Class in mendel.comm
Defines an internal event to respond to queries that have been processed back to the client.
QueryResponse(List<QueryResult>, String, long, String) - Constructor for class mendel.comm.QueryResponse
Constructs a QueryResponse to the query with the specified ID.
QueryResponse(SerializationInputStream) - Constructor for class mendel.comm.QueryResponse
 
QueryResult - Class in mendel.query
 
QueryResult(Sequence, Sequence) - Constructor for class mendel.query.QueryResult
 
QueryResult(SerializationInputStream) - Constructor for class mendel.query.QueryResult
 
QueryTest - Class in mendel.test
 
QueryTest() - Constructor for class mendel.test.QueryTest
 
queryTimer - Static variable in class mendel.test.ExpectationCalc
 
queryTimer - Static variable in class mendel.test.ScalabilityBenchmark
 
QueryTracker - Class in mendel.dht
Tracks query ids to its originating source while being passed around the system.
QueryTracker(EventContext) - Constructor for class mendel.dht.QueryTracker
 

R

randomHash() - Method in interface mendel.dht.hash.HashFunction
Returns a random location in the hash space.
randomHash() - Method in class mendel.dht.hash.SHA1
 
randomHash() - Method in class mendel.dht.hash.VPHashTree
 
randomize - Variable in class mendel.dht.hash.BalancedHashRing
If set to True, the first position in the hash ring is randomized.
read(SelectionKey) - Method in class mendel.network.MessageRouter
Read data from a SocketChannel.
READ_BUFFER_PROPERTY - Static variable in class mendel.network.MessageRouter
System property that overrides the read buffer size.
readBufferSize - Variable in class mendel.network.MessageRouter
 
readCompressableField() - Method in class mendel.serialize.SerializationInputStream
 
readField() - Method in class mendel.serialize.SerializationInputStream
 
readNetworkDescription(String) - Static method in class mendel.config.NetworkConfig
Reads a network description directory from disk.
readNodesFile(File) - Static method in class mendel.config.NetworkConfig
Read host:port pairs from a Mendel node configuration file and create the network overlay description GroupInfo.
readPrefix(ByteBuffer, TransmissionTracker) - Static method in class mendel.network.MessageRouter
Read the payload size prefix from a channel.
readSerializableCollection(Class<T>, Collection<T>) - Method in class mendel.serialize.SerializationInputStream
 
readSimpleMap(Class<T>, SimpleMap<?, T>) - Method in class mendel.serialize.SerializationInputStream
 
readString() - Method in class mendel.serialize.SerializationInputStream
 
readStringCollection(Collection<String>) - Method in class mendel.serialize.SerializationInputStream
 
rebuildPaths(File) - Method in class mendel.fs.MendelFileSystem
Scans the directory structure on disk to find all the blocks stored.
recordIterator() - Method in class mendel.data.parse.FastaParser
Returns a FastaParser.FastaRecordIterator over the FASTA file.
recover(List<String>) - Method in class mendel.fs.MendelFileSystem
Does a full recovery from disk on a particular Mendel partition; this scans every block in the partition, reads its metadata, and performs a checksum to verify block integrity.
recover() - Method in class mendel.fs.RecoveryManager
Recovers the Path Journal from disk.
RecoveryManager - Class in mendel.fs
 
RecoveryManager(String) - Constructor for class mendel.fs.RecoveryManager
 
reload() - Static method in class mendel.config.SystemConfig
Reloads the Mendel system configuration.
remove(T) - Method in class mendel.vptree.VPNode
Removes a point from this node's internal list of elements.
remove(Object) - Method in class mendel.vptree.VPTree
Removes a point from this vp-tree.
remove(E, boolean, Set<VPNode<E>>) - Method in class mendel.vptree.VPTree
Removes a point from this vp-tree and optionally defers pruning of nodes left empty after the removal of their last point.
removeAll(Collection<?>) - Method in class mendel.vptree.VPTree
Removes all of the points in the given collection from this vp-tree.
restore(Class<T>, File) - Static method in class mendel.serialize.Serializer
Loads a ByteSerializable object's binary form from disk and then instantiates a new object using the SerializationInputStream constructor.
restore(Class<T>, String) - Static method in class mendel.serialize.Serializer
Loads a ByteSerializable object's binary form from disk and then instantiates a new object using the SerializationInputStream constructor.
reverseCharMap - Static variable in class mendel.data.Nucleotide
 
reverseComplementCharMap - Static variable in class mendel.data.Nucleotide
 
root - Variable in class mendel.vptree.VPTree
 
run() - Method in class mendel.network.ClientMessageRouter
 
run() - Method in class mendel.network.MessageRouter
As long as the MessageRouter is online, monitor connection operations through the Selector instance.
running - Variable in class mendel.util.PerformanceTimer.PerformanceSample
 

