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java.lang.Objectorg.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.
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 |
public static final FiniteAlphabet QUALITY
public static final AtomicSymbol _0
public static final AtomicSymbol _1
public static final java.lang.Object SEQUENCE
public static final java.lang.Object SUPPORT
Constructor Detail |
public ABITools()
Method Detail |
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.
abiSeq
- the SymbolList over the QUALITY alphabet to view
IllegalAlphabetException
- if abiSeq is not over QUALITY
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