ABITools (biojava-legacy 1.9.5 API)

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	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 Description

ABITools()

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method	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