Package org.biojava.bio.chromatogram
Class ChromatogramFactory
java.lang.Object
org.biojava.bio.chromatogram.ChromatogramFactory
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
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic Chromatogram
Creates a newChromatogram
object from the named file.static Chromatogram
create
(InputStream in) Creates a newChromatogram
object from the supplied stream.
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Field Details
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SCF_MAGIC
The magic number for SCF files.- See Also:
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ABI_MAGIC
The magic number for ABIF files.- See Also:
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Constructor Details
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ChromatogramFactory
public ChromatogramFactory()
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Method Details
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create
public static Chromatogram create(File f) throws IOException, UnsupportedChromatogramFormatException Creates a newChromatogram
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 occursUnsupportedChromatogramFormatException
- when the file doesn't contain a chromatogram in a supported format
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create
public static Chromatogram create(InputStream in) throws IOException, UnsupportedChromatogramFormatException Creates a newChromatogram
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 useCachingInputStream
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 streamUnsupportedChromatogramFormatException
- when the file doesn't contain a chromatogram in a supported format
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