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[jalview.git] / forester / java / src / org / forester / evoinference / parsimony / FitchParsimony.java

diff --git a/forester/java/src/org/forester/evoinference/parsimony/FitchParsimony.java b/forester/java/src/org/forester/evoinference/parsimony/FitchParsimony.java
index df22cbc..7c7c9f2 100644 (file)
--- a/forester/java/src/org/forester/evoinference/parsimony/FitchParsimony.java
+++ b/forester/java/src/org/forester/evoinference/parsimony/FitchParsimony.java
@@ -148,7 +148,7 @@ public class FitchParsimony<STATE_TYPE> {
 
     /**
      * Returns a view of the internal states prior to trace-back.
-     * 
+     *
      * @return
      */
     public CharacterStateMatrix<List<STATE_TYPE>> getInternalStatesMatrixPriorToTraceback() {
@@ -200,13 +200,13 @@ public class FitchParsimony<STATE_TYPE> {
      * 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: 
+     * (given the enum BinaryStates sorts in the following order:
      * ABSENT, UNKNOWN, PRESENT).
-     * 
-     * 
+     *
+     *
      * @param use_last
      */
     public void setUseLast( final boolean use_last ) {
@@ -245,7 +245,7 @@ public class FitchParsimony<STATE_TYPE> {
             final PhylogenyNode node_child = node.getChildNode( i );
             if ( !states.containsKey( node_child ) ) {
                 throw new AssertionError( "this should not have happened: node [" + node_child.getName()
-                        + "] not found in node state map" );
+                                          + "] not found in node state map" );
             }
             if ( i == 0 ) {
                 states_in_child_nodes.addAll( states.get( node_child ) );
@@ -282,7 +282,7 @@ public class FitchParsimony<STATE_TYPE> {
             final STATE_TYPE state = matrix.getState( indentifier_index, character_index );
             if ( state == null ) {
                 throw new IllegalArgumentException( "value at [" + indentifier_index + ", " + character_index
-                        + "] is null" );
+                                                    + "] is null" );
             }
             final SortedSet<STATE_TYPE> l = new TreeSet<STATE_TYPE>();
             l.add( state );
@@ -299,7 +299,7 @@ public class FitchParsimony<STATE_TYPE> {
             final STATE_TYPE state = matrix.getState( indentifier_index, character_index );
             if ( state == null ) {
                 throw new IllegalArgumentException( "value at [" + indentifier_index + ", " + character_index
-                        + "] is null" );
+                                                    + "] is null" );
             }
             states.put( p.getNode( matrix.getIdentifier( indentifier_index ) ), state );
         }
@@ -313,7 +313,7 @@ public class FitchParsimony<STATE_TYPE> {
             final PhylogenyNode node_child = node.getChildNode( i );
             if ( !states.containsKey( node_child ) ) {
                 throw new AssertionError( "this should not have happened: node [" + node_child.getName()
-                        + "] not found in node state map" );
+                                          + "] not found in node state map" );
             }
             states_in_child_nodes.addAll( states.get( node_child ) );
         }
@@ -340,8 +340,8 @@ public class FitchParsimony<STATE_TYPE> {
             nodes.add( postorder.next() );
         }
         setGainLossMatrix( new BasicCharacterStateMatrix<CharacterStateMatrix.GainLossStates>( nodes.size(),
-                                                                                               external_node_states_matrix
-                                                                                                       .getNumberOfCharacters() ) );
+                external_node_states_matrix
+                .getNumberOfCharacters() ) );
         int identifier_index = 0;
         for( final PhylogenyNode node : nodes ) {
             getGainLossMatrix().setIdentifier( identifier_index++,
@@ -364,11 +364,11 @@ public class FitchParsimony<STATE_TYPE> {
             }
         }
         setInternalStatesMatrixPriorToTraceback( new BasicCharacterStateMatrix<List<STATE_TYPE>>( internal_nodes.size(),
-                                                                                                  external_node_states_matrix
-                                                                                                          .getNumberOfCharacters() ) );
+                external_node_states_matrix
+                .getNumberOfCharacters() ) );
         setInternalStatesMatrixTraceback( new BasicCharacterStateMatrix<STATE_TYPE>( internal_nodes.size(),
-                                                                                     external_node_states_matrix
-                                                                                             .getNumberOfCharacters() ) );
+                external_node_states_matrix
+                .getNumberOfCharacters() ) );
         int identifier_index = 0;
         for( final PhylogenyNode node : internal_nodes ) {
             getInternalStatesMatrix().setIdentifier( identifier_index,
@@ -384,7 +384,7 @@ public class FitchParsimony<STATE_TYPE> {
                                                     external_node_states_matrix.getCharacter( character_index ) );
             getInternalStatesMatrixPriorToTraceback().setCharacter( character_index,
                                                                     external_node_states_matrix
-                                                                            .getCharacter( character_index ) );
+                                                                    .getCharacter( character_index ) );
         }
     }
 
@@ -482,7 +482,7 @@ public class FitchParsimony<STATE_TYPE> {
                 else if ( current_binary_state == ABSENT ) {//new
                     setGainLossState( character_state_column, current_node, UNCHANGED_ABSENT );//new
                 }//new
-                 // setGainLossState( character_state_column, current_node, UNKNOWN_GAIN_LOSS );
+                // setGainLossState( character_state_column, current_node, UNKNOWN_GAIN_LOSS );
             }
         }
     }
@@ -507,26 +507,26 @@ public class FitchParsimony<STATE_TYPE> {
                                    final PhylogenyNode node,
                                    final GainLossStates state ) {
         getGainLossMatrix().setState( ForesterUtil.isEmpty( node.getName() ) ? node.getId() + "" : node.getName(),
-                                      character_state_column,
-                                      state );
+                character_state_column,
+                state );
     }
 
     private void setInternalNodeState( final Map<PhylogenyNode, STATE_TYPE> states,
                                        final int character_state_column,
                                        final PhylogenyNode node ) {
         getInternalStatesMatrix()
-                .setState( ForesterUtil.isEmpty( node.getName() ) ? node.getId() + "" : node.getName(),
-                           character_state_column,
-                           states.get( node ) );
+        .setState( ForesterUtil.isEmpty( node.getName() ) ? node.getId() + "" : node.getName(),
+                character_state_column,
+                states.get( node ) );
     }
 
     private void setInternalNodeStatePriorToTraceback( final Map<PhylogenyNode, SortedSet<STATE_TYPE>> states,
                                                        final int character_state_column,
                                                        final PhylogenyNode node ) {
         getInternalStatesMatrixPriorToTraceback()
-                .setState( ForesterUtil.isEmpty( node.getName() ) ? String.valueOf( node.getId() ) : node.getName(),
-                           character_state_column,
-                           toListSorted( states.get( node ) ) );
+        .setState( ForesterUtil.isEmpty( node.getName() ) ? String.valueOf( node.getId() ) : node.getName(),
+                character_state_column,
+                toListSorted( states.get( node ) ) );
     }
 
     private void setInternalStatesMatrixPriorToTraceback( final CharacterStateMatrix<List<STATE_TYPE>> internal_states_matrix_prior_to_traceback ) {