- public final void decorateTree( final Phylogeny phy, final List<MsaProperties> msa_props, final boolean chart_only ) {
+ private final static void addSeqs2Tree( final Msa msa, final Phylogeny phy ) {
+ for( int i = 0; i < msa.getNumberOfSequences(); ++i ) {
+ final MolecularSequence seq = msa.getSequence( i );
+ final String seq_name = seq.getIdentifier();
+ final PhylogenyNode n = phy.getNode( seq_name );
+ if ( !n.getNodeData().isHasSequence() ) {
+ n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() );
+ }
+ else {
+ throw new IllegalArgumentException( "this should not have happened" );
+ }
+ n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() );
+ n.getNodeData().getSequence().setMolecularSequenceAligned( true );
+ n.getNodeData().getSequence().setName( seq_name );
+ }
+ }
+
+ private final static void decorateTree( final Phylogeny phy,
+ final List<MsaProperties> msa_props,
+ final boolean chart_only ) {