Package | Description |
---|---|
jebl.evolution.alignments | |
jebl.evolution.graphs | |
jebl.evolution.sequences | |
jebl.evolution.taxa | |
jebl.evolution.trees | |
jebl.util |
Modifier and Type | Class and Description |
---|---|
class |
ConsensusSequence |
Modifier and Type | Interface and Description |
---|---|
interface |
Edge
Represents a node in a graph or tree.
|
interface |
Graph |
interface |
Node
Represents a node in a graph or tree.
|
Modifier and Type | Interface and Description |
---|---|
interface |
Sequence
A biomolecular sequence.
|
Modifier and Type | Class and Description |
---|---|
class |
BasicSequence
A default implementation of the Sequence interface.
|
class |
CanonicalSequence
A default implementation of the Sequence interface
that converts sequence characters to
States such that calling getString() will always return
uppercase residues with nucleotide U residues converted to T
|
class |
CodonSequence
A codon implementation of the Sequence interface.
|
class |
FilteredSequence |
class |
GaplessSequence |
class |
TranslatedSequence |
Modifier and Type | Class and Description |
---|---|
class |
Taxon |
Modifier and Type | Interface and Description |
---|---|
interface |
RootedTree
A tree with a root (node with maximum height).
|
interface |
Tree
A rooted or unrooted tree.
|
Modifier and Type | Class and Description |
---|---|
class |
BaseEdge
Common implementation of Attributable interface used by Nodes.
|
class |
BaseNode
Common implementation of Attributable interface used by Nodes.
|
class |
CompactRootedTree
A memory efficient rooted tree.
|
class |
FilteredRootedTree |
class |
MutableRootedTree
A simple rooted tree providing some ability to manipulate the tree.
|
class |
ReRootedTree |
class |
RootedFromUnrooted
Root an unrooted tree.
|
class |
RootedSubtree
A simple, immutable rooted tree implementation that is a subtree of an existing tree
subtending a specified set of taxa..
|
class |
SimpleRootedTree
A simple, and initially immutable rooted tree implementation.
|
class |
SimpleTree
A basic implementation on an unrooted tree.
|
class |
SortedRootedTree |
class |
TransformedRootedTree
This RootedTree class wraps another RootedTree and transforms
the branch lengths and node heights using various functions.
|
Modifier and Type | Class and Description |
---|---|
class |
AttributableHelper |
http://code.google.com/p/jebl2/