| AMOS::AlignmentException_t | An exception for alignment failures |
| AMOS::AllocException_t | An exception for alloc failures, better than std::bad_alloc |
| AMOS::ArgumentException_t | An exception for invalid arguments |
| AMOS::Bank_t | An AMOS data bank for efficiently storing Bankable data types |
| AMOS::Bank_t::BankPartition_t | A single partition of the file-based bank |
| AMOS::BankFlags_t | 8 bit flag set for IBankable types |
| AMOS::BankSet_t | A non-redundant, complete collection of AMOS banks |
| AMOS::BankSet_t::const_iterator | |
| AMOS::BankSet_t::iterator | |
| AMOS::BankStream_t | Provides stream functionality for an AMOS data bank |
| AMOS::BankStreamSet_t | A non-redundant, complete collection of AMOS banks |
| AMOS::BankStreamSet_t::const_iterator | |
| AMOS::BankStreamSet_t::iterator | |
| AMOS::Contig_t | A tiling of assembled sequence reads |
| AMOS::ContigEdge_t | Reliable linking information between two contigs |
| AMOS::ContigLink_t | Linking information between two contigs |
| AMOS::Distribution_t | A set of statistics that define a distribution |
| AMOS::Edge_t | Reliable linking information between two nodes |
| AMOS::Exception_t | The base AMOS excpetion class |
| AMOS::Feature_t | Notes remarkable features of other objects |
| AMOS::Fragment_t | Single piece of DNA |
| AMOS::Group_t | A homogenous grouping of AMOS objects |
| AMOS::IBankable_t | Interface for classes that can be stored in an AMOS bank |
| AMOS::IDMap_t | An IID/EID double hash for mapping IIDs and EIDs to BIDs |
| AMOS::IDMap_t::const_iterator | Const_iterator for moving through the map |
| AMOS::IDMap_t::HashTriple_t | HashTriple for IDMap |
| AMOS::IEdge_t | Interface for Edge_t |
| AMOS::IMessagable_t | Interface for classes that can interpret messages |
| AMOS::Index_t | An association index between two types of AMOS objects |
| AMOS::IOException_t | An exception for IO errors |
| AMOS::Kmer_t | String of K bases present in the assembly |
| AMOS::Layout_t | A layout of sequences |
| AMOS::Library_t | A collection of cloned, size-controlled DNA molecules |
| AMOS::Link_t | Linking information between two nodes, such as between contigs |
| AMOS::Message_t | A generic AMOS message object for reading and writing data |
| AMOS::Overlap_t | An overlap relation between to sequencing reads |
| AMOS::Range_t | A gapped coordinate range |
| AMOS::Read_t | A DNA sequencing read |
| AMOS::Scaffold_t | A ordered, oriented and positioned list of contigs |
| AMOS::ScaffoldEdge_t | Reliable linking information between two scaffolds |
| AMOS::ScaffoldLink_t | Linking information between two scaffolds |
| AMOS::Sequence_t | Sequence bases with quality scores |
| AMOS::Tile_t | A singe sequence's location and orientation in a larger sequence |
| AMOS::Universal_t | A universal base class that can be used by Banks or Messages |
| AMOS::UniversalSet_t | A non-redundant, complete collection of Universal objects |
| AMOS::UniversalSet_t::const_iterator | |
| AMOS::UniversalSet_t::iterator |
1.3.8