else {
states = createMatrixOfBinaryDomainCombinationPresenceOrAbsence( getGenomeWideCombinableDomainsList() );
}
- fitch.execute( getPhylogeny(), states );
+ fitch.execute( getPhylogeny(), states, true );
setGainLossMatrix( fitch.getGainLossMatrix() );
setBinaryInternalStatesMatrix( fitch.getInternalStatesMatrix() );
setCost( fitch.getCost() );
}
final CharacterStateMatrix<BinaryStates> states = createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence( getGenomeWideCombinableDomainsList(),
newmap );
- fitch.execute( getPhylogeny(), states );
+ fitch.execute( getPhylogeny(), states, true );
setGainLossMatrix( fitch.getGainLossMatrix() );
setBinaryInternalStatesMatrix( fitch.getInternalStatesMatrix() );
setCost( fitch.getCost() );