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

Class ExpressionDataWriterUtils

java.lang.Object

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

public class ExpressionDataWriterUtils
extends Object

Author:

keshav

Constructor Summary

Constructors

Constructor	Description
ExpressionDataWriterUtils()

Method Summary

Modifier and Type	Method	Description
static void	appendBaseHeader(String fileTypeStr, BuildInfo buildInfo, Writer buf)	Append a base header to a file.
static void	appendBaseHeader(ExpressionExperiment experiment, String fileTypeStr, String experimentUrl, BuildInfo buildInfo, Writer buf)	Appends base header information (about the experiment) to a file.
static String	constructFactorValueName(FactorValue factorValue)	Produce a value for representing a factor value.
static String	constructSampleExternalId(BioMaterial bioMaterial, Collection<BioAssay> bioAssays)
static String	constructSampleName(BulkExpressionDataMatrix<?> matrix, int assayColumnIndex)	Constructs a sample name for a given column of a data matrix.
static String	constructSampleName(BioMaterial bioMaterial, Collection<BioAssay> bioAssays)	Construct a BioAssay column name prefixed by the BioMaterial from which it originates.
static String	constructSampleName(BioMaterial bm, BioAssay ba)	Construct a sample name in case there is only one BioAssay attached to the corresponding BioMaterial.

Methods inherited from class java.lang.Object

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

Constructor Detail

ExpressionDataWriterUtils

public ExpressionDataWriterUtils()

Method Detail

appendBaseHeader

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

Append a base header to a file.

Throws:

IOException

appendBaseHeader

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

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

Parameters:

buf - buffer

fileTypeStr - file type str

experiment - ee

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

Throws:

IOException

constructSampleName

public static String constructSampleName(BulkExpressionDataMatrix<?> matrix,
                                         int assayColumnIndex)

Constructs a sample name for a given column of a data matrix.

Parameters:

matrix - matrix

assayColumnIndex - The column index in the matrix.

Returns:

BA name

constructSampleName

public static String constructSampleName(BioMaterial bm,
                                         BioAssay ba)

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

constructSampleName

public static String constructSampleName(BioMaterial bioMaterial,
                                         Collection<BioAssay> bioAssays)

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

constructFactorValueName

public static String constructFactorValueName(FactorValue factorValue)

Produce a value for representing a factor value.

In the context of the design file, this is focusing on the value (i.e. subjects or measurement value) itself and not its metadata which are instead exposed in the file header.

Replaces spaces and hyphens with underscores.

Parameters:

factorValue - FV

Returns:

replaced string

constructSampleExternalId

public static String constructSampleExternalId(BioMaterial bioMaterial,
                                               Collection<BioAssay> bioAssays)

Parameters:

bioAssays - BAs

bioMaterial - BM

Returns:

String representing the external identifier of the biomaterial. This will usually be a GEO or ArrayExpression accession id, or else blank.