Package ubic.gemma.core.analysis.service

Interface DifferentialExpressionAnalysisResultListFileService

All Superinterfaces:

FileService<List<DifferentialExpressionAnalysisResult>>, TsvFileService<List<DifferentialExpressionAnalysisResult>>

All Known Implementing Classes:

DifferentialExpressionAnalysisResultListFileServiceImpl

public interface DifferentialExpressionAnalysisResultListFileService
extends TsvFileService<List<DifferentialExpressionAnalysisResult>>

File service for arbitrary list of DifferentialExpressionAnalysisResult.

Use DifferentialExpressionAnalysisResultListFileService for producing results from a single result set.

Author:

poirigui

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> payload, 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 interface ubic.gemma.core.analysis.service.FileService

write, write

Method Detail

writeTsv

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

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 TsvFileService<List<DifferentialExpressionAnalysisResult>>

Throws:

IOException

writeTsv

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

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

Throws:

IOException