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

public class ABIFChromatogram
extends AbstractChromatogram
implements Serializable

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:

ABIFParser, Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	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.

Field Summary

Fields inherited from interface org.biojava.bio.chromatogram.Chromatogram

DNA, OFFSETS

Constructor Summary

Constructors

Constructor	Description
ABIFChromatogram()

Method Summary

Modifier and Type	Method	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().

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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ABIFChromatogram

public ABIFChromatogram()

Method Detail

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).

Throws:

IOException

UnsupportedChromatogramFormatException

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 stream

UnsupportedChromatogramFormatException

load

protected ABIFChromatogram load(File f)
                         throws IOException,
                                UnsupportedChromatogramFormatException

Throws:

IOException

UnsupportedChromatogramFormatException

load

protected ABIFChromatogram load(InputStream in)
                         throws IOException,
                                UnsupportedChromatogramFormatException

Throws:

IOException

UnsupportedChromatogramFormatException

reverseComplementInstance

protected AbstractChromatogram reverseComplementInstance()

Description copied from class: AbstractChromatogram

Returns a new instance of this AbstractChromatogram subclass for use in AbstractChromatogram.reverseComplement().

Specified by:

reverseComplementInstance in class AbstractChromatogram

Returns:

a reverse-complemented AbstractChromatogram