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 String	JSON_BULK_DATA_FILE_SUFFIX
static String	MEX_SC_DATA_SUFFIX
static String	TABULAR_BULK_DATA_FILE_SUFFIX
static String	TABULAR_SC_DATA_SUFFIX

Constructor Summary

Constructors

Constructor	Description
ExpressionDataFileUtils()

Method Summary

Modifier and Type	Method	Description
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	getEEFolderName(ExpressionExperiment ee)	Forms a folder name where the given experiments metadata will be located (within the #metadataDir directory).
static String	getEigenGenesFilename(ExpressionExperiment ee)
static String	getMeanVarianceRelationFilename(ExpressionExperiment ee)

Methods inherited from class java.lang.Object

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

Field Detail

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

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 Detail

ExpressionDataFileUtils

public ExpressionDataFileUtils()

Method Detail

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.

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)

getEEFolderName

public static String getEEFolderName(ExpressionExperiment ee)

Forms a folder name where the given experiments metadata will be located (within the #metadataDir directory).

Parameters:

ee - the experiment to get the folder name for.

Returns:

folder name based on the given experiments properties. Usually this will be the experiments short name, without any splitting suffixes (e.g. for GSE123.1 the folder name would be GSE123). If the short name is empty for any reason, the experiments ID will be used.