public class ABIFChromatogram extends AbstractChromatogram implements Serializable
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.htmlABIFParser,
Serialized Form| Modifier and Type | Class and Description |
|---|---|
protected class |
ABIFChromatogram.Parser
An extension of
ABIFParser that reads the particular fields from
the ABIF that contain the chromatogram data and initializes the fields
in its enclosing ABIFChromatogram instance. |
DNA, OFFSETS| Constructor and Description |
|---|
ABIFChromatogram() |
| Modifier and Type | Method and Description |
|---|---|
static ABIFChromatogram |
create(File f)
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 |
load(File f) |
protected ABIFChromatogram |
load(InputStream in) |
protected AbstractChromatogram |
reverseComplementInstance()
Returns a new instance of this AbstractChromatogram subclass for use in
AbstractChromatogram.reverseComplement(). |
clearTraces, createImmutableAlignment, createImmutableSymbolList, getBaseCalls, getMax, getMax, getSequenceLength, getSignificantBits, getTrace, getTraceLength, reverse, reverseComplement, reverseComplementBaseCallList, reverseComplementBaseCalls, setBaseCallAlignment, setBits, setTracepublic ABIFChromatogram()
public static ABIFChromatogram create(File f) throws IOException, UnsupportedChromatogramFormatException
This method is more efficent than create(InputStream).
public static ABIFChromatogram create(InputStream in) throws IOException, UnsupportedChromatogramFormatException
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.
in - the stream from which to readIOException - if there is a problem with the underlying streamUnsupportedChromatogramFormatExceptionprotected ABIFChromatogram load(File f) throws IOException, UnsupportedChromatogramFormatException
protected ABIFChromatogram load(InputStream in) throws IOException, UnsupportedChromatogramFormatException
protected AbstractChromatogram reverseComplementInstance()
AbstractChromatogramAbstractChromatogram.reverseComplement().reverseComplementInstance in class AbstractChromatogramCopyright © 2014 BioJava. All rights reserved.