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java.lang.Object net.sf.basedb.util.importer.spotdata.GenericIntensityParser
public class GenericIntensityParser
Generic spot intensity parser implementation that looks for 'intensity1', ..., 'intensityN' data columns for any number of channels.
Field Summary | |
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private int |
channels
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private int[] |
index
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Constructor Summary | |
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GenericIntensityParser(int channels)
Creates a new parser for the specified number of channels. |
Method Summary | |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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private final int channels
private int[] index
Constructor Detail |
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public GenericIntensityParser(int channels)
Method Detail |
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public boolean hasRequiredAssayFields(BaseFileParser parser, FlatFileParser ffp, List<String> assayFields)
SpotIntensityParser
hasRequiredAssayFields
in interface SpotIntensityParser
parser
- The master BASEfile parserffp
- The flat file parser that parses the current fileassayFields
- The list of assay fields
public void beginSection(BaseFileParser parser, FlatFileParser ffp, List<String> assayFields)
SpotIntensityParser
beginSection
in interface SpotIntensityParser
parser
- The master BASEfile parserffp
- The flat file parser that parses the current fileassayFields
- The list of assay fieldspublic boolean setIntensities(FlatFileParser.Data data, float[] intensities, int firstIndex)
SpotIntensityParser
setIntensities
in interface SpotIntensityParser
data
- The current data lineintensities
- An array that should be populate with intensity valuesfirstIndex
- The index of the first data column that contains data
for the current bioassay
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