Package ubic.gemma.core.util

Class TsvUtils

java.lang.Object

ubic.gemma.core.util.TsvUtils

public class TsvUtils
extends Object

Bunch of utilities for writing data to TSV.

Author:

poirigui

Field Summary

Fields

Modifier and Type	Field	Description
static final char	COMMENT
static final String	NA	Indicator used for a missing value (e.g.
static final char	SUB_DELIMITER	Delimiter used when printing a list of strings in a column.
static final String	SUB_DELIMITER_STR

Constructor Summary

Constructors

Constructor	Description
TsvUtils()

Method Summary

Modifier and Type	Method	Description
static void	appendBaseHeader(String what, BuildInfo buildInfo, Date timestamp, Writer buf)	Append a base header to a file.
static String	format(double d)
static String	format(int i)
static String	format(long l)
static String	format(Double d)	Format a Double for TSV.
static String	format(Integer i)
static String	format(Long l)
static String	format(Object object)
static String	format(String s)	Format a String for TSV.
static String	format(String[] values)	Join multiple values into a single string, separated by the SUB_DELIMITER.
static String	format(Collection<String> values)
static String	format(Date d)
static String	formatComment(String comment)	Format a string as a TSV comment.
static String	formatComment(String format, Object... args)
static String	formatFast(double value)	Quickly format a double value.
static String	formatFast(float value)
static String	formatFast(int value)
static String	formatFast(long value)
static org.apache.commons.csv.CSVFormat.Builder	getTsvFormatBuilder(String what, BuildInfo buildInfo, Date timestamp, String... extraHeaderComments)	Preconfigure a CSVFormat.Builder with desirable defaults.o
static Boolean	parseBoolean(String val)
static double	parseDouble(String val)
static Integer	parseInt(String val)
static Long	parseLong(String val)

Methods inherited from class java.lang.Object

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

Field Details

COMMENT

public static final char COMMENT

See Also:

• Constant Field Values

SUB_DELIMITER

public static final char SUB_DELIMITER

Delimiter used when printing a list of strings in a column.

When replacing the delimiter in a value, the occurrences of the delimiter itself should be replaced with an '_'. This is done automatically in format(String[]) and format(Collection).

See Also:

• Constant Field Values

SUB_DELIMITER_STR

public static final String SUB_DELIMITER_STR

NA

public static final String NA

Indicator used for a missing value (e.g. NaN or null) in a TSV file.

See Also:

• Constant Field Values

Constructor Details

TsvUtils

public TsvUtils()

Method Details

appendBaseHeader

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

Append a base header to a file.

Parameters:

what - a short description of what data is being written

buildInfo - build information to include in the header

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

Throws:

IOException

getTsvFormatBuilder

public static org.apache.commons.csv.CSVFormat.Builder getTsvFormatBuilder(String what,
 BuildInfo buildInfo,
 Date timestamp,
 String... extraHeaderComments)

Preconfigure a CSVFormat.Builder with desirable defaults.o

The format will include a header as per appendBaseHeader(String, BuildInfo, Date, Writer).

Parameters:

what - a short description of what data is being written

buildInfo - build information to include in the header

extraHeaderComments - additional header comments that will be included at the top of the TSV file, right after the Constants.GEMMA_CITATION_NOTICE and Constants.GEMMA_LICENSE_NOTICE

parseDouble

public static double parseDouble(@Nullable
 String val)

parseLong

@Nullable
public static Long parseLong(@Nullable
 String val)

parseInt

@Nullable
public static Integer parseInt(@Nullable
 String val)

parseBoolean

@Nullable
public static Boolean parseBoolean(@Nullable
 String val)

format

public static String format(@Nullable
 String[] values)

Join multiple values into a single string, separated by the SUB_DELIMITER.

If the delimiter appears in a value, it will be replaced with a _ character.

format

public static String format(@Nullable
 Collection<String> values)

format

public static 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

format

public static String format(double d)

format

public static String format(@Nullable
 Integer i)

format

public static String format(int i)

format

public static String format(@Nullable
 Long l)

format

public static String format(long l)

format

public static String format(@Nullable
 String s)

Format a String for TSV.

format

public static String format(@Nullable
 Date d)

format

public static String format(@Nullable
 Object object)

formatFast

public static String formatFast(double value)

Quickly format a double value.

If writing a large number of doubles, format(double) is usually way too slow. This method will use Java's native number formatting instead.

formatFast

public static String formatFast(float value)

formatFast

public static String formatFast(long value)

formatFast

public static String formatFast(int value)

formatComment

public static String formatComment(@Nullable
 String comment)

Format a string as a TSV comment.

This will prepend a COMMENT on each line that do not start with the character.

formatComment

public static String formatComment(String format,
 Object... args)