SankoffParsimony (Forester 1.038 API)

public class SankoffParsimony<STATE_TYPE>
extends Object

IN PROGRESS! DO NOT USE!

Constructors
Constructor and Description
`SankoffParsimony()`

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`execute(Phylogeny p, CharacterStateMatrix<STATE_TYPE> external_node_states_matrix)`
`int`	`getCost()`
`CharacterStateMatrix<CharacterStateMatrix.GainLossStates>`	`getGainLossMatrix()`
`CharacterStateMatrix<STATE_TYPE>`	`getInternalStatesMatrix()`
`CharacterStateMatrix<List<STATE_TYPE>>`	`getInternalStatesMatrixPriorToTraceback()` Returns a view of the internal states prior to trace-back.
`int`	`getTotalGains()`
`int`	`getTotalLosses()`
`int`	`getTotalUnchanged()`
`void`	`setRandomize(boolean randomize)`
`void`	`setRandomNumberSeed(long random_number_seed)`
`void`	`setReturnGainLossMatrix(boolean return_gain_loss)`
`void`	`setReturnInternalStates(boolean return_internal_states)`
`void`	`setUseLast(boolean use_last)` This sets whether to use the first or last state in the sorted states at the undecided internal nodes.

public void execute(Phylogeny p,
                    CharacterStateMatrix<STATE_TYPE> external_node_states_matrix)

public CharacterStateMatrix<CharacterStateMatrix.GainLossStates> getGainLossMatrix()

public CharacterStateMatrix<STATE_TYPE> getInternalStatesMatrix()

public void setRandomize(boolean randomize)

public void setRandomNumberSeed(long random_number_seed)

public void setReturnGainLossMatrix(boolean return_gain_loss)

public void setReturnInternalStates(boolean return_internal_states)

Class SankoffParsimony<STATE_TYPE>