Package org.biojava.nbio.phylo
Class ForesterWrapper
- java.lang.Object
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- org.biojava.nbio.phylo.ForesterWrapper
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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
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static BasicSymmetricalDistanceMatrix
cloneDM(BasicSymmetricalDistanceMatrix distM)
Helper function to clone a forester symmetrical DistanceMatrix.static <C extends Sequence<D>,D extends Compound>
Msaconvert(MultipleSequenceAlignment<C,D> msa)
Convert a BioJavaMultipleSequenceAlignment
to a foresterMsa
.static java.lang.String
getNewickString(Phylogeny phylo, boolean writeDistances)
Convert a Phylogenetic tree to its Newick representation, so that it can be exported to an external application.
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Method Detail
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convert
public static <C extends Sequence<D>,D extends Compound> Msa convert(MultipleSequenceAlignment<C,D> msa) throws java.io.IOException
Convert a BioJavaMultipleSequenceAlignment
to a foresterMsa
. The easiest way to convert them is writting the msa as a FASTA file and then parsing it with the foresterFastaParser
.- Parameters:
msa
- BioJava MultipleSequenceAlignment- Returns:
- forester Msa object
- Throws:
java.io.IOException
- if the conversion was not possible
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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 treewriteDistances
- write the branch lengths if true- Returns:
- Throws:
java.io.IOException
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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
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