Alignments

Class DuplicationAlignment

java.lang.Object

Alignments.DuplicationAlignment

public class DuplicationAlignment
extends java.lang.Object

Static classes for reading/writing duplication "alignments" - a set of gene families with their associated size in each species

Version:

2.0

Method Summary

Methods

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

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 duplication alignment from a file. File is tab separated. First row is a header file. First field is ignored while subsequent fields are the name of the species. Each additional row represents a family. The first field is an ID for the family while subsequent fields are the size of the family in the appropriate species. A family name of *class* is assumed not to be a taxa but rather gives the class of each site (which can be any string).

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 any family contains the wrong number of species

fromFile

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

Creates a duplication alignment which contains ambiguous data. File format is described 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 any family contains the wrong number of species

writeFile

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

Writes a alignment to a file in the duplication alignment format described above.

Parameters:

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

f - The file to write to

Throws:

OutputException - Thrown if there is a problem creating the file