---

AMOS Compound Members

a | b | c | d | e | f | g | i | k | l | m | n | o | p | q | r | s | t | u | w | ~

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

- a -

• a_id() : AMOS::AlignmentException_t
• addPartition() : AMOS::Bank_t
• ADENINE_BITS : AMOS::Sequence_t, AMOS::Kmer_t
• ALIGNMENT : AMOS::ContigLink_t
• AlignmentException_t() : AMOS::AlignmentException_t
• AllocException_t() : AMOS::AllocException_t
• ANTINORMAL : AMOS::Overlap_t, AMOS::ContigLink_t
• append() : AMOS::Bank_t
• ArgumentException_t() : AMOS::ArgumentException_t

- b -

• b_id() : AMOS::AlignmentException_t
• BAC : AMOS::Read_t, AMOS::Fragment_t
• Bank_t : AMOS::Bank_t, AMOS::IDMap_t, AMOS::IBankable_t
• banktype_m : AMOS::Bank_t
• begin : AMOS::Range_t

- c -

• clean() : AMOS::Bank_t
• clear() : AMOS::Universal_t, AMOS::Sequence_t, AMOS::Scaffold_t, AMOS::Read_t, AMOS::Overlap_t, AMOS::Message_t, AMOS::Matepair_t, AMOS::Library_t, AMOS::Kmer_t, AMOS::IDMap_t, AMOS::Fragment_t, AMOS::Example_t, AMOS::Tile_t, AMOS::Range_t, AMOS::Distribution_t, AMOS::ContigLink_t, AMOS::ContigEdge_t, AMOS::Contig_t, AMOS::Bank_t, AMOS::IBankable_t
• close() : AMOS::Bank_t
• compress() : AMOS::Sequence_t, AMOS::Kmer_t
• COMPRESS_BIT : AMOS::Sequence_t
• concat() : AMOS::Bank_t
• CONTIG : AMOS::Read_t
• Contig_t() : AMOS::Contig_t
• ContigEdge_t() : AMOS::ContigEdge_t
• ContigLink_t() : AMOS::ContigLink_t
• create() : AMOS::Bank_t
• CYTOSINE_BITS : AMOS::Sequence_t, AMOS::Kmer_t

- d -

• destroy() : AMOS::Bank_t
• Distribution_t() : AMOS::Distribution_t

- e -

• empty() : AMOS::IDMap_t
• END : AMOS::Read_t, AMOS::Matepair_t
• end : AMOS::Range_t
• Example_t() : AMOS::Example_t
• Exception_t() : AMOS::Exception_t
• exists() : AMOS::Message_t, AMOS::IDMap_t, AMOS::Bank_t

- f -

• fetch() : AMOS::Bank_t
• file() : AMOS::Exception_t
• FIRST_BIT : AMOS::Overlap_t
• fix_size_m : AMOS::Bank_t
• flags_m : AMOS::IBankable_t
• flip() : AMOS::Overlap_t, AMOS::Matepair_t, AMOS::ContigLink_t
• flush() : AMOS::Bank_t
• Fragment_t() : AMOS::Fragment_t

