Package org.biojava.bio.program.abi
Class ABIFChromatogram
java.lang.Object
org.biojava.bio.chromatogram.AbstractChromatogram
org.biojava.bio.program.abi.ABIFChromatogram
- All Implemented Interfaces:
Serializable
,Chromatogram
An implementation of
Chromatogram
to
encapulsulate chromatogram data extracted from the files produced by ABI
sequencers, such as the the 377 and the 3700. The format was described by
Clark Tibbetts in his paper "Raw Data File Formats, and the Digital and
Analog Raw Data Streams of the ABI PRISM 377 DNA Sequencer." Available
online
http://www-2.cs.cmu.edu/afs/cs/project/genome/WWW/Papers/clark.html- Author:
- Rhett Sutphin (UI CBCB), Richard Holland
- See Also:
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionprotected class
An extension ofABIFParser
that reads the particular fields from the ABIF that contain the chromatogram data and initializes the fields in its enclosingABIFChromatogram
instance. -
Field Summary
Fields inherited from interface org.biojava.bio.chromatogram.Chromatogram
DNA, OFFSETS
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic ABIFChromatogram
Create a new ABIF object from a file.static ABIFChromatogram
create
(InputStream in) Create a new ABIF object from a stream of bytes.protected ABIFChromatogram
protected ABIFChromatogram
load
(InputStream in) protected AbstractChromatogram
Returns a new instance of this AbstractChromatogram subclass for use inAbstractChromatogram.reverseComplement()
.Methods inherited from class org.biojava.bio.chromatogram.AbstractChromatogram
clearTraces, createImmutableAlignment, createImmutableSymbolList, getBaseCalls, getMax, getMax, getSequenceLength, getSignificantBits, getTrace, getTraceLength, reverse, reverseComplement, reverseComplementBaseCallList, reverseComplementBaseCalls, setBaseCallAlignment, setBits, setTrace
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Constructor Details
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ABIFChromatogram
public ABIFChromatogram()
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Method Details
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create
public static ABIFChromatogram create(File f) throws IOException, UnsupportedChromatogramFormatException Create a new ABIF object from a file.This method is more efficent than
create(InputStream)
. -
create
public static ABIFChromatogram create(InputStream in) throws IOException, UnsupportedChromatogramFormatException Create a new ABIF object from a stream of bytes.Due to the non-single-pass design of the ABI format, this method will wrap the InputStream in an
CachingInputStream
. For this reason,create(File)
should be preferred.- Parameters:
in
- the stream from which to read- Returns:
- a new ABIFChromatogram object
- Throws:
IOException
- if there is a problem with the underlying streamUnsupportedChromatogramFormatException
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load
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load
protected ABIFChromatogram load(InputStream in) throws IOException, UnsupportedChromatogramFormatException -
reverseComplementInstance
Description copied from class:AbstractChromatogram
Returns a new instance of this AbstractChromatogram subclass for use inAbstractChromatogram.reverseComplement()
.- Specified by:
reverseComplementInstance
in classAbstractChromatogram
- Returns:
- a reverse-complemented AbstractChromatogram
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