Package ubic.gemma.core.analysis.service

Class AbstractFileService<T>

java.lang.Object

ubic.gemma.core.analysis.service.AbstractFileService<T>

All Implemented Interfaces:

FileService<T>, JsonFileService<T>, TsvFileService<T>

Direct Known Subclasses:

ExpressionAnalysisResultSetFileServiceImpl, ExpressionDataFileServiceImpl, MatrixWriter

public abstract class AbstractFileService<T>
extends Object
implements TsvFileService<T>, JsonFileService<T>

Provide base implementation for all sorts of file services that serialize data in tabular format.

Constructor Summary

Constructors

Constructor	Description
AbstractFileService()

Method Summary

Modifier and Type	Method	Description
protected String	escapeTsv(String s)
protected String	format(Double d)	Format a Double for TSV.
protected String	getSubDelimiter()	Get the delimiter used within column.
protected org.apache.commons.csv.CSVFormat.Builder	getTsvFormatBuilder(String... extraHeaderComments)	Preconfigure a CSVFormat.Builder with desirable defaults.
void	write(T entity, File file, String contentType)
void	write(T entity, Writer writer, String contentType)	Write a given entity to an appendable with a given content type.
void	writeJson(T entity, File file)
void	writeJson(T entity, Writer writer)	Write a given entity to JSON.
void	writeTsv(T entity, File file)

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.gemma.core.analysis.service.TsvFileService

writeTsv

Constructor Detail

AbstractFileService

public AbstractFileService()

Method Detail

getTsvFormatBuilder

protected org.apache.commons.csv.CSVFormat.Builder getTsvFormatBuilder(String... extraHeaderComments)

Preconfigure a CSVFormat.Builder with desirable defaults.

Parameters:

extraHeaderComments - additional header comments that will be included at the top of the TSV file.

getSubDelimiter

protected String getSubDelimiter()

Get the delimiter used within column.

format

protected String format(@Nullable
                        Double d)

Format a Double for TSV.

Parameters:

d - a double to format

Returns:

a formatted double, an empty string if d is null or NaN or inf/-inf if infinite

escapeTsv

protected String escapeTsv(String s)

writeTsv

public void writeTsv(T entity,
                     File file)
              throws IOException

Specified by:

writeTsv in interface TsvFileService<T>

Throws:

IOException

writeJson

public void writeJson(T entity,
                      Writer writer)
               throws IOException

Description copied from interface: JsonFileService

Write a given entity to JSON.

Specified by:

writeJson in interface JsonFileService<T>

Throws:

IOException

writeJson

public void writeJson(T entity,
                      File file)
               throws IOException

Specified by:

writeJson in interface JsonFileService<T>

Throws:

IOException

write

public void write(T entity,
                  Writer writer,
                  String contentType)
           throws IOException

Description copied from interface: FileService

Write a given entity to an appendable with a given content type.

Specified by:

write in interface FileService<T>

Throws:

IOException

write

public void write(T entity,
                  File file,
                  String contentType)
           throws IOException

Specified by:

write in interface FileService<T>

Throws:

IOException