Class BaseFileInfo.SpotSectionInfo
- java.lang.Object
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- net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
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- Enclosing class:
- BaseFileInfo
public static class BaseFileInfo.SpotSectionInfo extends Object
Keeps information about headers and more in a 'spot' section.
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Field Summary
Fields Modifier and Type Field Description private List<String>
assayFields
private List<Integer>
assays
private List<ExtraFloatParser>
extraFloats
private int
firstAssayFieldIndex
private int
positionIndex
private SpotIntensityParser
spiParser
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Constructor Summary
Constructors Constructor Description SpotSectionInfo()
Creates a new object.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description 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.
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Field Detail
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positionIndex
private int positionIndex
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firstAssayFieldIndex
private int firstAssayFieldIndex
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extraFloats
private List<ExtraFloatParser> extraFloats
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spiParser
private SpotIntensityParser spiParser
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Method Detail
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getPositionIndex
public int getPositionIndex()
The index of the 'position' data column.
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setPositionIndex
public void setPositionIndex(int positionIndex)
Set the column index of the 'position' data column.
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getFirstAssayFieldIndex
public int getFirstAssayFieldIndex()
The index of the first data column that contains assay data.
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setFirstAssayFieldIndex
public void setFirstAssayFieldIndex(int firstAssayFieldIndex)
Set the index of the first data column that contains assay data.
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getAssayFields
public List<String> getAssayFields()
Get a list with all assay data fields, in the order they appear in the file.
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setAssayFields
public void setAssayFields(List<String> assayFields)
Set the list of all assay data fields, in the order the appear in the file.
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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.
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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.
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getSpotIntensityParser
public SpotIntensityParser getSpotIntensityParser()
Get the spot intensity parser that should be used for parsing spot intensities in this section.
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setSpotIntensityParser
public void setSpotIntensityParser(SpotIntensityParser spiParser)
Set the spot intensity parser for the section.
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getExtraFloatParsers
public List<ExtraFloatParser> getExtraFloatParsers()
Get the list of extra value parsers that exists for this section.
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addExtraFloatParser
public void addExtraFloatParser(ExtraFloatParser extraFloatParser)
Add an extra value parser to this section.
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