Package | Description |
---|---|
pal.alignment |
Classes dealing with sequence alignments, including methods for reading
and printing in several possible formats, as well as rearranging and
concatenating.
|
pal.gui |
GUI components for some special objects (e.g., trees).
|
pal.misc |
Classes that don't fit elsewhere ;^)
|
pal.tree |
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
|
Constructor | Description |
---|---|
SimpleAlignment(Alignment a,
LabelMapping lm) |
Clone constructor.
|
Modifier and Type | Method | Description |
---|---|---|
void |
TreeComponent.setLabelMapping(LabelMapping lm) |
|
void |
TreePainter.setLabelMapping(LabelMapping lp) |
Modifier and Type | Method | Description |
---|---|---|
LabelMapping |
LabelMapping.getRelabeled(LabelMapping.Relabeller relabeller) |
|
LabelMapping |
LabelMapping.getUniquifiedMappings() |
If a mapping occurs more than once will rename instance to "x 1", "x 2"...
|
Modifier and Type | Method | Description |
---|---|---|
protected void |
SimpleNode.init(Node n,
boolean keepId,
LabelMapping lm) |
Initialized node instance variables based on given Node.
|
Constructor | Description |
---|---|
SimpleNode(Node n,
LabelMapping lm) |
|
SimpleTree(Tree tree,
LabelMapping lm) |
clone constructor
|