An interface that
A document storing a table of codon usage frequencies.
An implementation of a
An implementation of a Phylogeny document.
A default implementation of a plugin document holding a list of trees.
Provides convenience functionality to create a SequenceGraphFactory which draws a bar graph from some simpler interfaces.
Provides methods to supply a score for a given set of sequence residues and provide a color for a given score.
Provides methods to supply a score for a given sequence residue and provide a color for a given score.
A default implementation of a plugin document holding a tree.
Calculates, and provides a method to determine whether residues in a set of sequences are end gaps.
Given a set of aligned sequences, provides methods for quickly finding all sequences that intersect a given base number, ignoring those sequences in end gap regions.
Used for building an
Just like a double, but the toString() method displays it as a nicely formatted e value
Keeps track of which sequences in a list of sequences are paired together and their paired distances.
Allows for the construction of a PairedReadManager where the data resides on disk instead of in memory.
Just like a double, but the toString() method displays it as a percentage with the specified number of decimal places.
Provides methods for extracting a portion of a sequence to a new sequence document.
Represents options controlling how sequence extraction works in
Precalculates information about the location of gaps ('-') in a CharSequence, and can efficiently calculate translate between indices in the gapped and ungapped sequence.
A document containing text that can be marked up in various formats such as html.
Represents the relative orientation for a set of interlaced reads.
Format of the text