ForesterWrapper

java.lang.Object
- org.biojava.nbio.phylo.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 Summary

All Methods Static Methods Concrete Methods
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> Msa`	`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.

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> Msa 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
  - 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

Class ForesterWrapper

Method Summary

Methods inherited from class java.lang.Object

Method Detail

convert

getNewickString

cloneDM