Class SankoffParsimony<STATE_TYPE>
- java.lang.Object
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- org.forester.evoinference.parsimony.SankoffParsimony<STATE_TYPE>
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- Type Parameters:
STATE_TYPE
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public class SankoffParsimony<STATE_TYPE> extends java.lang.Object
IN PROGRESS! DO NOT USE!
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Constructor Summary
Constructors Constructor Description SankoffParsimony()
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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)
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.
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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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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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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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