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

Class MAParser

java.lang.Object

net.sf.basedb.util.importer.spotdata.MAParser

All Implemented Interfaces:

SpotIntensityParser

public class MAParser
extends Object
implements SpotIntensityParser

Spot intensity parser implementation for 2-channel data that looks for M/A values in the spot data and converts them to ch1/ch2 intensity values. The required assay fields are: l2ratio1_2 (M) and l10intgmean1_2 (A).

NOTE! The column names for the M/A values can be redefined by calling BaseFileParser.setRedefinedColumnName(String, String, String).

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 static final String	aColumn
private int	aIndex
private static final String	mColumn
private int	mIndex

Constructor Summary

Constructors

Constructor	Description
MAParser()	Creates a new MA-parser.

Method Summary

Modifier and Type	Method	Description
void	beginSection(BaseFileParser parser, FlatFileParser ffp, List<String> assayFields)	Prepare for parsing the data section.
boolean	hasRequiredAssayFields(BaseFileParser parser, FlatFileParser ffp, List<String> assayFields)	Check the list of assay fields to see if all columns that are required are present or not.
boolean	setIntensities(FlatFileParser.Data data, float[] intensities, int firstIndex)	Extract the intensity values from the current data line for a single bioassay.

Methods inherited from class java.lang.Object

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

Field Details

mIndex

private int mIndex

aIndex

private int aIndex

mColumn

private static final String mColumn

See Also:

• Constant Field Values

aColumn

private static final String aColumn

See Also:

• Constant Field Values

Constructor Details

MAParser

public MAParser()

Creates a new MA-parser.

Method Details

hasRequiredAssayFields

public boolean hasRequiredAssayFields(BaseFileParser parser,
 FlatFileParser ffp,
 List<String> assayFields)

Description copied from interface: SpotIntensityParser

Check the list of assay fields to see if all columns that are required are present or not. This method is called in the first pass to decide which spot intensity parser that should be used in the second pass.

Specified by:

hasRequiredAssayFields in interface SpotIntensityParser

Parameters:

parser - The master BASEfile parser

ffp - The flat file parser that parses the current file

assayFields - The list of assay fields

Returns:

TRUE if all required fields are present, FALSE otherwise

beginSection

public void beginSection(BaseFileParser parser,
 FlatFileParser ffp,
 List<String> assayFields)

Description copied from interface: SpotIntensityParser

Prepare for parsing the data section. Preparations typically include extracting the column indexes of the data columns. This method is called in the second pass before starting to parse data for a 'spot' section. NOTE! The same object instance may be used to parse more than one section in a serial BASEfile.

Specified by:

beginSection in interface SpotIntensityParser

Parameters:

parser - The master BASEfile parser

ffp - The flat file parser that parses the current file

assayFields - The list of assay fields

setIntensities

public boolean setIntensities(FlatFileParser.Data data,
 float[] intensities,
 int firstIndex)

Description copied from interface: SpotIntensityParser

Extract the intensity values from the current data line for a single bioassay. If the section contains data for multiple bioassays (eg. a matrix BASEfile) this method is called multiple times (with different 'firstIndex' value) for each row.

Specified by:

setIntensities in interface SpotIntensityParser

Parameters:

data - The current data line

intensities - An array that should be populate with intensity values

firstIndex - The index of the first data column that contains data for the current bioassay

Returns:

TRUE if the values could be set correctly, FALSE otherwise (which means that the spot data will not be inserted)