Package ubic.gemma.core.analysis.service

Class ExpressionAnalysisResultSetFileServiceImpl

java.lang.Object

ubic.gemma.core.analysis.service.AbstractFileService<ExpressionAnalysisResultSet>

ubic.gemma.core.analysis.service.ExpressionAnalysisResultSetFileServiceImpl

All Implemented Interfaces:

ExpressionAnalysisResultSetFileService, FileService<ExpressionAnalysisResultSet>, JsonFileService<ExpressionAnalysisResultSet>, TsvFileService<ExpressionAnalysisResultSet>

@Service
public class ExpressionAnalysisResultSetFileServiceImpl
extends AbstractFileService<ExpressionAnalysisResultSet>
implements ExpressionAnalysisResultSetFileService

Constructor Summary

Constructors

Constructor	Description
ExpressionAnalysisResultSetFileServiceImpl()

Method Summary

Modifier and Type	Method	Description
void	writeTsv(ExpressionAnalysisResultSet entity, Writer writer)	Write the analysis result set to an Appendable using a tabular format.
void	writeTsv(ExpressionAnalysisResultSet analysisResultSet, Baseline baseline, Map<Long,List<Gene>> resultId2Genes, Writer appendable)	Write the analysis result set with result-to-gene mappings.

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

ExpressionAnalysisResultSetFileServiceImpl

public ExpressionAnalysisResultSetFileServiceImpl()

Method Detail

writeTsv

public void writeTsv(ExpressionAnalysisResultSet entity,
                     Writer writer)
              throws IOException

Description copied from interface: ExpressionAnalysisResultSetFileService

Write the analysis result set to an Appendable using a tabular format.

The format is borrowed from ExpressionDataFileService and contains the following columns:

- result id - probe id - probe name - pvalue - corrected pvalue (a.k.a. qvalue) - rank Then for each contrast, a column with the contrast_ prefix: - coefficient - log2 fold-change - t statistic - pvalue

Specified by:

writeTsv in interface ExpressionAnalysisResultSetFileService

Specified by:

writeTsv in interface TsvFileService<ExpressionAnalysisResultSet>

Throws:

IOException

writeTsv

public void writeTsv(ExpressionAnalysisResultSet analysisResultSet,
                     @Nullable
                     Baseline baseline,
                     Map<Long,List<Gene>> resultId2Genes,
                     Writer appendable)
              throws IOException

Description copied from interface: ExpressionAnalysisResultSetFileService

Write the analysis result set with result-to-gene mappings.

The tabular format has the following additional columns: - gene id - gene name - gene NCBI ID - gene official symbol - gene official name

Specified by:

writeTsv in interface ExpressionAnalysisResultSetFileService

baseline - baseline to include in the TSV header

resultId2Genes - mapping of results to genes

Throws:

IOException