Package ubic.gemma.core.datastructure.matrix.io

Class ExpressionDataWriterUtils

java.lang.Object

ubic.gemma.core.datastructure.matrix.io.ExpressionDataWriterUtils

public class ExpressionDataWriterUtils
extends Object

Utilities for writing expression data files.

Author:

keshav

Constructor Summary

Constructors

Constructor	Description
ExpressionDataWriterUtils()

Method Summary

Modifier and Type	Method	Description
static void	appendBaseHeader(String fileTypeStr, BuildInfo buildInfo, Date timestamp, Writer buf)
static void	appendBaseHeader(ExpressionExperiment experiment, String fileTypeStr, String experimentUrl, BuildInfo buildInfo, Date timestamp, Writer buf)	Appends base header information (about the experiment) to a file.
static void	appendBaseHeader(ExpressionExperiment experiment, QuantitationType quantitationType, Class<? extends DataVector> dataVectorType, String fileTypeStr, String experimentUrl, BuildInfo buildInfo, Date timestamp, Writer buf)	Append base header information (about the experiment) to a file with some information about the quantitation type.
static String	constructAssayName(BioAssay ba, boolean useIds, boolean useRawColumnNames)	Construct a BioAssay column name, unprefixed by the BioMaterial from which it originates.
static String	constructAssaysName(Collection<BioAssay> bas, boolean useIds, boolean useRawColumnNames, char assayDelimiter)
static String	constructCellIdName(BioAssay ba, String cellId, boolean useBioAssayIds, boolean useRawColumnNames)	Construct a BioAssay column name, unprefixed by the BioMaterial from which it originates.
static String	constructExperimentalFactorName(ExperimentalFactor ef)	Construct an ExperimentalFactor column name.
static String[]	constructExperimentalFactorNames(List<ExperimentalFactor> factors)	Construct an ExperimentalFactor column names for a list of factors.
static String	constructSampleName(BioMaterial bioMaterial, boolean useIds, boolean useRawColumnNames)
static String	constructSampleName(BioMaterial bioMaterial, Collection<BioAssay> bioAssays, boolean useIds, boolean useRawColumnNames, char assayDelimiter)	Construct a BioAssay column name prefixed by the BioMaterial from which it originates.
static String	constructSampleName(BioMaterial bm, BioAssay ba, boolean useIds, boolean useRawColumnNames)	Construct a sample name in case there is only one BioAssay attached to the corresponding BioMaterial.
static String	formatQuantitationType(QuantitationType quantitationType, Class<? extends DataVector> dataVectorType)

Methods inherited from class java.lang.Object

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

Constructor Details

ExpressionDataWriterUtils

public ExpressionDataWriterUtils()

Method Details

appendBaseHeader

public static void appendBaseHeader(String fileTypeStr,
 BuildInfo buildInfo,
 Date timestamp,
 Writer buf)
                             throws IOException

Throws:

IOException

appendBaseHeader

public static void appendBaseHeader(ExpressionExperiment experiment,
 String fileTypeStr,
 @Nullable
 String experimentUrl,
 BuildInfo buildInfo,
 Date timestamp,
 Writer buf)
                             throws IOException

Appends base header information (about the experiment) to a file.

Parameters:

experiment - ee

fileTypeStr - file type str

experimentUrl - an URL for the expriment, or null to omit

timestamp - timestamp to include in the header that reflect the time of file generation

buf - buffer

Throws:

IOException

appendBaseHeader

public static void appendBaseHeader(ExpressionExperiment experiment,
 QuantitationType quantitationType,
 Class<? extends DataVector> dataVectorType,
 String fileTypeStr,
 @Nullable
 String experimentUrl,
 BuildInfo buildInfo,
 Date timestamp,
 Writer buf)
                             throws IOException

Append base header information (about the experiment) to a file with some information about the quantitation type.

Throws:

IOException

formatQuantitationType

public static String formatQuantitationType(QuantitationType quantitationType,
 Class<? extends DataVector> dataVectorType)

constructSampleName

public static String constructSampleName(BioMaterial bm,
 BioAssay ba,
 boolean useIds,
 boolean useRawColumnNames)

Construct a sample name in case there is only one BioAssay attached to the corresponding BioMaterial.

See Also:

• constructSampleName(BioMaterial, Collection, boolean, boolean, char)

constructSampleName

public static String constructSampleName(BioMaterial bioMaterial,
 boolean useIds,
 boolean useRawColumnNames)

constructAssaysName

public static String constructAssaysName(Collection<BioAssay> bas,
 boolean useIds,
 boolean useRawColumnNames,
 char assayDelimiter)

constructSampleName

public static String constructSampleName(BioMaterial bioMaterial,
 Collection<BioAssay> bioAssays,
 boolean useIds,
 boolean useRawColumnNames,
 char assayDelimiter)

Construct a BioAssay column name prefixed by the BioMaterial from which it originates.

Parameters:

bioMaterial - the biomaterial

bioAssays - the bioassay(s) associated to the biomaterial

useIds - use biomaterial and bioassay IDs instead of names (or short names)

useRawColumnNames - do not clean up the names with StringUtil.makeNames(String) to make them R-friendly

assayDelimiter - the delimiter to use between bioassays, if that delimiter appears in the bioassay name, it will be replaced with a '_'. For this reason, this function does not allow '_' as a delimiter.

constructAssayName

public static String constructAssayName(BioAssay ba,
 boolean useIds,
 boolean useRawColumnNames)

Construct a BioAssay column name, unprefixed by the BioMaterial from which it originates.

constructCellIdName

public static String constructCellIdName(BioAssay ba,
 String cellId,
 boolean useBioAssayIds,
 boolean useRawColumnNames)

Construct a BioAssay column name, unprefixed by the BioMaterial from which it originates.

constructExperimentalFactorName

public static String constructExperimentalFactorName(ExperimentalFactor ef)

Construct an ExperimentalFactor column name.

See Also:

• StringUtil.makeNames(String)

constructExperimentalFactorNames

public static String[] constructExperimentalFactorNames(List<ExperimentalFactor> factors)

Construct an ExperimentalFactor column names for a list of factors.

See Also:

• StringUtil.makeNames(String[], boolean)