Class SecondPassSectionSpotsParser
- java.lang.Object
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- net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser
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- All Implemented Interfaces:
BaseFileSectionParser
public class SecondPassSectionSpotsParser extends Object implements BaseFileSectionParser
The second pass of the 'spots' section extracts spot and extra value data.- Version:
- 2.14
- Author:
- Nicklas
- Last modified
- $Date: 2019-03-20 14:31:03 +0100 (ons, 20 mars 2019) $
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Field Summary
Fields Modifier and Type Field Description private int
channels
private BioAssaySet
child
private DbControl
dc
private BaseFileInfo
info
private int
linesToParse
private int
nextProgressReport
private int
progressReportInterval
private int
sectionCount
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Constructor Summary
Constructors Constructor Description SecondPassSectionSpotsParser(DbControl dc, BaseFileInfo info, BioAssaySet child, int linesToParse)
Creates a new 'section spot' parser for the first pass.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
parseSection(BaseFileParser parser, FlatFileParser ffp)
Parse the current section.
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Field Detail
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dc
private final DbControl dc
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info
private final BaseFileInfo info
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child
private final BioAssaySet child
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linesToParse
private final int linesToParse
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progressReportInterval
private final int progressReportInterval
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nextProgressReport
private int nextProgressReport
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channels
private final int channels
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sectionCount
private int sectionCount
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Constructor Detail
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SecondPassSectionSpotsParser
public SecondPassSectionSpotsParser(DbControl dc, BaseFileInfo info, BioAssaySet child, int linesToParse)
Creates a new 'section spot' parser for the first pass. This parser will only extract header and reporter/position mapping information.- Parameters:
dc
- A DbControl to use for database accessinfo
- Information about the file we are parsingchild
- The new child bioassay set that we are importing data to
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Method Detail
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parseSection
public void parseSection(BaseFileParser parser, FlatFileParser ffp) throws IOException
Description copied from interface:BaseFileSectionParser
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.- Specified by:
parseSection
in interfaceBaseFileSectionParser
- 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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