Package ubic.gemma.core.analysis.service

Class ExpressionDataFileUtils

java.lang.Object

ubic.gemma.core.analysis.service.ExpressionDataFileUtils

public class ExpressionDataFileUtils
extends Object

Generate filenames for various types of data files.

Author:

poirigui

Field Summary

Fields

Modifier and Type	Field	Description
static final String	CELL_BROWSER_SC_DATA_SUFFIX
static final String	CELL_BROWSER_SC_METADATA_SUFFIX
static final String	JSON_BULK_DATA_FILE_SUFFIX
static final String	MEX_SC_DATA_SUFFIX
static final String	TABULAR_BULK_DATA_FILE_SUFFIX
static final String	TABULAR_SC_DATA_SUFFIX

Constructor Summary

Constructors

Constructor	Description
ExpressionDataFileUtils()

Method Summary

Modifier and Type	Method	Description
static String	formatBioAssayFilename(BioAssay ba)
static String	getCoexpressionDataFilename(ExpressionExperiment ee)	Obtain the filename for writing coexpression data.
static String	getDataOutputFilename(ExpressionExperiment ee, boolean filtered, String suffix)	Obtain a filename for writing the processed data.
static String	getDataOutputFilename(ExpressionExperiment ee, List<BioAssay> assays, boolean filtered, String suffix)
static String	getDataOutputFilename(ExpressionExperiment ee, List<BioAssay> assays, QuantitationType type, String suffix)	Obtain the filename for writing a specific QT.
static String	getDataOutputFilename(ExpressionExperiment ee, QuantitationType type, String suffix)	Obtain the filename for writing a specific QT.
static String	getDesignFileName(ExpressionExperiment ee)
static String	getDiffExArchiveFileName(DifferentialExpressionAnalysis diff)
static String	getEigenGenesFilename(ExpressionExperiment ee)
static String	getExpressionExperimentMetadataDirname(ExpressionExperiment ee)	Forms a folder name where the given experiments metadata will be located (within the ${gemma.appdata.home}/metadata directory).
static String	getMeanVarianceRelationFilename(ExpressionExperiment ee)
static String	getMetadataOutputFilename(ExpressionExperiment ee, QuantitationType qt, String suffix)

Methods inherited from class java.lang.Object

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

Field Details

MEX_SC_DATA_SUFFIX

public static final String MEX_SC_DATA_SUFFIX

See Also:

• Constant Field Values

TABULAR_SC_DATA_SUFFIX

public static final String TABULAR_SC_DATA_SUFFIX

See Also:

• Constant Field Values

CELL_BROWSER_SC_DATA_SUFFIX

public static final String CELL_BROWSER_SC_DATA_SUFFIX

See Also:

• Constant Field Values

CELL_BROWSER_SC_METADATA_SUFFIX

public static final String CELL_BROWSER_SC_METADATA_SUFFIX

See Also:

• Constant Field Values

TABULAR_BULK_DATA_FILE_SUFFIX

public static final String TABULAR_BULK_DATA_FILE_SUFFIX

See Also:

• Constant Field Values

JSON_BULK_DATA_FILE_SUFFIX

public static final String JSON_BULK_DATA_FILE_SUFFIX

See Also:

• Constant Field Values

Constructor Details

ExpressionDataFileUtils

public ExpressionDataFileUtils()

Method Details

getDataOutputFilename

public static String getDataOutputFilename(ExpressionExperiment ee,
 boolean filtered,
 String suffix)

Obtain a filename for writing the processed data.

getDataOutputFilename

public static String getDataOutputFilename(ExpressionExperiment ee,
 List<BioAssay> assays,
 boolean filtered,
 String suffix)

getDataOutputFilename

public static String getDataOutputFilename(ExpressionExperiment ee,
 QuantitationType type,
 String suffix)

Obtain the filename for writing a specific QT.

getDataOutputFilename

public static String getDataOutputFilename(ExpressionExperiment ee,
 List<BioAssay> assays,
 QuantitationType type,
 String suffix)

Obtain the filename for writing a specific QT.

getMetadataOutputFilename

public static String getMetadataOutputFilename(ExpressionExperiment ee,
 QuantitationType qt,
 String suffix)

getCoexpressionDataFilename

public static String getCoexpressionDataFilename(ExpressionExperiment ee)

Obtain the filename for writing coexpression data.

getDesignFileName

public static String getDesignFileName(ExpressionExperiment ee)

getDiffExArchiveFileName

public static String getDiffExArchiveFileName(DifferentialExpressionAnalysis diff)

getMeanVarianceRelationFilename

public static String getMeanVarianceRelationFilename(ExpressionExperiment ee)

getEigenGenesFilename

public static String getEigenGenesFilename(ExpressionExperiment ee)

getExpressionExperimentMetadataDirname

public static String getExpressionExperimentMetadataDirname(ExpressionExperiment ee)

Forms a folder name where the given experiments metadata will be located (within the ${gemma.appdata.home}/metadata directory).

formatBioAssayFilename

public static String formatBioAssayFilename(BioAssay ba)