S

samples - Variable in class mendel.util.PerformanceTimer
Timer samples (time intervals)
ScalabilityBenchmark - Class in mendel.test
The benchmarking code to time the same query over the same dataset on various cluster sizes.
ScalabilityBenchmark(String, int) - Constructor for class mendel.test.ScalabilityBenchmark
 
scanDirectory(File) - Method in class mendel.fs.MendelFileSystem
Scans a directory (and its subdirectories) for blocks.
scoreCount - Variable in class mendel.test.ExpectationCalc
 
selector - Variable in class mendel.network.MessageRouter
 
sendMessage(NetworkDestination, MendelMessage) - Method in class mendel.network.ClientConnectionPool
 
sendMessage(NetworkDestination, MendelMessage) - Method in class mendel.network.ClientMessageRouter
Sends a message to the specified network destination.
sendMessage(NodeInfo, MendelMessage) - Method in class mendel.network.ClientMessageRouter
Sends a message to the specified node.
sendMessage(MendelMessage) - Method in class mendel.network.MessageContext
Sends a message back to the originator of the message this context belongs to.
sendMessage(SelectionKey, MendelMessage) - Method in class mendel.network.MessageRouter
Adds a message to the pending write queue for a particular SelectionKey and submits a change request for its interest set.
sendMessage(NetworkDestination, MendelMessage) - Method in class mendel.network.ParallelMessageRouter
 
sendReply(Event) - Method in class mendel.event.EventContext
Send a reply back to the source that created the original event.
Sequence - Class in mendel.vptree.types
Implementation of a Sequence as a point in a VPTree.
Sequence(String) - Constructor for class mendel.vptree.types.Sequence
 
Sequence(Sequence) - Constructor for class mendel.vptree.types.Sequence
 
Sequence(VPPoint) - Constructor for class mendel.vptree.types.Sequence
 
Sequence(SerializationInputStream) - Constructor for class mendel.vptree.types.Sequence
 
sequenceID - Variable in class mendel.vptree.types.Sequence
 
sequenceLength - Variable in class mendel.vptree.types.Sequence
 
sequencePos - Variable in class mendel.vptree.types.Sequence
 
SerializationException - Exception in mendel.serialize
 
SerializationException() - Constructor for exception mendel.serialize.SerializationException
 
SerializationException(String) - Constructor for exception mendel.serialize.SerializationException
 
SerializationException(String, Throwable) - Constructor for exception mendel.serialize.SerializationException
 
SerializationInputStream - Class in mendel.serialize
 
SerializationInputStream(InputStream) - Constructor for class mendel.serialize.SerializationInputStream
 
SerializationOutputStream - Class in mendel.serialize
 
SerializationOutputStream(OutputStream) - Constructor for class mendel.serialize.SerializationOutputStream
 
serialize(SerializationOutputStream) - Method in class mendel.comm.QueryEvent
 
serialize(SerializationOutputStream) - Method in class mendel.comm.QueryRequest
 
serialize(SerializationOutputStream) - Method in class mendel.comm.QueryResponse
 
serialize(SerializationOutputStream) - Method in class mendel.comm.StorageEvent
 
serialize(SerializationOutputStream) - Method in class mendel.comm.StorageRequest
 
serialize(SerializationOutputStream) - Method in class mendel.data.DNASequence
 
serialize(SerializationOutputStream) - Method in class mendel.data.Metadata
 
serialize(SerializationOutputStream) - Method in class mendel.event.EventWithSynopsis
 
