Alignments

Class PhylipAlignment

java.lang.Object

Alignments.PhylipAlignment

public class PhylipAlignment
extends java.lang.Object

Static classes for reading/writing sequence alignment in Phylip format

Version:

2.0

Method Summary

Methods

Modifier and Type	Method and Description
static Alignment	fromFile(java.io.File f) Creates a sequence alignment from a file.
static Alignment	fromFile(java.io.File f, Ambiguous ambig) Creates a sequence alignment from a file with ambiguous data.
static void	writeFile(Alignment a, java.io.File f) Writes a alignment to a file in the format described in fromFile(java.io.File).
static void	writeFilePAML(Alignment a, java.io.File f) Writes a alignment to a file in the format described in fromFile(java.io.File).

Methods inherited from class java.lang.Object

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

Method Detail

fromFile

public static Alignment fromFile(java.io.File f)
                          throws InputException,
                                 AlignmentException

Creates a sequence alignment from a file. File should be in a format similar to Phylip. The first non-blank line, which normally gives the number and length of the sequence, is ignored. Further non-blank lines represent each sequence, one per line. Anything from the start of the line to the first white space is considered the taxa's name. Anything after the first whitespace is the sequence. Whitespace in the sequence is ignored. A taxa name of *class* is assumed not to be a taxa but rather gives the class of each site (which can be any single character).

Parameters:

f - The input file

Returns:

The alignment created from the file

Throws:

InputException - Thrown if there is a problem reading the file

AlignmentException - Thrown if there is something wrong with the alignment, e.g. different length sequences

fromFile

public static Alignment fromFile(java.io.File f,
                 Ambiguous ambig)
                          throws InputException,
                                 AlignmentException

Creates a sequence alignment from a file with ambiguous data. File should be in the format described at fromFile(java.io.File)

Parameters:

f - The input file

ambig - Description o the ambiguous data

Returns:

The alignment created from the file

Throws:

InputException - Thrown if there is a problem with the input file

AlignmentException - Thrown if there is something wrong with the alignment, e.g. different length sequences

writeFile

public static void writeFile(Alignment a,
             java.io.File f)
                      throws OutputException

Writes a alignment to a file in the format described in fromFile(java.io.File).

Parameters:

a - The alignment to write to the file. Need not be a sequence alignment

f - The file to write to

Throws:

OutputException - Thrown if there is a problem creating the file

writeFilePAML

public static void writeFilePAML(Alignment a,
                 java.io.File f)
                          throws OutputException

Writes a alignment to a file in the format described in fromFile(java.io.File).

Parameters:

a - The alignment to write to the file. Need not be a sequence alignment

f - The file to write to

Throws:

OutputException - Thrown if there is a problem creating the file