Package org.biojava.nbio.phylo

Class ForesterWrapper

java.lang.Object
org.biojava.nbio.phylo.ForesterWrapper
public class ForesterWrapper extends Object
This class contains wrapper methods for communication between BioJava and forester (e.g, Data Structure conversion).
Since:
4.1.1
Author:
Aleix Lafita

  • Method Details

    • convert

      public static <C extends Sequence<D>, D extends Compound> Msa convert(MultipleSequenceAlignment<C,D> msa) throws IOException
      Convert a BioJava MultipleSequenceAlignment to a forester Msa. The easiest way to convert them is writting the msa as a FASTA file and then parsing it with the forester FastaParser.
      Parameters:
      msa - BioJava MultipleSequenceAlignment
      Returns:
      forester Msa object
      Throws:
      IOException - if the conversion was not possible

    • getNewickString

      public static String getNewickString(Phylogeny phylo, boolean writeDistances) throws IOException
      Convert a Phylogenetic tree to its Newick representation, so that it can be exported to an external application.
      Parameters:
      phylo - Phylogeny phylogenetic tree
      writeDistances - write the branch lengths if true
      Returns:
      Throws:
      IOException

    • cloneDM

      public static BasicSymmetricalDistanceMatrix cloneDM(BasicSymmetricalDistanceMatrix distM)
      Helper function to clone a forester symmetrical DistanceMatrix.
      Parameters:
      distM - forester symmetrical DistanceMatrix
      Returns:
      identical copy of the forester symmetrical DistanceMatrix