serialize(SerializationOutputStream) - Method in class mendel.event.StubEvent
 
serialize(SerializationOutputStream) - Method in class mendel.fs.Block
 
serialize(SerializationOutputStream) - Method in class mendel.network.NodeInfo
 
serialize(SerializationOutputStream) - Method in class mendel.query.QueryResult
 
serialize(SerializationOutputStream) - Method in class mendel.query.SimilarityQuery
 
serialize(SerializationOutputStream) - Method in interface mendel.serialize.ByteSerializable
Serializes this object to binary form by passing it through a serialization stream.
serialize(ByteSerializable) - Static method in class mendel.serialize.Serializer
Dumps a ByteSerializable object to a portable byte array.
serialize(SerializationOutputStream) - Method in class mendel.vptree.types.Sequence
 
serialize(SerializationOutputStream) - Method in class mendel.vptree.VPNode
 
serialize(SerializationOutputStream) - Method in class mendel.vptree.VPTree
 
Serializer - Class in mendel.serialize
This class provides convenience functions to make the Serialization and Deserialization process easier.
Serializer() - Constructor for class mendel.serialize.Serializer
 
ServerMessageRouter - Class in mendel.network
Handles message routing on a ServerSocketChannel.
ServerMessageRouter() - Constructor for class mendel.network.ServerMessageRouter
 
ServerMessageRouter(int, int) - Constructor for class mendel.network.ServerMessageRouter
 
setCompressionLevel(int) - Method in class mendel.serialize.SerializationOutputStream
Sets the compression level (1-9) when writing serializable fields using gzip.
setConsecScore(double) - Method in class mendel.query.QueryResult
 
setContigName(String) - Method in class mendel.data.parse.FastaParser.FastaRecord
 
setFinished() - Method in class mendel.network.Transmission
Updates the status of this transmission to completed and notifies any waiting threads.
setIdentityScore(double) - Method in class mendel.query.QueryResult
 
setSequence(String) - Method in class mendel.data.parse.FastaParser.FastaRecord
 
setSequenceID(String) - Method in class mendel.vptree.types.Sequence
 
setSequenceLength(int) - Method in class mendel.vptree.types.Sequence
 
setSequencePos(int) - Method in class mendel.vptree.types.Sequence
 
setup() - Method in class mendel.test.VPTreeTest
 
setWholeSequence(String) - Method in class mendel.vptree.types.Sequence
 
SHA1 - Class in mendel.dht.hash
Provides an SHA1 HashFunction.
SHA1() - Constructor for class mendel.dht.hash.SHA1
 
SHA1Partitioner - Class in mendel.dht.partition
Partition using a SHA1 based hash.
SHA1Partitioner(StorageNode, NetworkInfo) - Constructor for class mendel.dht.partition.SHA1Partitioner
 
shutdown() - Method in class mendel.fs.MendelFileSystem
Performs a clean shutdown of the FileSystem instance.
shutdown() - Method in class mendel.fs.RecoveryManager
Closes open index files and stops accepting new data.
shutdown() - Method in class mendel.network.ClientMessageRouter
Shuts down the message processor and disconnects from the server(s).
shutdown() - Method in class mendel.network.ParallelMessageRouter
 
shutdown() - Method in class mendel.network.ServerMessageRouter
Closes the server socket channel and stops processing incoming messages.
SimilarityQuery - Class in mendel.query
Encapsulates a similarity query in Mendel for protein sequences.
SimilarityQuery(String, String) - Constructor for class mendel.query.SimilarityQuery
Constructs a SimilarityQuery with a single sequence segment from a base query.
SimilarityQuery(List<String>, String) - Constructor for class mendel.query.SimilarityQuery
Constructs a SimilarityQuery containing multiple sequence segments from a base query.
SimilarityQuery(SerializationInputStream) - Constructor for class mendel.query.SimilarityQuery
 
SimpleMap<K,V extends ByteSerializable> - Interface in mendel.serialize
Defines a very basic serializable map that consists of Key, Value pairs wherein the Key can be ascertained by the Value directly.
size() - Method in interface mendel.serialize.SimpleMap
Reports the current size of the data structure.
size() - Method in class mendel.util.PerformanceTimer
Retrieves the number of samples recorded by this PerformanceTimer instance.
size() - Method in class mendel.vptree.VPNode
Returns the number of elements contained in this node and its child nodes.
size() - Method in class mendel.vptree.VPTree
Returns the total number of points stored in this vp-tree.
SmithWaterman - Class in mendel.util
 
