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

Class FirstPassSectionSpotsParser

java.lang.Object

net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser

All Implemented Interfaces:

BaseFileSectionParser

public class FirstPassSectionSpotsParser
extends Object
implements BaseFileSectionParser

Parses a 'spots' section of a BASEfile with bioassay set spot data. This section is optional but can also appear more than once (eg. serial BASEfile). The section must have an 'assays' header that contains the id:s of the bioassays that have spot data in this section. The id values should either reference an id from the 'assays' section or the id of an existing bioassay in the database.

The section must also contain a 'columns' header that includes at least 'position', 'reporter' and 'assayData' columns. The 'assayData' is a meta column that expands to the columns defined by the required 'assayFields' header. This header must define as many 'intensityN' columns as there are channels in the experiment. For two-channel data, it may instead optionally use M (l2ratio1_2) and A (l10intgmean1_2). Columns with extra values can be defined by including a 'setExtraFloats' header. This header just enumerates the extra columns. A macthing column must also be presen in the 'assayFields' header.

NOTE! Column names can be redefined by calling BaseFileParser.setRedefinedColumnName(String, String, String).

Here is an example of the headers and the first data line of a matrix BASEfile which has two two-channel assays and one extra value column.

section spots
assays  101     102
columns position        reporter        assayData
assayFields intensity1 intensity2 extra1
setExtraFloats extra1
%
1       1       1.0     2.0     0.5     2.0     3.0     0.2

The first pass will check the headers and extract position/reporter mappings. This is important because we need to know if the child bioassay set has the same or a different position/reporter mapping than the parent bioassay set.

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 DbControl	dc
private BaseFileInfo	info
private boolean	mapZeroToNull
private long	nextProgressReport
private BioAssaySet	parent
private long	progressReportInterval
static String	SECTION	The section of the BASEfile this parser can parse, eg.
private int	sectionCount
private List<SpotIntensityParser>	spotIntensityParsers
private String	totalBytes

Constructor Summary

Constructors

Constructor	Description
FirstPassSectionSpotsParser(DbControl dc, BaseFileInfo info, BioAssaySet parent)	Creates a new 'section spot' parser for the first pass.

Method Summary

Modifier and Type	Method	Description
void	addSpotIntensityParser(SpotIntensityParser parser)	Adds a spot intensity parser to the list of used parsers.
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

SECTION

public static final String SECTION

The section of the BASEfile this parser can parse, eg. 'spots'.

See Also:

Constant Field Values

dc

private final DbControl dc

info

private final BaseFileInfo info

parent

private final BioAssaySet parent

totalBytes

private final String totalBytes

progressReportInterval

private final long progressReportInterval

nextProgressReport

private long nextProgressReport

sectionCount

private int sectionCount

mapZeroToNull

private boolean mapZeroToNull

spotIntensityParsers

private List<SpotIntensityParser> spotIntensityParsers

Constructor Details

FirstPassSectionSpotsParser

public FirstPassSectionSpotsParser(DbControl dc,
BaseFileInfo info,
BioAssaySet parent)

Creates a new 'section spot' parser for the first pass. This parser will extract header information and position/reporter mapping information.

Parameters:

dc - A DbControl to use for database access

info - Information about the file we are parsing

parent - The parent bioassay set

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

addSpotIntensityParser

public void addSpotIntensityParser(SpotIntensityParser parser)

Adds a spot intensity parser to the list of used parsers. The first found parser that signals that all required assay fields are present will be used to parse the spot intensity data.

See Also:

GenericIntensityParser, MAParser