- g -

• gaps : AMOS::Tile_t
• getAdjacency() : AMOS::Overlap_t, AMOS::ContigLink_t
• getAhang() : AMOS::Overlap_t
• getBankCode() : AMOS::Bank_t
• getBase() : AMOS::Sequence_t, AMOS::Kmer_t
• getBegin() : AMOS::Range_t
• getBhang() : AMOS::Overlap_t
• getClearRange() : AMOS::Read_t
• getComment() : AMOS::Universal_t
• getContigEdges() : AMOS::Scaffold_t
• getContigLinks() : AMOS::ContigEdge_t
• getContigs() : AMOS::ContigLink_t
• getContigTiling() : AMOS::Scaffold_t
• getCount() : AMOS::Kmer_t
• getDistribution() : AMOS::Library_t
• getEID() : AMOS::Universal_t
• getEnd() : AMOS::Range_t
• getField() : AMOS::Message_t
• getFragment() : AMOS::Read_t
• getIID() : AMOS::IBankable_t
• getLastIID() : AMOS::Bank_t
• getLength() : AMOS::Sequence_t, AMOS::Kmer_t, AMOS::Range_t
• getLibrary() : AMOS::Fragment_t
• getMessageCode() : AMOS::Message_t
• getNCode() : AMOS::Universal_t, AMOS::Sequence_t, AMOS::Scaffold_t, AMOS::Read_t, AMOS::Overlap_t, AMOS::IMessagable_t, AMOS::Matepair_t, AMOS::Library_t, AMOS::Kmer_t, AMOS::IDMap_t, AMOS::Fragment_t, AMOS::Example_t, AMOS::Tile_t, AMOS::Distribution_t, AMOS::ContigLink_t, AMOS::ContigEdge_t, AMOS::Contig_t, AMOS::IBankable_t
• getPartition() : AMOS::Bank_t
• getPolymorphism() : AMOS::Scaffold_t, AMOS::Contig_t
• getQualityClearRange() : AMOS::Read_t
• getQualString() : AMOS::Sequence_t
• getReads() : AMOS::Overlap_t, AMOS::Matepair_t, AMOS::Kmer_t
• getReadTiling() : AMOS::Contig_t
• getSD() : AMOS::ContigLink_t
• getSeqString() : AMOS::Sequence_t, AMOS::Kmer_t
• getSize() : AMOS::Fragment_t, AMOS::ContigLink_t
• getSource() : AMOS::Fragment_t, AMOS::ContigLink_t
• getSubMessages() : AMOS::Message_t
• getType() : AMOS::Read_t, AMOS::Matepair_t, AMOS::Fragment_t, AMOS::ContigLink_t
• getUngappedQualString() : AMOS::Contig_t
• getUngappedSeqString() : AMOS::Contig_t
• getVectorClearRange() : AMOS::Read_t
• GUANINE_BITS : AMOS::Sequence_t, AMOS::Kmer_t

- i -

• IBankable_t() : AMOS::IBankable_t
• id : AMOS::Tile_t
• idmap_m : AMOS::Bank_t
• IDMap_t() : AMOS::IDMap_t
• iid_m : AMOS::IBankable_t
• IMessagable_t() : AMOS::IMessagable_t
• init() : AMOS::Bank_t
• INNIE : AMOS::Overlap_t, AMOS::ContigLink_t
• insert() : AMOS::IDMap_t
• INSERT : AMOS::Fragment_t
• invert() : AMOS::IDMap_t
• IOException_t() : AMOS::IOException_t
• is_open_m : AMOS::Bank_t
• isCompressed() : AMOS::Sequence_t
• isFlagA() : AMOS::IBankable_t
• isFlagB() : AMOS::IBankable_t
• isModified() : AMOS::IBankable_t
• isOpen() : AMOS::Bank_t
• isRemoved() : AMOS::IBankable_t

- k -

• Kmer_t() : AMOS::Kmer_t

- l -

• last_iid_m : AMOS::Bank_t
• last_partition_m : AMOS::Bank_t
• Library_t() : AMOS::Library_t
• line() : AMOS::Exception_t
• lookup() : AMOS::IDMap_t, AMOS::Bank_t

- m -

• map() : AMOS::Bank_t
• MATEPAIR : AMOS::ContigLink_t
• Matepair_t() : AMOS::Matepair_t
• max_iid_m : AMOS::Bank_t
• MAX_LENGTH : AMOS::Kmer_t
• mean : AMOS::Distribution_t
• Message_t() : AMOS::Message_t

- n -

• NCode() : AMOS::Universal_t, AMOS::Sequence_t, AMOS::Scaffold_t, AMOS::Read_t, AMOS::Overlap_t, AMOS::Matepair_t, AMOS::Library_t, AMOS::Kmer_t, AMOS::IDMap_t, AMOS::Fragment_t, AMOS::Example_t, AMOS::ContigLink_t, AMOS::ContigEdge_t, AMOS::Contig_t
• NORMAL : AMOS::Overlap_t, AMOS::ContigLink_t
• NULL_ADJACENCY : AMOS::Overlap_t, AMOS::ContigLink_t
• NULL_FRAGMENT : AMOS::Fragment_t
• NULL_LINK : AMOS::ContigLink_t
• NULL_MATE : AMOS::Matepair_t
• NULL_READ : AMOS::Read_t