SmithWaterman(String, String, String, String) - Constructor for class mendel.util.SmithWaterman
 
socketToDestination - Variable in class mendel.network.ClientMessageRouter
 
socketToTracker - Variable in class mendel.network.ClientMessageRouter
 
splitExtension(File) - Static method in class mendel.util.FileNames
 
stageData() - Method in class mendel.dht.partition.VPHashPartitioner
 
start() - Method in class mendel.event.ConcurrentEventReactor
Initializes the event reactor by creating worker threads and having them block on the event queue.
start() - Method in class mendel.fs.RecoveryManager
Prepares the journal files and allows new entries to be written.
start - Variable in class mendel.util.PerformanceTimer.PerformanceSample
 
start() - Method in class mendel.util.PerformanceTimer
Starts a time interval.
stop() - Method in class mendel.event.ConcurrentEventReactor
Gracefully shuts down all the worker threads being maintained by this event reactor.
stop() - Method in class mendel.util.PerformanceTimer
Stops the currently-running time interval.
stopAndPrint() - Method in class mendel.util.PerformanceTimer
Stops the currently-running time interval and prints its duration.
StorageEvent - Class in mendel.comm
Represents an internal storage event at a StorageNode to store sequence segments within the storage blocks.
StorageEvent(Block) - Constructor for class mendel.comm.StorageEvent
Constructs a StorageEvent to store the given Block.
StorageEvent(SerializationInputStream) - Constructor for class mendel.comm.StorageEvent
 
storageNode - Variable in class mendel.dht.partition.Partitioner
 
StorageNode - Class in mendel.dht
 
StorageNode() - Constructor for class mendel.dht.StorageNode
 
StorageNode(boolean) - Constructor for class mendel.dht.StorageNode
 
StorageRequest - Class in mendel.comm
Represents a client's request for storing an inverted indexing block(s) at a Mendel StorageNode.
StorageRequest(Block) - Constructor for class mendel.comm.StorageRequest
Constructs a StorageRequest to store a Block on an individual StorageNode.
StorageRequest(SerializationInputStream) - Constructor for class mendel.comm.StorageRequest
 
store(ProteinSequence) - Method in class mendel.test.ClientTest
 
store(Block) - Method in class mendel.test.ClientTest
 
store(String) - Method in class mendel.test.ExpectationCalc
 
store(Block) - Method in class mendel.test.ExpectationCalc
 
store(ProteinSequence, NetworkDestination) - Method in class mendel.test.ExpectationCalc
 
store(List<ProteinSequence>, NetworkDestination) - Method in class mendel.test.ExpectationCalc
 
store(String) - Method in class mendel.test.FileUploadTest
 
store(Block) - Method in class mendel.test.FileUploadTest
 
store(ProteinSequence, NetworkDestination) - Method in class mendel.test.FileUploadTest
 
store(String) - Method in class mendel.test.ScalabilityBenchmark
 
store(Block) - Method in class mendel.test.ScalabilityBenchmark
 
store(ProteinSequence, NetworkDestination) - Method in class mendel.test.ScalabilityBenchmark
 
store(List<ProteinSequence>, NetworkDestination) - Method in class mendel.test.ScalabilityBenchmark
 
storeBlock(Block) - Method in interface mendel.fs.FileSystem
Stores a Block at the specified path on disk.
storeBlock(Block) - Method in class mendel.fs.MendelFileSystem
 
storeMetadata(Metadata, String) - Method in interface mendel.fs.FileSystem
Stores a Metadata at the specified location.
storeMetadata(Metadata, String) - Method in class mendel.fs.MendelFileSystem
 
StubEvent - Class in mendel.event
Represents an event that is just a 'stub' -- doesn't actually do anything other than serve as an identifier.
StubEvent() - Constructor for class mendel.event.StubEvent
 
StubEvent(SerializationInputStream) - Constructor for class mendel.event.StubEvent
 
SUB_MATRIX - Static variable in class mendel.vptree.types.SubMatrix
An iteration on the Blosum62 substitution matrix with diagonals normalized to 0 to be used as a valid metric to define distances between sequences.
SubMatrix - Class in mendel.vptree.types
 
