- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- publishEvent(NetworkDestination, Event) - Method in class mendel.event.EventProducer
-
- put(V) - Method in interface mendel.serialize.SimpleMap
-
Places an item in this data structure.
- 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
-
- 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
-
- SynopsisWrapper() - Constructor for class mendel.event.SynopsisWrapper
-
- SystemConfig - Class in mendel.config
-
Provides general system configuration information.
- SystemConfig() - Constructor for class mendel.config.SystemConfig
-
- 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
-