Package net.sf.basedb.util.basefile
Interface BaseFileSectionParser
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- All Known Implementing Classes:
FirstPassSectionSpotsParser
,SecondPassSectionSpotsParser
,SectionAssaysParser
,SectionReporterListParser
public interface BaseFileSectionParser
A section parser is responsible for parsing and collecting data that is found in a section in a serial or matrix BASEfile. A section parser should check for user abort by callingThreadSignalHandler.checkInterrupted()
at regular intervals. The parser should also update progress by callingBaseFileParser.setProgress(long, String)
. Note that progress should be reported as the number of bytes parsed, which can simply can be retreived by callingFlatFileParser.getParsedBytes()
.- Version:
- 2.14
- Author:
- Nicklas
- Last modified
- $Date: 2011-03-16 12:48:47 +0100 (on, 16 mar 2011) $
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description void
parseSection(BaseFileParser parser, FlatFileParser ffp)
Parse the current section.
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Method Detail
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parseSection
void parseSection(BaseFileParser parser, FlatFileParser ffp) throws IOException
Parse the current section. The current parse position is right after the section marker. If the section contains headers theFlatFileParser.parseHeaders()
must be called. UseFlatFileParser.nextData()
to parse data lines.- Parameters:
parser
- The master BASEfile parser (can be used for reporting progress, checking for interrupts, etc.)ffp
- The actual file parser, use this to get the data- Throws:
IOException
- If there is a problem reading the data
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