Here is a list of all class members with links to the classes they belong to:

- i -

• i : crosspoint_t , score_t , CmdNotifyScore
• i0 : gap_sequence_t , SpecialRowWriter , SpecialRowsPartition , Partition
• i1 : gap_sequence_t , SpecialRowsPartition , Partition
• IAligner() : IAligner
• IAlignerParameters() : IAlignerParameters
• id : SpecialRowReader , SpecialRow
• ids : CmdTestRing
• ignoreBlock() : AbstractBlockAligner
• IllegalArgumentException() : IllegalArgumentException
• IManager() : IManager
• increaseBlockStat() : AbstractBlockAligner
• index : SequenceInfo
• info : Sequence
• info_filename : Job
• init() : SocketCellsReader , SocketCellsWriter , Timer
• initAutoFlush() : Buffer , FileBuffer , NullBuffer , SocketBuffer
• initAutoLoad() : NullBuffer , SocketBuffer , Buffer , FileBuffer
• initBuffer() : BufferedStream
• InitialCellsReader() : InitialCellsReader
• initialize() : AlignerPool , BlocksFile , InitialCellsReader , Job , Properties , FirstRow , SpecialRow , SpecialRowFile , SpecialRowRAM , AbstractBlockAligner , IAligner , AbstractBlockPruning , BlockPruningDiagonal , BlockPruningGenericN2 , MasaNetCLI
• initializeBlockPruning() : AbstractAligner
• initialized : BlocksFile
• initializeDiagonals() : AbstractDiagonalAligner
• initializeWorkPath() : Job
• initiator : Peer
• inputBuffer : Buffer
• inputBufferLogFile : Job
• interval : RecurrentTimer
• intervalElapsed() : Timer
• intervalEvent : Timer
• IOException() : IOException
• isAllowed() : BestScoreList
• isBlockPrunable() : AbstractBlockPruning
• isBlockPruned() : AbstractBlockAligner , BlockPruningGenericN2
• isBlockPruningEnabled() : Configs
• isBufferDestroyed() : BufferedStream
• isClearN() : SequenceModifiers
• isCompatible() : SequenceModifiers
• isComplement() : SequenceModifiers
• isConnected() : Peer
• isDerived() : BestScoreList
• isDestroyed() : Buffer , Buffer2
• isEmpty() : Status
• isEqual() : SequenceInfo
• isFinalized() : Alignment
• isFirstNode() : AlignerPool
• isFoundCrosspoint() : AlignerManager
• isInitialized() : BlocksFile
• isInitiator() : Peer
• isLastNode() : AlignerPool
• isLogging : Buffer , Buffer2
• isPersistent() : SpecialRowsPartition
• isReverse() : SequenceModifiers
• isReversed() : Sequence
• isSpecialColumn() : AbstractBlockAligner
• isSpecialRow() : AbstractBlockAligner , AbstractDiagonalAligner