public class ForesterWrapper
extends java.lang.Object
Modifier and Type | Method and Description |
---|---|
static BasicSymmetricalDistanceMatrix |
cloneDM(BasicSymmetricalDistanceMatrix distM)
Helper function to clone a forester symmetrical DistanceMatrix.
|
static <C extends Sequence<D>,D extends Compound> |
convert(MultipleSequenceAlignment<C,D> msa)
Convert a BioJava
MultipleSequenceAlignment to a forester
Msa . |
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.
|
public static <C extends Sequence<D>,D extends Compound> Msa convert(MultipleSequenceAlignment<C,D> msa) throws java.io.IOException
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
.msa
- BioJava MultipleSequenceAlignmentjava.io.IOException
- if the conversion was not possiblepublic static java.lang.String getNewickString(Phylogeny phylo, boolean writeDistances) throws java.io.IOException
phylo
- Phylogeny phylogenetic treewriteDistances
- write the branch lengths if truejava.io.IOException
public static BasicSymmetricalDistanceMatrix cloneDM(BasicSymmetricalDistanceMatrix distM)
distM
- forester symmetrical DistanceMatrix