org.biojava.bio.program.abi
Class ABITools

java.lang.Object
  extended byorg.biojava.bio.program.abi.ABITools

public class ABITools
extends java.lang.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
static AtomicSymbol _0
          The poorly supported symbol.
static AtomicSymbol _1
          The well supported symbol.
static FiniteAlphabet QUALITY
          The quality alphabet.
static java.lang.Object SEQUENCE
          Alignment label for the DNA sequence row.
static java.lang.Object SUPPORT
          Alignment label for the support row.
 
Constructor Summary
ABITools()
           
 
Method Summary
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 java.lang.Object SEQUENCE
Alignment label for the DNA sequence row.


SUPPORT

public static final java.lang.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