net.sf.basedb.util.importer.spotdata
Class BaseFileInfo.SpotSectionInfo

java.lang.Object
  net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo

Enclosing class:

BaseFileInfo

public static class BaseFileInfo.SpotSectionInfo
extends Object

Keeps information about headers and more in a 'spot' section.

Field Summary

private List<String>	assayFields
private List<Integer>	assays
private List<ExtraFloatParser>	extraFloats
private int	firstAssayFieldIndex
private int	positionIndex
private SpotIntensityParser	spiParser

Constructor Summary

BaseFileInfo.SpotSectionInfo()
Creates a new object.

Method Summary

void	addExtraFloatParser(ExtraFloatParser extraFloatParser) Add an extra value parser to this section.
List<String>	getAssayFields() Get a list with all assay data fields, in the order they appear in the file.
List<Integer>	getAssays() Get a list with the ID:s of all assays in the section, in the order they appear in the data columns.
List<ExtraFloatParser>	getExtraFloatParsers() Get the list of extra value parsers that exists for this section.
int	getFirstAssayFieldIndex() The index of the first data column that contains assay data.
int	getPositionIndex() The index of the 'position' data column.
SpotIntensityParser	getSpotIntensityParser() Get the spot intensity parser that should be used for parsing spot intensities in this section.
void	setAssayFields(List<String> assayFields) Set the list of all assay data fields, in the order the appear in the file.
void	setAssays(List<Integer> assays) Set a list with the ID:s of all assays, in the order the appearu in the data columns.
void	setFirstAssayFieldIndex(int firstAssayFieldIndex) Set the index of the first data column that contains assay data.
void	setPositionIndex(int positionIndex) Set the column index of the 'position' data column.
void	setSpotIntensityParser(SpotIntensityParser spiParser) Set the spot intensity parser for the section.

Methods inherited from class java.lang.Object

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

Field Detail

positionIndex

private int positionIndex

firstAssayFieldIndex

private int firstAssayFieldIndex

assays

private List<Integer> assays

assayFields

private List<String> assayFields

extraFloats

private List<ExtraFloatParser> extraFloats

spiParser

private SpotIntensityParser spiParser

Constructor Detail

BaseFileInfo.SpotSectionInfo

public BaseFileInfo.SpotSectionInfo()

Creates a new object.

Method Detail

getPositionIndex

public int getPositionIndex()

The index of the 'position' data column.

setPositionIndex

public void setPositionIndex(int positionIndex)

Set the column index of the 'position' data column.

getFirstAssayFieldIndex

public int getFirstAssayFieldIndex()

The index of the first data column that contains assay data.

setFirstAssayFieldIndex

public void setFirstAssayFieldIndex(int firstAssayFieldIndex)

Set the index of the first data column that contains assay data.

getAssayFields

public List<String> getAssayFields()

Get a list with all assay data fields, in the order they appear in the file.

setAssayFields

public void setAssayFields(List<String> assayFields)

Set the list of all assay data fields, in the order the appear in the file.

getAssays

public List<Integer> getAssays()

Get a list with the ID:s of all assays in the section, in the order they appear in the data columns.

setAssays

public void setAssays(List<Integer> assays)

Set a list with the ID:s of all assays, in the order the appearu in the data columns.

getSpotIntensityParser

public SpotIntensityParser getSpotIntensityParser()

Get the spot intensity parser that should be used for parsing spot intensities in this section.

setSpotIntensityParser

public void setSpotIntensityParser(SpotIntensityParser spiParser)

Set the spot intensity parser for the section.

getExtraFloatParsers

public List<ExtraFloatParser> getExtraFloatParsers()

Get the list of extra value parsers that exists for this section.

addExtraFloatParser

public void addExtraFloatParser(ExtraFloatParser extraFloatParser)

Add an extra value parser to this section.