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java.lang.Object net.sf.basedb.util.importer.spotdata.MAParser
public class MAParser
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)
.
Field Summary | |
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private static String |
aColumn
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private int |
aIndex
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private static String |
mColumn
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private int |
mIndex
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Constructor Summary | |
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MAParser()
Creates a new MA-parser. |
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 int mIndex
private int aIndex
private static final String mColumn
private static final String aColumn
Constructor Detail |
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public MAParser()
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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