htsjdk.samtools.util

Class AbstractProgressLogger

java.lang.Object

htsjdk.samtools.util.AbstractProgressLogger

All Implemented Interfaces:

ProgressLoggerInterface

Direct Known Subclasses:

ProgressLogger

public abstract class AbstractProgressLogger
extends java.lang.Object
implements ProgressLoggerInterface

Abstract implementation of a Little progress logging class to facilitate consistent output of useful information when progressing through a stream of SAM records. Concrete subclasses must provide the logger

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractProgressLogger(java.lang.String noun, java.lang.String verb, int n) Construct an AbstractProgressLogger.

Method Summary

Modifier and Type	Method and Description
long	getCount() Returns the count of records processed.
long	getElapsedSeconds() Returns the number of seconds since progress tracking began.
protected abstract void	log(java.lang.String... message) Log a message to whatever logger is being used
boolean	record(SAMRecord... recs) Records multiple SAMRecords and triggers logging if necessary.
boolean	record(SAMRecord rec) Records that a given record has been processed and triggers logging if necessary.
boolean	record(java.lang.String chrom, int pos)

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractProgressLogger

protected AbstractProgressLogger(java.lang.String noun,
                                 java.lang.String verb,
                                 int n)

Construct an AbstractProgressLogger. This must be called by any subclasses

Parameters:

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"

Method Detail

log

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

Log a message to whatever logger is being used

Parameters:

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

record

public boolean record(java.lang.String chrom,
                      int pos)

Specified by:

record in interface ProgressLoggerInterface

record

public boolean record(SAMRecord rec)

Records that a given record has been processed and triggers logging if necessary.

Specified by:

record in interface ProgressLoggerInterface

Returns:

boolean true if logging was triggered, false otherwise

record

public boolean record(SAMRecord... recs)

Records multiple SAMRecords and triggers logging if necessary.

Specified by:

record in interface ProgressLoggerInterface

getCount

public long getCount()

Returns the count of records processed.

getElapsedSeconds

public long getElapsedSeconds()

Returns the number of seconds since progress tracking began.