org.biojava.bio.program.abi

Class ABITools

java.lang.Object

org.biojava.bio.program.abi.ABITools

public class ABITools
extends Object

Useful functionality for working with fasta files where the quality of the DNA is encoded as upper and lower case DNA characters.

Author:

Matthew Pocock

Field Summary

Fields

Modifier and Type	Field and Description
static AtomicSymbol	_0 The poorly supported symbol.
static AtomicSymbol	_1 The well supported symbol.
static FiniteAlphabet	QUALITY The quality alphabet.
static Object	SEQUENCE Alignment label for the DNA sequence row.
static Object	SUPPORT Alignment label for the support row.

Constructor Summary

Constructors

Constructor and Description
ABITools()

Method Summary

Methods

Modifier and Type	Method and Description
static Alignment	getAlignment(SymbolList abiSeq) View a symbol list over the QUALITY alphabet as an alignment.

Methods inherited from class java.lang.Object

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

Field Detail

QUALITY

public static final FiniteAlphabet QUALITY

The quality alphabet. This is equivalent to DNA x [0,1] where 0 represents poorly supported (lower case) and 1 represents strongly supported (upper case).

_0

public static final AtomicSymbol _0

The poorly supported symbol.

_1

public static final AtomicSymbol _1

The well supported symbol.

SEQUENCE

public static final Object SEQUENCE

Alignment label for the DNA sequence row.

SUPPORT

public static final Object SUPPORT

Alignment label for the support row.

Constructor Detail

ABITools

public ABITools()

Method Detail

getAlignment

public static Alignment getAlignment(SymbolList abiSeq)
                              throws IllegalAlphabetException

View a symbol list over the QUALITY alphabet as an alignment.

The alignment will have labels of SEQUENCE and SUPPORT that retrieve the DNA sequence and the binary support values respectively.

Parameters:

abiSeq - the SymbolList over the QUALITY alphabet to view

Returns:

an Alignment view of abiSeq

Throws:

IllegalAlphabetException - if abiSeq is not over QUALITY