org.biojava.bio.chromatogram

Class ChromatogramFactory

java.lang.Object

org.biojava.bio.chromatogram.ChromatogramFactory

public class ChromatogramFactory
extends Object

A factory that creates Chromatogram objects from files or streams. In either case, the type of object to create is determined from the first four bytes of the stream (the magic number).

Since:

1.3

Author:

Rhett Sutphin (UI CBCB), Matthew Pocock

Field Summary

Fields

Modifier and Type	Field and Description
static int	ABI_MAGIC The magic number for ABIF files.
static int	SCF_MAGIC The magic number for SCF files.

Constructor Summary

Constructors

Constructor and Description
ChromatogramFactory()

Method Summary

Methods

Modifier and Type	Method and Description
static Chromatogram	create(File f) Creates a new Chromatogram object from the named file.
static Chromatogram	create(InputStream in) Creates a new Chromatogram object from the supplied stream.

Methods inherited from class java.lang.Object

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

Field Detail

SCF_MAGIC

public static final int SCF_MAGIC

The magic number for SCF files.

See Also:

Constant Field Values

ABI_MAGIC

public static final int ABI_MAGIC

The magic number for ABIF files.

See Also:

Constant Field Values

Constructor Detail

ChromatogramFactory

public ChromatogramFactory()

Method Detail

create

public static Chromatogram create(File f)
                           throws IOException,
                                  UnsupportedChromatogramFormatException

Creates a new Chromatogram object from the named file.

Parameters:

f - the file to read

Returns:

a new Chromatogram

Throws:

IOException - when the file can't be read or some other I/O error occurs

UnsupportedChromatogramFormatException - when the file doesn't contain a chromatogram in a supported format

create

public static Chromatogram create(InputStream in)
                           throws IOException,
                                  UnsupportedChromatogramFormatException

Creates a new Chromatogram object from the supplied stream. Note that for some chromatogram formats, this can be much more memory-intensive than reading from a file.

Note also that if the provided stream is a CachingInputStream, it will be seeked back to 0 before being passed to the parser. This is because the parsers that use CachingInputStream assume that the "file" starts at 0.

Parameters:

in - the stream from which to read the chromatogram.

Returns:

a new Chromatogram

Throws:

IOException - when there's a problem with the stream

UnsupportedChromatogramFormatException - when the file doesn't contain a chromatogram in a supported format