in progress

[jalview.git] / forester / java / src / org / forester / surfacing / DomainParsimonyCalculator.java

diff --git a/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java b/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java
index e2db537..4de0b35 100644 (file)
--- a/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java
+++ b/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java
@@ -206,7 +206,7 @@ public final class DomainParsimonyCalculator {
         else {
             states = createMatrixOfBinaryDomainCombinationPresenceOrAbsence( getGenomeWideCombinableDomainsList() );
         }
-        fitch.execute( getPhylogeny(), states );
+        fitch.execute( getPhylogeny(), states, true );
         setGainLossMatrix( fitch.getGainLossMatrix() );
         setBinaryInternalStatesMatrix( fitch.getInternalStatesMatrix() );
         setCost( fitch.getCost() );
@@ -242,7 +242,7 @@ public final class DomainParsimonyCalculator {
         }
         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() );