STATE_TYPE
- public class SankoffParsimony<STATE_TYPE>
extends java.lang.Object
Constructor and Description |
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SankoffParsimony() |
Modifier and Type | Method and Description |
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void |
execute(Phylogeny p,
CharacterStateMatrix<STATE_TYPE> external_node_states_matrix) |
int |
getCost() |
CharacterStateMatrix<CharacterStateMatrix.GainLossStates> |
getGainLossMatrix() |
CharacterStateMatrix<STATE_TYPE> |
getInternalStatesMatrix() |
CharacterStateMatrix<java.util.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 int getCost()
public CharacterStateMatrix<CharacterStateMatrix.GainLossStates> getGainLossMatrix()
public CharacterStateMatrix<STATE_TYPE> getInternalStatesMatrix()
public CharacterStateMatrix<java.util.List<STATE_TYPE>> getInternalStatesMatrixPriorToTraceback()
public int getTotalGains()
public int getTotalLosses()
public int getTotalUnchanged()
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)
public void setUseLast(boolean use_last)
use_last
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