Package org.biojava.bio.program.abi
Class ABITools
java.lang.Object
org.biojava.bio.program.abi.ABITools
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
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final AtomicSymbol
The poorly supported symbol.static final AtomicSymbol
The well supported symbol.static final FiniteAlphabet
The quality alphabet.static final Object
Alignment label for the DNA sequence row.static final Object
Alignment label for the support row. -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic Alignment
getAlignment
(SymbolList abiSeq) View a symbol list over the QUALITY alphabet as an alignment.
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Field Details
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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
The poorly supported symbol. -
_1
The well supported symbol. -
SEQUENCE
Alignment label for the DNA sequence row. -
SUPPORT
Alignment label for the support row.
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Constructor Details
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ABITools
public ABITools()
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Method Details
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getAlignment
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
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