Package org.biojava.bio.program.abi

Class ABIFParser

java.lang.Object

org.biojava.bio.program.abi.ABIFParser

Direct Known Subclasses:

ABIFChromatogram.Parser

public class ABIFParser
extends Object

A general base parser for files produced by ABI software. This includes chromatograms derived from ABI sequencers and potentially other data files as well. 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

Briefly, the format consists of a set of named fixed-length "tagged data records" which may contain data themselves, or pointers to data elsewhere in the file. This class reads these records and exposes them to subclasses through the getDataRecord(java.lang.String, int) method. The attributes of the records as described in Tibbets' paper are exposed through public (final) fields of ABIFParser.TaggedDataRecord instances.

If a record only contains a pointer to the desired data (see ABIFParser.TaggedDataRecord.hasOffsetData, subclasses may get at the raw data by using ABIFParser.TaggedDataRecord.offsetData:

This parser provides methods and classes for dealing with the files as streams or local files (local files being more memory-efficient).

Author:

Rhett Sutphin (UI CBCB), Richard Holland

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static interface	ABIFParser.DataAccess	Concatenation of the Seekable and DataInput interfaces.
static class	ABIFParser.TaggedDataRecord	An aggregate immutable type for an ABIF tagged data record.

Constructor Summary

Constructors

Constructor	Description
ABIFParser(File f)	Creates a new ABIFParser for a file.
ABIFParser(InputStream in)	Creates a new ABIFParser for an input stream.
ABIFParser(ABIFParser.DataAccess toParse)	Creates a new ABIFParser for the specified ABIFParser.DataAccess object.

Method Summary

Modifier and Type	Method	Description
static Symbol	decodeDNAToken(char token)	Decodes a character into a Symbol in the DNA alphabet.
Map	getAllDataRecords()	Obtain all data records.
ABIFParser.DataAccess	getDataAccess()	Returns the accessor for the raw data being parsed by this parser.
ABIFParser.TaggedDataRecord	getDataRecord(String tagName, int tagNumber)	Get the entry from the file TOC with the given name and tag number.

Methods inherited from class java.lang.Object

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

Constructor Detail

ABIFParser

public ABIFParser(File f)
           throws IOException

Creates a new ABIFParser for a file.

Throws:

IOException

ABIFParser

public ABIFParser(InputStream in)
           throws IOException

Creates a new ABIFParser for an input stream. Note that the stream will be wrapped in a CachingInputStream if it isn't one already. If it is, it will be seeked to 0.

Throws:

IOException

ABIFParser

public ABIFParser(ABIFParser.DataAccess toParse)
           throws IOException

Creates a new ABIFParser for the specified ABIFParser.DataAccess object. If you need to read from something other than a file or a stream, you'll have to implement a ABIFParser.DataAccess-implementing class wrapping your source and then pass an instance to this constructor.

Throws:

IOException

Method Detail

getDataAccess

public final ABIFParser.DataAccess getDataAccess()

Returns the accessor for the raw data being parsed by this parser.

decodeDNAToken

public static Symbol decodeDNAToken(char token)
                             throws IllegalSymbolException

Decodes a character into a Symbol in the DNA alphabet. Uses a definition of characters that is compatible with the ABI format.

Parameters:

token - the character to decode

Throws:

IllegalSymbolException - when token isn't in { a, A, c, C, g, G, t, T, n, N, - }

getDataRecord

public ABIFParser.TaggedDataRecord getDataRecord(String tagName,
                                                 int tagNumber)
                                          throws IllegalArgumentException,
                                                 IllegalStateException

Get the entry from the file TOC with the given name and tag number.

Parameters:

tagName - the four-character string name of the desired data record

tagNumber - which one of the tags with this name to return (must be positive)

Returns:

the requested data record, or null if no such record exists

Throws:

IllegalArgumentException - if tagName is the wrong length or tagNumber is 0 or negative

IllegalStateException - if the initial parsing is not complete

getAllDataRecords

public Map getAllDataRecords()

Obtain all data records. Keys of the map are strings consisting of tag names with tag numbers concatenated immediately afterwards. Values are TaggedDataRecord objects. The map has no particular order and so cannot be relied on to iterate over records in the same order they were read from the file.

Returns:

the map of all data records.