Package org.biojava.bio.program.fastq
Interface ParseListener
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public interface ParseListener
Low-level event based parser callback.- Since:
- 1.8.2
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description void
appendQuality(String quality)
Notify this listener of a quality line.void
appendSequence(String sequence)
Notify this parse listener of an additional sequence line.void
complete()
Notify this listener the FASTQ formatted sequence is complete.void
description(String description)
Notify this parse listener of a description line.void
quality(String quality)
Notify this listener of a quality line.void
repeatDescription(String repeatDescription)
Notify this parse listener of a repeat description line.void
sequence(String sequence)
Notify this parse listener of a sequence line.
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Method Detail
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description
void description(String description) throws IOException
Notify this parse listener of a description line.- Parameters:
description
- description line- Throws:
IOException
- if an I/O error occurs
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sequence
void sequence(String sequence) throws IOException
Notify this parse listener of a sequence line.Note that the sequence in FASTQ format may contain end-of-line characters, so both this method and
appendSequence(String)
may be called per FASTQ formatted sequence.- Parameters:
sequence
- sequence line- Throws:
IOException
- if an I/O error occurs
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appendSequence
void appendSequence(String sequence) throws IOException
Notify this parse listener of an additional sequence line.Note that the sequence in FASTQ format may contain end-of-line characters, so this method may be called more than once per FASTQ formatted sequence.
- Parameters:
sequence
- additional sequence line- Throws:
IOException
- if an I/O error occurs
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repeatDescription
void repeatDescription(String repeatDescription) throws IOException
Notify this parse listener of a repeat description line.- Parameters:
repeatDescription
- repeat description line- Throws:
IOException
- if an I/O error occurs
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quality
void quality(String quality) throws IOException
Notify this listener of a quality line.Note that the quality scores in FASTQ format may contain end-of-line characters, so both this method and
appendQuality(String)
may be called per FASTQ formatted sequence.- Parameters:
quality
- quality line- Throws:
IOException
- if an I/O error occurs
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appendQuality
void appendQuality(String quality) throws IOException
Notify this listener of a quality line.Note that the quality scores in FASTQ format may contain end-of-line characters, so this method may be called more than once per FASTQ formatted sequence.
- Parameters:
quality
- additional quality line- Throws:
IOException
- if an I/O error occurs
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complete
void complete() throws IOException
Notify this listener the FASTQ formatted sequence is complete.- Throws:
IOException
- if an I/O error occurs
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