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Class Summary |
| BitMap |
module for managing a fast bitmap |
| BPExn |
module for handling base pair exceptions (non-ACGT) in a sequence |
| ExnType |
this is a useful hack until Titanium adds some mechanism for querying exception type directly |
| FASTAInputFile |
FASTA file input support |
| FASTAOutputFile |
FASTA file output support |
| FindOligos |
module encapsulating the framework for extracting Oligos of given tm and SSenergy |
| GeneData |
represents the Oligos and associated scores for a particular gene tail |
| HashTable |
module for managing a fast bitmap using a hashtable representation |
| Hybridization |
Performs hybridization energy calculations and stores useful energy constants |
| IterationDone |
This exception gets thrown by various methods to indicate iteration completion |
| MGFInputFile |
MGF file input support |
| MGFOutputFile |
MGF file output support |
| Oligo |
represents a Oligo offset, with tm info |
| Seq |
Abstraction of a base pair sequence, stored in a packed binary form with storage sharing
storage-sharing is transparent to the user, it just adds efficiency
keeps BP Exceptions (non-ATCG) in a separate list
can be built from Strings, byte arrays, or files |
| SeqBPIterator |
a fast sequential Iterator object for the base pairs in a Seq |
| SeqDBPIterator |
a fast sequential Iterator object for the base pair pairs in a Seq |
| SeqNBPIterator |
a fast sequential Iterator object for the base pair n-mers in a Seq |
| SortEntry |
Generic sorting utility |
| SSCalc |
Performs secondary structure prediction on a Seq |
| TmCalc |
Object that performs Tm calculation on a Seq and returns qualifying oligos |
| Z |
module containing lots of useful global constants and functions used elsewhere |