org.biojava.bio.program.abi
Class ABIFChromatogram
java.lang.Object
org.biojava.bio.chromatogram.AbstractChromatogram
org.biojava.bio.program.abi.ABIFChromatogram
- All Implemented Interfaces:
- Chromatogram
- public class ABIFChromatogram
- extends AbstractChromatogram
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)
- See Also:
ABIFParser
Nested Class Summary |
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. |
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 |
ABIFChromatogram
public ABIFChromatogram()
create
public static ABIFChromatogram create(java.io.File f)
throws java.io.IOException,
UnsupportedChromatogramFormatException
- Create a new ABIF object from a file.
This method is more efficent than create(InputStream)
.
- Throws:
java.io.IOException
UnsupportedChromatogramFormatException
create
public static ABIFChromatogram create(java.io.InputStream in)
throws java.io.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:
java.io.IOException
- if there is a problem with the underlying stream
UnsupportedChromatogramFormatException
load
protected ABIFChromatogram load(java.io.File f)
throws java.io.IOException,
UnsupportedChromatogramFormatException
- Throws:
java.io.IOException
UnsupportedChromatogramFormatException
load
protected ABIFChromatogram load(java.io.InputStream in)
throws java.io.IOException,
UnsupportedChromatogramFormatException
- Throws:
java.io.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