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 Summary

Methods

Modifier and Type	Method and Description
static org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix	cloneDM(org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix distM) Helper function to clone a forester symmetrical DistanceMatrix.
static <C extends Sequence<D>,D extends Compound> org.forester.msa.Msa	convert(MultipleSequenceAlignment<C,D> msa) Convert a BioJava MultipleSequenceAlignment to a forester Msa.
static String	getNewickString(org.forester.phylogeny.Phylogeny phylo, boolean writeDistances) Convert a Phylogenetic tree to its Newick representation, so that it can be exported to an external application.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

convert

public static <C extends Sequence<D>,D extends Compound> org.forester.msa.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(org.forester.phylogeny.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 org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix cloneDM(org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix distM)

Helper function to clone a forester symmetrical DistanceMatrix.

Parameters:

distM - forester symmetrical DistanceMatrix

Returns:

identical copy of the forester symmetrical DistanceMatrix