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

Method Summary
`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.

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