Package org.biojava.bio.program.fastq
Interface FastqReader
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- All Known Implementing Classes:
IlluminaFastqReader
,SangerFastqReader
,SolexaFastqReader
public interface FastqReader
Reader for FASTQ formatted sequences.
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description java.lang.Iterable<Fastq>
read(java.io.File file)
Read zero or more FASTQ formatted sequences from the specified file.java.lang.Iterable<Fastq>
read(java.io.InputStream inputStream)
Read zero or more FASTQ formatted sequences from the specified input stream.java.lang.Iterable<Fastq>
read(java.net.URL url)
Read zero or more FASTQ formatted sequences from the specified url.
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Method Detail
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read
java.lang.Iterable<Fastq> read(java.io.File file) throws java.io.IOException
Read zero or more FASTQ formatted sequences from the specified file.- Parameters:
file
- file to read from, must not be null- Returns:
- zero or more FASTQ formatted sequences read from the specified file
- Throws:
java.io.IOException
- if an IO error occurs
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read
java.lang.Iterable<Fastq> read(java.net.URL url) throws java.io.IOException
Read zero or more FASTQ formatted sequences from the specified url.- Parameters:
url
- URL to read from, must not be null- Returns:
- zero or more FASTQ formatted sequences read from the specified url
- Throws:
java.io.IOException
- if an IO error occurs
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read
java.lang.Iterable<Fastq> read(java.io.InputStream inputStream) throws java.io.IOException
Read zero or more FASTQ formatted sequences from the specified input stream.- Parameters:
inputStream
- input stream to read from, must not be null- Returns:
- zero or more FASTQ formatted sequences read from the specified input stream
- Throws:
java.io.IOException
- if an IO error occurs
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