File List

Here is a list of all files with brief descriptions:

AbstractAligner.cpp [code]
AbstractAligner.hpp [code]
AbstractAlignerParameters.cpp [code]
AbstractAlignerParameters.hpp [code]
AbstractAlignerSafe.cpp [code]
AbstractAlignerSafe.hpp [code]
AbstractBlockAligner.cpp [code]
AbstractBlockAligner.hpp [code]
AbstractBlockProcessor.cpp [code]
AbstractBlockProcessor.hpp [code]
AbstractBlockPruning.cpp [code]
AbstractBlockPruning.hpp [code]
AbstractDiagonalAligner.cpp [code]
AbstractDiagonalAligner.hpp [code]
AlignerManager.cpp [code]
AlignerManager.hpp [code]
AlignerPool.cpp [code]
AlignerPool.hpp [code]
AlignerTester.cpp [code]
AlignerTester.hpp [code]
AlignerUtils.cpp [code]
AlignerUtils.hpp [code]
Alignment.cpp [code]
Alignment.hpp [code]
AlignmentBinaryFile.cpp [code]
AlignmentBinaryFile.hpp [code]
AlignmentParams.cpp [code]
AlignmentParams.hpp [code]
BestScoreList.cpp [code]
BestScoreList.hpp [code]
biology.hpp [code]
BlockAlignerParameters.cpp [code]
BlockAlignerParameters.hpp [code]
BlockPruningDiagonal.cpp [code]
BlockPruningDiagonal.hpp [code]
BlockPruningGenericN2.cpp [code]
BlockPruningGenericN2.hpp [code]
BlocksFile.cpp [code]
BlocksFile.hpp [code]
Buffer.cpp [code]
Buffer.hpp [code]
Buffer2.cpp [code]
Buffer2.hpp [code]
BufferedCellsReader.cpp [code]
BufferedCellsReader.hpp [code]
BufferedCellsWriter.cpp [code]
BufferedCellsWriter.hpp [code]
BufferedStream.cpp [code]
BufferedStream.hpp [code]
BufferFactory.cpp [code]
BufferFactory.hpp [code]
buffer/BufferLogger.cpp [code]
io/BufferLogger.cpp [code]
buffer/BufferLogger.hpp [code]
io/BufferLogger.hpp [code]
capabilities.hpp [code]
CellsReader.hpp [code]
CellsWriter.hpp [code]
CmdCreateRing.cpp [code]
CmdCreateRing.hpp [code]
CmdDiscover.cpp [code]
CmdDiscover.hpp [code]
CmdJoin.cpp [code]
CmdJoin.hpp [code]
CmdNotifyScore.cpp [code]
CmdNotifyScore.hpp [code]
CmdPeerList.cpp [code]
CmdPeerList.hpp [code]
CmdPeerRequest.cpp [code]
CmdPeerRequest.hpp [code]
CmdPeerResponse.cpp [code]
CmdPeerResponse.hpp [code]
CmdStatusRequest.cpp [code]
CmdStatusRequest.hpp [code]
CmdStatusResponse.cpp [code]
CmdStatusResponse.hpp [code]
CmdTestRing.cpp [code]
CmdTestRing.hpp [code]
CmdUndiscover.cpp [code]
CmdUndiscover.hpp [code]
Command.cpp [code]
Command.hpp [code]
Common.hpp [code]
config.h [code]
ConfigParser.cpp [code]
ConfigParser.hpp [code]
Configs.cpp [code]
Configs.hpp [code]
Constants.hpp [code]
CPUBlockProcessor.cpp [code]
CPUBlockProcessor.hpp [code]
Crosspoint.hpp [code]
CrosspointsFile.cpp [code]
CrosspointsFile.hpp [code]
default.h [code]
DummyCellsReader.cpp [code]
DummyCellsReader.hpp [code]
DummyCellsWriter.cpp [code]
DummyCellsWriter.hpp [code]
exceptions.hpp [code]
FileBuffer.cpp [code]
FileBuffer.hpp [code]
FileCellsReader.cpp [code]
FileCellsReader.hpp [code]
FileCellsWriter.cpp [code]
FileCellsWriter.hpp [code]
FileStream.cpp [code]
FileStream.hpp [code]
FirstRow.cpp [code]
FirstRow.hpp [code]
Grid.cpp [code]
Grid.hpp [code]
IAligner.hpp [code]
IAlignerParameter.hpp [code]
IllegalArgumentException.cpp [code]
IllegalArgumentException.hpp [code]
IManager.hpp [code]
InitialCellsReader.cpp [code]
InitialCellsReader.hpp [code]
IOException.cpp [code]
IOException.hpp [code]
Job.cpp [code]
Job.hpp [code]
libmasa.cpp [code]
libmasa.hpp [code]
libmasaTypes.hpp [code]
macros.hpp [code]
MasaNet.cpp [code]
MasaNet.hpp [code]
MasaNetCallbacks.hpp [code]
MasaNetCLI.cpp [code]
MasaNetCLI.hpp [code]
MasaNetJob.cpp [code]
MasaNetJob.hpp [code]
MasaNetStatus.cpp [code]
MasaNetStatus.hpp [code]
NullBuffer.cpp [code]
NullBuffer.hpp [code]
Partition.cpp [code]
Partition.hpp [code]
Peer.cpp [code]
Peer.hpp [code]
PeerList.cpp [code]
PeerList.hpp [code]
Properties.cpp [code]
Properties.hpp [code]
RecurrentTimer.cpp [code]
RecurrentTimer.hpp [code]
ReversedCellsReader.cpp [code]
ReversedCellsReader.hpp [code]
SeekableCellsReader.hpp [code]
Sequence.cpp [code]
Sequence.hpp [code]
SequenceData.cpp [code]
SequenceData.hpp [code]
SequenceInfo.cpp [code]
SequenceInfo.hpp [code]
SequenceModifiers.cpp [code]
SequenceModifiers.hpp [code]
SocketBuffer.cpp [code]
SocketBuffer.hpp [code]
SocketCellsReader.cpp [code]
SocketCellsReader.hpp [code]
SocketCellsWriter.cpp [code]
SocketCellsWriter.hpp [code]
SpecialRow.cpp [code]
SpecialRow.hpp [code]
SpecialRowFile.cpp [code]
SpecialRowFile.hpp [code]
SpecialRowRAM.cpp [code]
SpecialRowRAM.hpp [code]
SpecialRowReader.cpp [code]
SpecialRowReader.hpp [code]
SpecialRowsArea.cpp [code]
SpecialRowsArea.hpp [code]
SpecialRowsPartition.cpp [code]
SpecialRowsPartition.hpp [code]
SpecialRowWriter.cpp [code]
SpecialRowWriter.hpp [code]
SplitCellsReader.cpp [code]
SplitCellsReader.hpp [code]
sra.hpp [code]
Status.cpp [code]
Status.hpp [code]
sw_stage1.cpp [code]
sw_stage1.h [code]
sw_stage2.cpp [code]
sw_stage2.h [code]
sw_stage3.cpp [code]
sw_stage3.h [code]
sw_stage4.cpp [code]
sw_stage4.h [code]
sw_stage5.cpp [code]
sw_stage5.h [code]
sw_stage6.cpp [code]
sw_stage6.h [code]
TeeCellsReader.cpp [code]
TeeCellsReader.hpp [code]
testing.cpp [code]
Timer.cpp [code]
Timer.hpp [code]
URLCellsReader.cpp [code]
URLCellsReader.hpp [code]
URLCellsWriter.cpp [code]
URLCellsWriter.hpp [code]
utils.cpp [code]
utils.hpp [code]