- o -

• offset : AMOS::Tile_t
• open() : AMOS::Bank_t
• opened_m : AMOS::Bank_t
• openPartition() : AMOS::Bank_t
• operator++() : AMOS::Kmer_t
• operator=() : AMOS::Sequence_t, AMOS::Kmer_t, AMOS::IDMap_t, AMOS::Example_t
• OTHER : AMOS::Read_t, AMOS::Matepair_t, AMOS::Fragment_t, AMOS::ContigLink_t
• OUTIE : AMOS::Overlap_t, AMOS::ContigLink_t
• OVERLAP : AMOS::ContigLink_t
• Overlap_t() : AMOS::Overlap_t

- p -

• partition_size_m : AMOS::Bank_t
• partitions_m : AMOS::Bank_t
• PHYSICAL : AMOS::ContigLink_t

- q -

• QUAL_BITS : AMOS::Sequence_t

- r -

• range : AMOS::Tile_t
• Range_t() : AMOS::Range_t
• read() : AMOS::Message_t
• Read_t() : AMOS::Read_t
• readMessage() : AMOS::Universal_t, AMOS::Sequence_t, AMOS::Scaffold_t, AMOS::Read_t, AMOS::Overlap_t, AMOS::IMessagable_t, AMOS::Matepair_t, AMOS::Library_t, AMOS::Kmer_t, AMOS::IDMap_t, AMOS::Fragment_t, AMOS::Tile_t, AMOS::Distribution_t, AMOS::ContigLink_t, AMOS::ContigEdge_t, AMOS::Contig_t
• readRecord() : AMOS::Universal_t, AMOS::Sequence_t, AMOS::Scaffold_t, AMOS::Read_t, AMOS::Overlap_t, AMOS::Matepair_t, AMOS::Library_t, AMOS::Kmer_t, AMOS::Fragment_t, AMOS::Example_t, AMOS::ContigLink_t, AMOS::ContigEdge_t, AMOS::Contig_t, AMOS::IBankable_t
• readUMD() : AMOS::Contig_t
• remove() : AMOS::IDMap_t, AMOS::Bank_t
• removeField() : AMOS::Message_t
• replace() : AMOS::Bank_t
• restore() : AMOS::Bank_t

- s -

• Scaffold_t() : AMOS::Scaffold_t
• sd : AMOS::Distribution_t
• SECOND_BIT : AMOS::Overlap_t
• SEQ_BITS : AMOS::Sequence_t, AMOS::Kmer_t
• Sequence_t() : AMOS::Sequence_t
• setAdjacency() : AMOS::Overlap_t, AMOS::ContigLink_t
• setAhang() : AMOS::Overlap_t
• setBase() : AMOS::Sequence_t, AMOS::Kmer_t
• setBegin() : AMOS::Range_t
• setBhang() : AMOS::Overlap_t
• setClearRange() : AMOS::Read_t
• setComment() : AMOS::Universal_t
• setContigEdges() : AMOS::Scaffold_t
• setContigLinks() : AMOS::ContigEdge_t
• setContigs() : AMOS::ContigLink_t
• setContigTiling() : AMOS::Scaffold_t
• setCount() : AMOS::Kmer_t
• setDistribution() : AMOS::Library_t
• setEID() : AMOS::Universal_t
• setEnd() : AMOS::Range_t
• setField() : AMOS::Message_t
• setFlagA() : AMOS::IBankable_t
• setFlagB() : AMOS::IBankable_t
• setFragment() : AMOS::Read_t
• setIID() : AMOS::IBankable_t
• setLibrary() : AMOS::Fragment_t
• setMessageCode() : AMOS::Message_t
• setPolymorphism() : AMOS::Scaffold_t, AMOS::Contig_t
• setQualityClearRange() : AMOS::Read_t
• setRange() : AMOS::Range_t
• setReads() : AMOS::Overlap_t, AMOS::Matepair_t, AMOS::Kmer_t
• setReadTiling() : AMOS::Contig_t
• setSD() : AMOS::ContigLink_t
• setSeqString() : AMOS::Kmer_t
• setSequence() : AMOS::Sequence_t
• setSize() : AMOS::Fragment_t, AMOS::ContigLink_t
• setSource() : AMOS::Fragment_t, AMOS::ContigLink_t
• setSubMessages() : AMOS::Message_t
• setType() : AMOS::Read_t, AMOS::Matepair_t, AMOS::Fragment_t, AMOS::ContigLink_t
• setVectorClearRange() : AMOS::Read_t
• size() : AMOS::IDMap_t
• sizeVar() : AMOS::Universal_t, AMOS::Sequence_t, AMOS::Scaffold_t, AMOS::Read_t, AMOS::Overlap_t, AMOS::Matepair_t, AMOS::Library_t, AMOS::Kmer_t, AMOS::Fragment_t, AMOS::Example_t, AMOS::ContigLink_t, AMOS::ContigEdge_t, AMOS::Contig_t, AMOS::IBankable_t
• skew : AMOS::Distribution_t
• skip() : AMOS::Message_t
• store_dir_m : AMOS::Bank_t
• store_pfx_m : AMOS::Bank_t
• Swap() : AMOS::Range_t
• SYNTENY : AMOS::ContigLink_t

