Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

AbstractAligner	Abstract class that executes the Alignment procedure
AbstractAlignerParameters	The customized parameters of a MASA Extension, used for receiving, manipulating and customizing command line parameters
AbstractAlignerSafe	A thread-safe AbstractAligner extension
AbstractBlockAligner	Abstract class that processes blocks individually considering some schedule mechanism
AbstractBlockProcessor
AbstractBlockPruning
AbstractDiagonalAligner	Abstract class that processes diagonal of blocks
aligner_capabilities_t	Struct that informs to the MASA framework which capabilities the MASA extension implements
AlignerManager
AlignerPool
AlignerTester
AlignerUtils
Alignment
AlignmentBinaryFile
AlignmentParams
BestScoreList
BlockAlignerParameters	This class contains the parameters for the AbstractBlockAligner
BlockPruningDiagonal
BlockPruningGenericN2
BlocksFile
Buffer
Buffer2
buffer2_statistics_t
buffer_statistics_t
BufferedCellsReader
BufferedCellsWriter
BufferedStream
BufferFactory
BufferLogger
cell_t	Struct that represents a cell in the DP matrix
CellsReader
CellsWriter
classcomp
CmdCreateRing
CmdDiscover
CmdJoin
CmdNotifyScore
CmdPeerList
CmdPeerRequest
CmdPeerResponse
CmdStatusRequest
CmdStatusResponse
CmdTestRing
CmdUndiscover
Command
command_t
config_option_t
ConfigParser
Configs
coordinate_t
CPUBlockProcessor
crosspoint_t	Represents a crosspoint between the optimal alignment and a special row
CrosspointsFile
dispatch_job_t
dispatch_job_t::dispatch_params_t
DummyCellsReader
DummyCellsWriter
FileBuffer
FileCellsReader
FileCellsWriter
FileStream
FirstRow	Class that reads and stores an Special Row considering a the affine gap formula in the first row
gap_sequence_t
gap_t
Grid
IAligner	Interface between the MASA extension and the MASA framework
IAlignerParameters	The customized parameters of a MASA Extension, used for receiving, manipulating and customizing command line parameters
IllegalArgumentException	Argument exception class
IManager	Interface that manages the MASA extension execution
InitialCellsReader
IOException	IO exception class
Job
MasaNet
MasaNetCallbacks
MasaNetCLI
MasaNetJob
MasaNetStatus
match_result_t	Struct that notifies the match result in the Mayers-Miller matching procedure
NullBuffer
output_format_t
dispatch_job_t::dispatch_params_t::params_score_t
Partition
Peer
PeerList
Properties
RecurrentTimer
ReversedCellsReader
score_params_t	Defines the match/mismatch score and affine gap penalties
score_t	Represents a score in the DP matrix
SeekableCellsReader
Sequence
SequenceData
SequenceInfo
SequenceModifiers
SocketBuffer
SocketCellsReader
SocketCellsWriter
SpecialRow	Abstract class that represents an Special Row
SpecialRowFile	Class that reads and stores an Special Row in the disk
SpecialRowRAM	Class that reads and stores an Special Row in the RAM memory
SpecialRowReader
SpecialRowsArea
SpecialRowsPartition
SpecialRowWriter
split_args_t
SplitCellsReader
Timer::stat_t
Status
TeeCellsReader
Timer
total_score_t
URLCellsReader
URLCellsWriter