SubMatrix() - Constructor for class mendel.vptree.types.SubMatrix
 
SynopsisWrapper - Class in mendel.event
Wrapper for simple EventWithSynopsis events.
SynopsisWrapper() - Constructor for class mendel.event.SynopsisWrapper
 
SystemConfig - Class in mendel.config
Provides general system configuration information.
SystemConfig() - Constructor for class mendel.config.SystemConfig
 

T

tearDown() - Method in class mendel.test.VPNodeTest
 
testNth_element() - Method in class mendel.test.VPNodeTest
 
testVPTree() - Method in class mendel.test.VPTreeTest
 
timeInMs() - Method in class mendel.util.PerformanceTimer.PerformanceSample
 
toArray() - Method in class mendel.vptree.VPTree
Returns an array containing all of the points in this vp-tree.
toArray(T[]) - Method in class mendel.vptree.VPTree
 
toSortedList(VPPoint) - Method in class mendel.vptree.BoundedPriorityQueue
Returns a list of the points in this result set sorted in order of increasing distance from the query point provided at construction time.
toString() - Method in class mendel.data.parse.FastaParser.FastaRecord
 
toString() - Method in class mendel.dht.hash.BalancedHashRing
Formats the hash ring as node-to-predecessor pair Strings.
toString() - Method in class mendel.network.GroupInfo
 
toString() - Method in class mendel.network.NetworkDestination
 
toString() - Method in class mendel.network.NetworkInfo
 
toString() - Method in class mendel.network.NodeInfo
 
toString() - Method in class mendel.query.QueryResult
 
toString() - Method in class mendel.query.SimilarityQuery
 
toString() - Method in class mendel.util.Pair
 
toString() - Method in class mendel.util.PerformanceTimer.PerformanceSample
 
toString() - Method in class mendel.util.PerformanceTimer
 
toString() - Method in class mendel.util.SmithWaterman
 
toString() - Method in class mendel.vptree.types.Sequence
 
Transmission - Class in mendel.network
Represents the transmission of one unit of data (MendelMessage).
Transmission(ByteBuffer) - Constructor for class mendel.network.Transmission
 

U

unwrap(MendelMessage) - Method in class mendel.event.BasicEventWrapper
 
unwrap(MendelMessage) - Method in interface mendel.event.EventWrapper
Unwraps a MendelMessage to extract the Event it contains.
unwrap(MendelMessage) - Method in class mendel.event.SynopsisWrapper
 
update(int) - Method in class mendel.util.ProgressBar
Set the current progress value to the specified argument.
updateIndex(Sequence) - Method in class mendel.dht.partition.VPHashPartitioner
 
updateIndex(List<ProteinSequence>) - Method in class mendel.dht.partition.VPHashPartitioner
 
updateInterestOps() - Method in class mendel.network.MessageRouter
Updates interest sets for any SelectionKey instances that require changes.

V

values() - Method in interface mendel.serialize.SimpleMap
Retrieves all the values contained in this data structure.
verifyMetricSpace() - Method in class mendel.vptree.types.Sequence
 
Version - Class in mendel.util
Utility for managing and displaying Mendel software versions and splash art.
Version() - Constructor for class mendel.util.Version
 
VERSION - Static variable in class mendel.util.Version
 
VPHashPartitioner - Class in mendel.dht.partition
 
VPHashPartitioner(StorageNode, NetworkInfo) - Constructor for class mendel.dht.partition.VPHashPartitioner
 
VPHashTree - Class in mendel.dht.hash
 
VPHashTree(int) - Constructor for class mendel.dht.hash.VPHashTree
Constructs a new, empty vp-tree with a default node capacity.
VPHashTree(int, int) - Constructor for class mendel.dht.hash.VPHashTree
Constructs a new, empty vp-tree with the specified node capacity.
VPHashTree(int, Collection<? extends VPPoint>) - Constructor for class mendel.dht.hash.VPHashTree
Constructs a new vp-tree that contains (and indexes) all of the points in the given collection.
VPHashTree(int, ArrayList<? extends VPPoint>, int) - Constructor for class mendel.dht.hash.VPHashTree
Constructs a new vp-tree that contains (and indexes) all of the points in the given collection and has leaf nodes with the given point capacity.
VPHashTreeTest - Class in mendel.test
 
