Package org.biojava.bio.program.fastq
Class SolexaFastqWriter
- java.lang.Object
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- org.biojava.bio.program.fastq.SolexaFastqWriter
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- All Implemented Interfaces:
FastqWriter
public final class SolexaFastqWriter extends java.lang.Object
Writer forFastqVariant.FASTQ_SOLEXA
formatted sequences.
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Constructor Summary
Constructors Constructor Description SolexaFastqWriter()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description <T extends java.lang.Appendable>
Tappend(T appendable, java.lang.Iterable<Fastq> fastq)
Append the specified FASTQ formatted sequences to the specified appendable.<T extends java.lang.Appendable>
Tappend(T appendable, Fastq... fastq)
Append the specified FASTQ formatted sequences to the specified appendable.protected void
validate(Fastq fastq)
Validate the specified FASTQ formatted sequence for writing.void
write(java.io.File file, java.lang.Iterable<Fastq> fastq)
Write the specified FASTQ formatted sequences to the specified file.void
write(java.io.File file, Fastq... fastq)
Write the specified FASTQ formatted sequences to the specified file.void
write(java.io.OutputStream outputStream, java.lang.Iterable<Fastq> fastq)
Write the specified FASTQ formatted sequences to the specified output stream.void
write(java.io.OutputStream outputStream, Fastq... fastq)
Write the specified FASTQ formatted sequences to the specified output stream.
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Method Detail
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validate
protected void validate(Fastq fastq) throws java.io.IOException
Validate the specified FASTQ formatted sequence for writing.- Parameters:
fastq
- FASTQ formatted sequence to validate, will not be null- Throws:
java.io.IOException
- if the specified FASTQ formatted sequence is not valid for writing
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append
public final <T extends java.lang.Appendable> T append(T appendable, Fastq... fastq) throws java.io.IOException
Append the specified FASTQ formatted sequences to the specified appendable.- Specified by:
append
in interfaceFastqWriter
- Type Parameters:
T
- extends Appendable- Parameters:
appendable
- appendable to append the specified FASTQ formatted sequences to, must not be nullfastq
- variable number of FASTQ formatted sequences to append, must not be null- Returns:
- the specified appendable with the specified FASTQ formatted sequences appended
- Throws:
java.io.IOException
- if an IO error occurs
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append
public final <T extends java.lang.Appendable> T append(T appendable, java.lang.Iterable<Fastq> fastq) throws java.io.IOException
Append the specified FASTQ formatted sequences to the specified appendable.- Specified by:
append
in interfaceFastqWriter
- Type Parameters:
T
- extends Appendable- Parameters:
appendable
- appendable to append the specified FASTQ formatted sequences to, must not be nullfastq
- zero or more FASTQ formatted sequences to append, must not be null- Returns:
- the specified appendable with the specified FASTQ formatted sequences appended
- Throws:
java.io.IOException
- if an IO error occurs
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write
public final void write(java.io.File file, Fastq... fastq) throws java.io.IOException
Write the specified FASTQ formatted sequences to the specified file.- Specified by:
write
in interfaceFastqWriter
- Parameters:
file
- file to write to, must not be nullfastq
- variable number of FASTQ formatted sequences to write, must not be null- Throws:
java.io.IOException
- if an IO error occurs
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write
public final void write(java.io.File file, java.lang.Iterable<Fastq> fastq) throws java.io.IOException
Write the specified FASTQ formatted sequences to the specified file.- Specified by:
write
in interfaceFastqWriter
- Parameters:
file
- file to write to, must not be nullfastq
- zero or more FASTQ formatted sequences to write, must not be null- Throws:
java.io.IOException
- if an IO error occurs
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write
public final void write(java.io.OutputStream outputStream, Fastq... fastq) throws java.io.IOException
Write the specified FASTQ formatted sequences to the specified output stream.- Specified by:
write
in interfaceFastqWriter
- Parameters:
outputStream
- output stream to write to, must not be nullfastq
- variable number of FASTQ formatted sequences to write, must not be null- Throws:
java.io.IOException
- if an IO error occurs
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write
public final void write(java.io.OutputStream outputStream, java.lang.Iterable<Fastq> fastq) throws java.io.IOException
Write the specified FASTQ formatted sequences to the specified output stream.- Specified by:
write
in interfaceFastqWriter
- Parameters:
outputStream
- output stream to write to, must not be nullfastq
- zero or more FASTQ formatted sequences to write, must not be null- Throws:
java.io.IOException
- if an IO error occurs
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