Package net.sf.basedb.util.importer.spotdata

Class SecondPassSectionSpotsParser

java.lang.Object

net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser

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) $

Field Summary

Fields

Modifier and Type	Field	Description
private final int	channels
private final BioAssaySet	child
private final DbControl	dc
private final BaseFileInfo	info
private final int	linesToParse
private int	nextProgressReport
private final int	progressReportInterval
private int	sectionCount

Constructor Summary

Constructors

Constructor	Description
SecondPassSectionSpotsParser(DbControl dc, BaseFileInfo info, BioAssaySet child, int linesToParse)	Creates a new 'section spot' parser for the first pass.

Method Summary

Modifier and Type	Method	Description
void	parseSection(BaseFileParser parser, FlatFileParser ffp)	Parse the current section.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

dc

private final DbControl dc

info

private final BaseFileInfo info

child

private final BioAssaySet child

linesToParse

private final int linesToParse

progressReportInterval

private final int progressReportInterval

nextProgressReport

private int nextProgressReport

channels

private final int channels

sectionCount

private int sectionCount

Constructor Details

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 access

info - Information about the file we are parsing

child - The new child bioassay set that we are importing data to

Method Details

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 the FlatFileParser.parseHeaders() must be called. Use FlatFileParser.nextData() to parse data lines.

Specified by:

parseSection in interface BaseFileSectionParser

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