VPHashTreeTest() - Constructor for class mendel.test.VPHashTreeTest
 
VPNode<T extends VPPoint> - Class in mendel.vptree
VPNodes are the nodes of a vantage point vp-tree.
VPNode(int, long, int) - Constructor for class mendel.vptree.VPNode
Constructs a new, empty node with the given capacity.
VPNode(T[], int, int, int, long, int) - Constructor for class mendel.vptree.VPNode
Constructs a new node that contains a subset of the given array of VPPoints.
VPNode(SerializationInputStream) - Constructor for class mendel.vptree.VPNode
 
VPNodeComparator - Class in mendel.vptree
 
VPNodeComparator(VPPoint) - Constructor for class mendel.vptree.VPNodeComparator
 
VPNodeTest - Class in mendel.test
 
VPNodeTest() - Constructor for class mendel.test.VPNodeTest
 
VPPoint - Interface in mendel.vptree
An interface that defines a single point in a vp-vptree.
VPTree<E extends VPPoint> - Class in mendel.vptree
 
VPTree() - Constructor for class mendel.vptree.VPTree
Constructs a new, empty vp-tree with a default node capacity.
VPTree(int) - Constructor for class mendel.vptree.VPTree
Constructs a new, empty vp-tree with the specified node capacity.
VPTree(Collection<E>) - Constructor for class mendel.vptree.VPTree
Constructs a new vp-tree that contains (and indexes) all of the points in the given collection.
VPTree(Collection<? extends VPPoint>, int) - Constructor for class mendel.vptree.VPTree
Constructs a new vp-tree that contains (and indexes) all of the points in the given collection and has leaf nodes with the given point capacity.
VPTree(SerializationInputStream) - Constructor for class mendel.vptree.VPTree
 
VPTreeTest - Class in mendel.test
Testing correctness of vp-tree implementation.
VPTreeTest() - Constructor for class mendel.test.VPTreeTest
 

W

wholeSequece - Variable in class mendel.vptree.types.Sequence
 
windowIterator() - Method in class mendel.data.parse.FastaParser
 
word - Variable in class mendel.vptree.types.Sequence
 
wrap(Event) - Method in class mendel.event.BasicEventWrapper
 
wrap(Event) - Method in interface mendel.event.EventWrapper
Wraps an Event up in a MendelMessage, ready to be transmitted across the network.
wrap(Event) - Method in class mendel.event.SynopsisWrapper
 
wrapEvent(Event) - Static method in class mendel.client.EventPublisher
Wraps a MendelEvent inside an EventContainer, and places the container inside a MendelMessage, ready to be transmitted across the network.
wrapEvent(Event) - Method in class mendel.event.EventReactor
Convenience function for wrapping an outgoing event with this EventReactor's EventWrapper implementation.
wrapWithPrefix(MendelMessage) - Static method in class mendel.network.MessageRouter
Wraps a given message in a ByteBuffer, including the payload size prefix.
WRITE_QUEUE_PROPERTY - Static variable in class mendel.network.MessageRouter
System property that overrides the write queue maximum size.
writeCompressableField(byte[], boolean) - Method in class mendel.serialize.SerializationOutputStream
Writes a field that can be compressed.
writeField(byte[]) - Method in class mendel.serialize.SerializationOutputStream
Writes a byte array (byte field) to the output stream.
writeIndex(VPTree) - Method in class mendel.fs.RecoveryManager
Adds a vp-tree VPTree to the index journal.
writeQueueSize - Variable in class mendel.network.MessageRouter
 
writeSerializable(ByteSerializable) - Method in class mendel.serialize.SerializationOutputStream
Writes a ByteSerializable object to this output stream.
writeSerializableCollection(Collection<? extends ByteSerializable>) - Method in class mendel.serialize.SerializationOutputStream
 
writeSimpleMap(SimpleMap<?, ? extends ByteSerializable>) - Method in class mendel.serialize.SerializationOutputStream
 
writeString(String) - Method in class mendel.serialize.SerializationOutputStream
Writes a String to the output stream.
writeStringCollection(Collection<String>) - Method in class mendel.serialize.SerializationOutputStream
 
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