Class FitchParsimony<STATE_TYPE>
- java.lang.Object
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- org.forester.evoinference.parsimony.FitchParsimony<STATE_TYPE>
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public class FitchParsimony<STATE_TYPE> extends java.lang.Object
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Constructor Summary
Constructors Constructor Description FitchParsimony()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
execute(Phylogeny p, CharacterStateMatrix<STATE_TYPE> external_node_states_matrix)
void
execute(Phylogeny p, CharacterStateMatrix<STATE_TYPE> external_node_states_matrix, boolean verbose)
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()
boolean
isVerbose()
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.void
setVerbose(boolean verbose)
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Method Detail
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execute
public void execute(Phylogeny p, CharacterStateMatrix<STATE_TYPE> external_node_states_matrix)
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execute
public void execute(Phylogeny p, CharacterStateMatrix<STATE_TYPE> external_node_states_matrix, boolean verbose)
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getCost
public int getCost()
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getGainLossMatrix
public CharacterStateMatrix<CharacterStateMatrix.GainLossStates> getGainLossMatrix()
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getInternalStatesMatrix
public CharacterStateMatrix<STATE_TYPE> getInternalStatesMatrix()
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getInternalStatesMatrixPriorToTraceback
public CharacterStateMatrix<java.util.List<STATE_TYPE>> getInternalStatesMatrixPriorToTraceback()
Returns a view of the internal states prior to trace-back.- Returns:
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getTotalGains
public int getTotalGains()
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getTotalLosses
public int getTotalLosses()
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getTotalUnchanged
public int getTotalUnchanged()
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isVerbose
public boolean isVerbose()
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setRandomize
public void setRandomize(boolean randomize)
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setRandomNumberSeed
public void setRandomNumberSeed(long random_number_seed)
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setReturnGainLossMatrix
public void setReturnGainLossMatrix(boolean return_gain_loss)
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setReturnInternalStates
public void setReturnInternalStates(boolean return_internal_states)
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setUseLast
public void setUseLast(boolean use_last)
This sets whether to use the first or last state in the sorted states at the undecided internal nodes. For randomized choices set randomize to true (and this to false). Note. It might be advisable to set this to false for BinaryStates if absence at the root is preferred (given the enum BinaryStates sorts in the following order: ABSENT, UNKNOWN, PRESENT).- Parameters:
use_last
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setVerbose
public void setVerbose(boolean verbose)
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