Alignments

Class FastaAlignment

java.lang.Object

Alignments.FastaAlignment

public class FastaAlignment
extends java.lang.Object

Static classes for reading/writing sequence alignment in FASTA 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).

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 Fasta format File should consist of a line beginning with a ">" followed by the taxa name - anything after a "|" is ignored. The following lines to the next line beginning with ">" are the sequence associated with that taxa. Blank lines are ignored. Comments, i.e. lines beginning with ";" are NOT supported. 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 with the input 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 fromFile(java.io.File)

Parameters:

f - The input file

ambig - Description of 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