htsjdk.samtools.util

Class ProgressLogger

java.lang.Object

htsjdk.samtools.util.AbstractProgressLogger

htsjdk.samtools.util.ProgressLogger

All Implemented Interfaces:

ProgressLoggerInterface

public class ProgressLogger
extends AbstractProgressLogger

Little progress logging class to facilitate consistent output of useful information when progressing through a stream of SAM records.

Constructor Summary

Constructors

Constructor and Description
ProgressLogger(Log log) Construct a progress logger with the desired log, the verb "Processed" and a period of 1m records.
ProgressLogger(Log log, int n) Construct a progress logger with the desired log and frequency and the verb "Processed".
ProgressLogger(Log log, int n, java.lang.String verb) Construct a progress logger.
ProgressLogger(Log log, int n, java.lang.String verb, java.lang.String noun) Construct a progress logger.

Method Summary

Modifier and Type	Method and Description
protected void	log(java.lang.String... message) Log a message to whatever logger is being used

Methods inherited from class htsjdk.samtools.util.AbstractProgressLogger

getCount, getElapsedSeconds, record, record, record

Methods inherited from class java.lang.Object

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

Constructor Detail

ProgressLogger

public ProgressLogger(Log log,
                      int n,
                      java.lang.String verb,
                      java.lang.String noun)

Construct a progress logger.

Parameters:

log - the Log object to write outputs to

n - the frequency with which to output (i.e. every N records)

verb - the verb to log, e.g. "Processed, Read, Written".

noun - the noun to use when logging, e.g. "Records, Variants, Loci"

ProgressLogger

public ProgressLogger(Log log,
                      int n,
                      java.lang.String verb)

Construct a progress logger.

Parameters:

log - the Log object to write outputs to

n - the frequency with which to output (i.e. every N records)

verb - the verb to log, e.g. "Processed, Read, Written".

ProgressLogger

public ProgressLogger(Log log,
                      int n)

Construct a progress logger with the desired log and frequency and the verb "Processed".

Parameters:

log - the Log object to write outputs to

n - the frequency with which to output (i.e. every N records)

ProgressLogger

public ProgressLogger(Log log)

Construct a progress logger with the desired log, the verb "Processed" and a period of 1m records.

Parameters:

log - the Log object to write outputs to

Method Detail

log

protected void log(java.lang.String... message)

Description copied from class: AbstractProgressLogger

Log a message to whatever logger is being used

Specified by:

log in class AbstractProgressLogger

Parameters:

message - a message to be logged by the logger (recommended output level is INFO or the equivalent)