Alignments

Class GenericAlignment

java.lang.Object

Alignments.GenericAlignment

public class GenericAlignment
extends java.lang.Object

Static classes for reading/writing sequence alignment in a generic 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. One sequence / taxa per line - taxa name followed by the sequence. Name is separated from sequence by whitespace. Sites in the sequence are separated by white space. Allows the use of states that are multiple characters long (e.g. codon). Blank lines are 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