SangerFastqReader (biojava-legacy 1.9.5 API)

java.lang.Object
- org.biojava.bio.program.fastq.SangerFastqReader

All Implemented Interfaces:: FastqReader

public final class SangerFastqReader
extends Object

Since:: 1.7.1

Constructor Summary

Constructors
Constructor Description

SangerFastqReader()

Constructors
Constructor	Description
`SangerFastqReader()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected FastqVariant`	`getVariant()`	Return the FASTQ sequence format variant for this reader.
`void`	`parse(Readable readable, ParseListener listener)`	Parse the specified readable.
`Iterable<Fastq>`	`read(File file)`	Read zero or more FASTQ formatted sequences from the specified file.
`Iterable<Fastq>`	`read(InputStream inputStream)`	Read zero or more FASTQ formatted sequences from the specified input stream.
`Iterable<Fastq>`	`read(URL url)`	Read zero or more FASTQ formatted sequences from the specified url.
`void`	`stream(Readable readable, StreamListener listener)`	Stream the specified readable.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - SangerFastqReader
```
public SangerFastqReader()
```
- Method Detail
  - getVariant
```
protected FastqVariant getVariant()
```
    Return the FASTQ sequence format variant for this reader.
    
    Returns:
    
    the FASTQ sequence format variant for this reader
  - parse
```
public final void parse(Readable readable,
                        ParseListener listener)
                 throws IOException
```
    Description copied from interface: FastqReader
    
    Parse the specified readable.
    
    Specified by:
    
    parse in interface FastqReader
    
    Parameters:
    
    readable - readable, must not be null
    
    listener - low-level event based parser callback, must not be null
    
    Throws:
    
    IOException - if an I/O error occurs
  - stream
```
public final void stream(Readable readable,
                         StreamListener listener)
                  throws IOException
```
    Description copied from interface: FastqReader
    
    Stream the specified readable.
    
    Specified by:
    
    stream in interface FastqReader
    
    Parameters:
    
    readable - readable, must not be null
    
    listener - event based reader callback, must not be null
    
    Throws:
    
    IOException - if an I/O error occurs
  - read
```
public final Iterable<Fastq> read(File file)
                           throws IOException
```
    Description copied from interface: FastqReader
    
    Read zero or more FASTQ formatted sequences from the specified file.
    
    Specified by:
    
    read in interface FastqReader
    
    Parameters:
    
    file - file to read from, must not be null
    
    Returns:
    
    zero or more FASTQ formatted sequences read from the specified file
    
    Throws:
    
    IOException - if an I/O error occurs
  - read
```
public final Iterable<Fastq> read(URL url)
                           throws IOException
```
    Description copied from interface: FastqReader
    
    Read zero or more FASTQ formatted sequences from the specified url.
    
    Specified by:
    
    read in interface FastqReader
    
    Parameters:
    
    url - URL to read from, must not be null
    
    Returns:
    
    zero or more FASTQ formatted sequences read from the specified url
    
    Throws:
    
    IOException - if an I/O error occurs
  - read
```
public final Iterable<Fastq> read(InputStream inputStream)
                           throws IOException
```
    Description copied from interface: FastqReader
    
    Read zero or more FASTQ formatted sequences from the specified input stream.
    
    Specified by:
    
    read in interface FastqReader
    
    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:
    
    IOException - if an I/O error occurs

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

SangerFastqReader

Method Detail

getVariant

parse

stream

read

read

read