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

Class ExperimentalDesignWriter

java.lang.Object

ubic.gemma.core.datastructure.matrix.io.ExperimentalDesignWriter

public class ExperimentalDesignWriter
extends Object

Output compatible with ExperimentalDesignImporterImpl.

Author:

keshav

See Also:

• ExperimentalDesignImporterImpl

Constructor Summary

Constructors

Constructor	Description
ExperimentalDesignWriter(EntityUrlBuilder entityUrlBuilder, BuildInfo buildInfo, boolean autoFlush)

Method Summary

Modifier and Type	Method	Description
void	setSeparateSampleFromAssaysIdentifiers(boolean separateSampleFromAssaysIdentifiers)	If true, write the sample identifier and the assay(s) identifiers in separate columns.
void	setUseBioAssayIds(boolean useBioAssayIds)	If true, use the IDs of the BioAssays (and BioMaterials.
void	setUseMultipleRowsForAssays(boolean useMultipleRowsForAssays)	Write assays over multiple rows.
void	setUseRawColumnNames(boolean useRawColumnNames)	If true, use column names as they appear in the database.
void	write(ExpressionExperiment ee, Writer writer)	Write the experimental design of the given ExpressionExperiment to the given Writer.
void	write(ExpressionExperiment ee, QuantitationType quantitationType, Class<? extends DataVector> vectorType, Collection<BioAssay> bioAssays, boolean writeBaseHeader, Writer writer)	Write the experimental design of the given ExpressionExperiment to the given Writer for a given collection of assays.

Methods inherited from class java.lang.Object

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

Constructor Details

ExperimentalDesignWriter

public ExperimentalDesignWriter(EntityUrlBuilder entityUrlBuilder,
 BuildInfo buildInfo,
 boolean autoFlush)

Method Details

write

public void write(ExpressionExperiment ee,
 Writer writer)
           throws IOException

Write the experimental design of the given ExpressionExperiment to the given Writer.

Throws:

IOException

See Also:

• write(ExpressionExperiment, QuantitationType, Class, Collection, boolean, Writer)

write

public void write(ExpressionExperiment ee,
 @Nullable
 QuantitationType quantitationType,
 @Nullable
 Class<? extends DataVector> vectorType,
 Collection<BioAssay> bioAssays,
 boolean writeBaseHeader,
 Writer writer)
           throws IOException

Write the experimental design of the given ExpressionExperiment to the given Writer for a given collection of assays.

Parameters:

ee - experiment for which the design is being written

quantitationType - the quantitation type for which the experimental design is being written, or null if not applicable. You want to use this when writing the design for a specific QT that might be applicable to a subset or sub-assays.

vectorType - if a quantitation type is supplied, this indicate the type of data vectors

bioAssays - assays to write, the order is defined by the order of their corresponding biomaterials as per BioMaterial.COMPARATOR.

writeBaseHeader - whether to write the base header (experiment URL, build info, etc.), see ExpressionDataWriterUtils.appendBaseHeader(ExpressionExperiment, String, String, BuildInfo, Date, Writer) for details

Throws:

IOException

setUseMultipleRowsForAssays

public void setUseMultipleRowsForAssays(boolean useMultipleRowsForAssays)

Write assays over multiple rows.

This simplifies merging the experimental design with the expression data as the "Bioassay" column will match exactly the columns of the matrix written by MatrixWriter.

If separating identifiers with separateSampleFromAssaysIdentifiers, MatrixWriter.setExcludeSampleIdentifiers(boolean) can be used to match the "Assay" column instead.

setSeparateSampleFromAssaysIdentifiers

public void setSeparateSampleFromAssaysIdentifiers(boolean separateSampleFromAssaysIdentifiers)

If true, write the sample identifier and the assay(s) identifiers in separate columns.

The column will be named "Sample" and "Assays" respectively. If useMultipleRowsForAssays is true, the assay column will be named "Assay".

The default column name for mangled sample and assay identifiers is "Bioassay".

setUseBioAssayIds

public void setUseBioAssayIds(boolean useBioAssayIds)

If true, use the IDs of the BioAssays (and BioMaterials.

setUseRawColumnNames

public void setUseRawColumnNames(boolean useRawColumnNames)

If true, use column names as they appear in the database.