Package ubic.gemma.core.analysis.service

Class DifferentialExpressionAnalysisResultListFileServiceImpl

java.lang.Object

ubic.gemma.core.analysis.service.AbstractFileService<List<DifferentialExpressionAnalysisResult>>

ubic.gemma.core.analysis.service.DifferentialExpressionAnalysisResultListFileServiceImpl

All Implemented Interfaces:

DifferentialExpressionAnalysisResultListFileService, FileService<List<DifferentialExpressionAnalysisResult>>, JsonFileService<List<DifferentialExpressionAnalysisResult>>, TsvFileService<List<DifferentialExpressionAnalysisResult>>

@Service
public class DifferentialExpressionAnalysisResultListFileServiceImpl
extends AbstractFileService<List<DifferentialExpressionAnalysisResult>>
implements DifferentialExpressionAnalysisResultListFileService

Constructor Summary

Constructors

Constructor	Description
DifferentialExpressionAnalysisResultListFileServiceImpl()

Method Summary

Modifier and Type	Method	Description
void	writeTsv(List<DifferentialExpressionAnalysisResult> entity, Writer writer)	Write the given entity to tabular format.
void	writeTsv(List<DifferentialExpressionAnalysisResult> entity, Gene gene, Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap, Writer writer)	Writes a list of DE results with additional columns for mapping them to source experiments and analyzed experiments (for subsets).

Methods inherited from class ubic.gemma.core.analysis.service.AbstractFileService

escapeTsv, format, getSubDelimiter, getTsvFormatBuilder, write, write, writeJson

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.gemma.core.analysis.service.FileService

write, write

Constructor Detail

DifferentialExpressionAnalysisResultListFileServiceImpl

public DifferentialExpressionAnalysisResultListFileServiceImpl()

Method Detail

writeTsv

public void writeTsv(List<DifferentialExpressionAnalysisResult> entity,
                     Writer writer)
              throws IOException

Description copied from interface: DifferentialExpressionAnalysisResultListFileService

Write the given entity to tabular format.

The format is similar to ExpressionAnalysisResultSetFileService.writeTsv(ExpressionAnalysisResultSet, Writer) except for how contrasts are encoded.

Because results may originate from different result sets, the contrasts are mangled into a single column in the tabular output and a column is added for the result set ID.

Specified by:

writeTsv in interface DifferentialExpressionAnalysisResultListFileService

Specified by:

writeTsv in interface TsvFileService<List<DifferentialExpressionAnalysisResult>>

Throws:

IOException

writeTsv

public void writeTsv(List<DifferentialExpressionAnalysisResult> entity,
                     Gene gene,
                     Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap,
                     Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap,
                     Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap,
                     Writer writer)
              throws IOException

Description copied from interface: DifferentialExpressionAnalysisResultListFileService

Writes a list of DE results with additional columns for mapping them to source experiments and analyzed experiments (for subsets).

The following additional columns are added: - source experiment ID - experiment analyzed ID

Specified by:

writeTsv in interface DifferentialExpressionAnalysisResultListFileService

Throws:

IOException