Class BaseFileInfo.SpotSectionInfo
java.lang.Object
net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
- Enclosing class:
- BaseFileInfo
Keeps information about headers and more in a 'spot' section.
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Field Summary
Modifier and TypeFieldDescriptionprivate List<ExtraFloatParser>
private int
private int
private SpotIntensityParser
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptionvoid
addExtraFloatParser
(ExtraFloatParser extraFloatParser) Add an extra value parser to this section.Get a list with all assay data fields, in the order they appear in the file.Get a list with the ID:s of all assays in the section, in the order they appear in the data columns.Get the list of extra value parsers that exists for this section.int
The index of the first data column that contains assay data.int
The index of the 'position' data column.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
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 Details
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positionIndex
private int positionIndex -
firstAssayFieldIndex
private int firstAssayFieldIndex -
assays
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assayFields
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extraFloats
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spiParser
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Constructor Details
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SpotSectionInfo
public SpotSectionInfo()Creates a new object.
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Method Details
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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
Get a list with all assay data fields, in the order they appear in the file. -
setAssayFields
Set the list of all assay data fields, in the order the appear in the file. -
getAssays
Get a list with the ID:s of all assays in the section, in the order they appear in the data columns. -
setAssays
Set a list with the ID:s of all assays, in the order the appearu in the data columns. -
getSpotIntensityParser
Get the spot intensity parser that should be used for parsing spot intensities in this section. -
setSpotIntensityParser
Set the spot intensity parser for the section. -
getExtraFloatParsers
Get the list of extra value parsers that exists for this section. -
addExtraFloatParser
Add an extra value parser to this section.
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