RbDe rbde-349 (20120127151154)

edu.mssm.crover.imports
Interface SequenceReader

All Known Implementing Classes:
FastaReader, PDBReader, PIRReader, SwissProtReader

public interface SequenceReader

SequenceReader are used by a SequenceReaderFactory. The factory is responsible for selecting the appropriate SequenceReader according to the format indicated by the user or the file extension. This allows to keep the Reader simple. A Reader should come with associated ReaderType objects that describe what the reader is supposed to be able to parse to create a BiologicalSequence. The ReaderType objects can be presented to the user to help his choice of a ReaderType suitable to read his/her file.


Method Summary
 ReaderType getSupportedType()
          Get information about the type of data supported by this sequence reader.
 AnnotatedBioSequence[] readFile(InputStream stream)
          Parses the content of the given stream extracts sequence informaton.
 

Method Detail

readFile

AnnotatedBioSequence[] readFile(InputStream stream)
                                throws IOException
Parses the content of the given stream extracts sequence informaton.

Parameters:
stream - The stream to process
Returns:
An array of sequences that were extracted from the stream
Throws:
IOException - if there is a problem reading from the stream

getSupportedType

ReaderType getSupportedType()
Get information about the type of data supported by this sequence reader.

Returns:
The reader type information for this reader

RbDe rbde-349 (20120127151154)

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