Class ForesterWrapper


  • public class ForesterWrapper
    extends java.lang.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 Detail

      • convert

        public static <C extends Sequence<D>,​D extends CompoundMsa convert​(MultipleSequenceAlignment<C,​D> msa)
                                                                            throws java.io.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:
        java.io.IOException - if the conversion was not possible
      • getNewickString

        public static java.lang.String getNewickString​(Phylogeny phylo,
                                                       boolean writeDistances)
                                                throws java.io.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:
        java.io.IOException