Package net.sf.basedb.util.basefile

Interface BaseFileSectionParser

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 calling ThreadSignalHandler.checkInterrupted() at regular intervals. The parser should also update progress by calling BaseFileParser.setProgress(long, String). Note that progress should be reported as the number of bytes parsed, which can simply can be retreived by calling FlatFileParser.getParsedBytes().
Version:
2.14
Author:
Nicklas
Last modified
$Date: 2011-03-16 12:48:47 +0100 (on, 16 mar 2011) $

  • Method Details

    • 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 the FlatFileParser.parseHeaders() must be called. Use FlatFileParser.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