Here is a list of all documented namespaces with brief descriptions:
[detail level 123]
| ▼Ndigest | Digest code |
| ▼Nds | |
| CAdaptive | Adaptive data structure. Selects between Naive and Naive2 based on the large window size |
| CAdaptive64 | Same as Adaptive but uses 64-bit hashes |
| CInterface | |
| CNaive | Naive data structure. Naively loops through the array to find the minimum |
| CNaive2 | Naive2 data structure. Remembers the last minimum index and only loops through the array when this index leaves the window |
| CSegmentTree | Segment Tree data structure. Supports log(n) point updates and range minimum queries |
| ▼Nthread_out | Possible implementation for multi-threading the digestion of a single sequence. The key thing to note is basically by carefully telling where each digester should start digesting you can make it so each kmer is only considered once. For more details on a function, click on more and it will take you to the description that is located in modules |
| CBadThreadOutParams | Exception thrown when invalid parameters are passed to the thread functions |
| CBadConstructionException | Exception thrown when initializing a Digister with k (kmer size) < 4 and start (starting index) < len (length of sequence) |
| CBadModException | Exception thrown when initializing a mod minimizer object where the target value after modding is greater than the mod value |
| CBadWindowSizeException | Exception thrown when initializing a Window Minimizer or Syncmer with a large window size of 0 |
| CDigester | Abstract class for Digester objects |
| CModMin | Child class of Digester that defines a minimizer as a kmer whose hash is equal to some target value after being modded. Parameters without a description are the same as the parameters in the Digester parent class. They are simply passed up to the parent constructor |
| CNotRolledTillEndException | Exception thrown when append_seq() is called before all kmers/large windows in the current sequence have been iterated over |
| CSyncmer | This class inherits from WindowMinimizer (implementation reasons), but the represent very different things. A Syncmer is defined as a large window where the minimal hash among all kmers in the large window belong to either the leftmost or rightmost kmer. Parameters without a description are the same as the parameters in the Digester parent class. They are simply passed up to the parent constructor |
| CWindowMin | Child class of Digester that defines a minimizer as a kmer whose hash is minimal among those in the large window. Parameters without a description are the same as the parameters in the Digester parent class. They are simply passed up to the parent constructor |
