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public interface ParseListener
Low-level event based parser callback.
Method Summary | |
---|---|
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. |
Method Detail |
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void description(String description) throws IOException
description
- description line
IOException
- if an I/O error occursvoid sequence(String sequence) throws IOException
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.
sequence
- sequence line
IOException
- if an I/O error occursvoid appendSequence(String sequence) throws IOException
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.
sequence
- additional sequence line
IOException
- if an I/O error occursvoid repeatDescription(String repeatDescription) throws IOException
repeatDescription
- repeat description line
IOException
- if an I/O error occursvoid quality(String quality) throws IOException
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.
quality
- quality line
IOException
- if an I/O error occursvoid appendQuality(String quality) throws IOException
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.
quality
- additional quality line
IOException
- if an I/O error occursvoid complete() throws IOException
IOException
- if an I/O error occurs
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