- t -

• THYMINE_BITS : AMOS::Sequence_t, AMOS::Kmer_t
• Tile_t() : AMOS::Tile_t
• transform() : AMOS::Bank_t
• TRANSPOSON : AMOS::Matepair_t, AMOS::Fragment_t

- u -

• uncompress() : AMOS::Sequence_t, AMOS::Kmer_t
• Universal_t() : AMOS::Universal_t

- w -

• WALK : AMOS::Read_t, AMOS::Fragment_t
• what() : AMOS::Exception_t
• write() : AMOS::Message_t
• writeMessage() : AMOS::Universal_t, AMOS::Sequence_t, AMOS::Scaffold_t, AMOS::Read_t, AMOS::Overlap_t, AMOS::IMessagable_t, AMOS::Matepair_t, AMOS::Library_t, AMOS::Kmer_t, AMOS::IDMap_t, AMOS::Fragment_t, AMOS::Tile_t, AMOS::Distribution_t, AMOS::ContigLink_t, AMOS::ContigEdge_t, AMOS::Contig_t
• writeRecord() : AMOS::Universal_t, AMOS::Sequence_t, AMOS::Scaffold_t, AMOS::Read_t, AMOS::Overlap_t, AMOS::Matepair_t, AMOS::Library_t, AMOS::Kmer_t, AMOS::Fragment_t, AMOS::Example_t, AMOS::ContigLink_t, AMOS::ContigEdge_t, AMOS::Contig_t, AMOS::IBankable_t
• writeUMD() : AMOS::Contig_t

- ~ -

• ~Bank_t() : AMOS::Bank_t
• ~Contig_t() : AMOS::Contig_t
• ~ContigEdge_t() : AMOS::ContigEdge_t
• ~ContigLink_t() : AMOS::ContigLink_t
• ~Distribution_t() : AMOS::Distribution_t
• ~Example_t() : AMOS::Example_t
• ~Exception_t() : AMOS::Exception_t
• ~Fragment_t() : AMOS::Fragment_t
• ~IBankable_t() : AMOS::IBankable_t
• ~IDMap_t() : AMOS::IDMap_t
• ~IMessagable_t() : AMOS::IMessagable_t
• ~Kmer_t() : AMOS::Kmer_t
• ~Library_t() : AMOS::Library_t
• ~Matepair_t() : AMOS::Matepair_t
• ~Message_t() : AMOS::Message_t
• ~Overlap_t() : AMOS::Overlap_t
• ~Range_t() : AMOS::Range_t
• ~Read_t() : AMOS::Read_t
• ~Scaffold_t() : AMOS::Scaffold_t
• ~Sequence_t() : AMOS::Sequence_t
• ~Tile_t() : AMOS::Tile_t
• ~Universal_t() : AMOS::Universal_t

---