ProgressMeter (gatk 4.2.0.0 API)

java.lang.Object
- org.broadinstitute.hellbender.engine.ProgressMeter

```
public final class ProgressMeter
extends java.lang.Object
```
A basic progress meter to print out the number of records processed (and other metrics) during a traversal at a configurable time interval. Clients set the update interval at construction, which controls how many seconds must elapse before printing an update. Then call start() at traversal start, update(Locatable) after processing each record from the primary input, and stop() at traversal end to print summary statistics. Note that start() must only be called once, before any update(Locatable). Note no update(Locatable) must be called after stop(). All output is made at INFO level via log4j.

Field Summary

Fields
Modifier and Type	Field and Description
`static java.lang.String`	`DEFAULT_RECORD_LABEL` Default label for records in logger messages.
`static long`	`DEFAULT_RECORDS_BETWEEN_TIME_CHECKS` We check the current time every time we process this many records, by default (to cut down on the number of system calls)
`static double`	`DEFAULT_SECONDS_BETWEEN_UPDATES` By default, we output a line to the logger after this many seconds have elapsed
`static java.util.function.LongSupplier`	`DEFAULT_TIME_FUNCTION` By default, we use this function to get the current time
`protected static org.apache.logging.log4j.Logger`	`logger`
`static long`	`MILLISECONDS_PER_MINUTE` Number of milliseconds in a minute
`static long`	`MILLISECONDS_PER_SECOND` Number of milliseconds in a second

Constructor Summary

Constructors
Constructor and Description
`ProgressMeter()` Create a progress meter with the default update interval of `DEFAULT_SECONDS_BETWEEN_UPDATES` seconds and the default time function `DEFAULT_TIME_FUNCTION`.
`ProgressMeter(double secondsBetweenUpdates)` Create a progress meter with a custom update interval and the default time function `DEFAULT_TIME_FUNCTION`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`setRecordLabel(java.lang.String label)` Change the label used for records in logger messages.
`void`	`setRecordsBetweenTimeChecks(long recordsBetweenTimeChecks)` Set the number of records we need to process before we check the current time
`void`	`start()` Start the progress meter and produce preliminary output such as column headings.
`boolean`	`started()` Returns whether the meter has been started.
`void`	`stop()` Stop the progress meter and output summary statistics to the logger
`boolean`	`stopped()` Returns whether the meter has been stopped.
`void`	`update(htsjdk.samtools.util.Locatable currentLocus)` Signal to the progress meter that an additional record has been processed.
`void`	`update(htsjdk.samtools.util.Locatable currentLocus, long recordCountIncrease)` Signal to the progress meter that several additional records hav been processed.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - logger
```
protected static final org.apache.logging.log4j.Logger logger
```
  - DEFAULT_SECONDS_BETWEEN_UPDATES
```
public static final double DEFAULT_SECONDS_BETWEEN_UPDATES
```
    By default, we output a line to the logger after this many seconds have elapsed
    
    See Also:
    
    Constant Field Values
  - DEFAULT_RECORDS_BETWEEN_TIME_CHECKS
```
public static final long DEFAULT_RECORDS_BETWEEN_TIME_CHECKS
```
    We check the current time every time we process this many records, by default (to cut down on the number of system calls)
    
    See Also:
    
    Constant Field Values
  - DEFAULT_TIME_FUNCTION
```
public static final java.util.function.LongSupplier DEFAULT_TIME_FUNCTION
```
    By default, we use this function to get the current time
  - MILLISECONDS_PER_SECOND
```
public static final long MILLISECONDS_PER_SECOND
```
    Number of milliseconds in a second
    
    See Also:
    
    Constant Field Values
  - MILLISECONDS_PER_MINUTE
```
public static final long MILLISECONDS_PER_MINUTE
```
    Number of milliseconds in a minute
    
    See Also:
    
    Constant Field Values
  - DEFAULT_RECORD_LABEL
```
public static final java.lang.String DEFAULT_RECORD_LABEL
```
    Default label for records in logger messages. For display purposes only.
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - ProgressMeter
```
public ProgressMeter()
```
    Create a progress meter with the default update interval of DEFAULT_SECONDS_BETWEEN_UPDATES seconds and the default time function DEFAULT_TIME_FUNCTION.
  - ProgressMeter
```
public ProgressMeter(double secondsBetweenUpdates)
```
    Create a progress meter with a custom update interval and the default time function DEFAULT_TIME_FUNCTION
    
    Parameters:
    
    secondsBetweenUpdates - number of seconds that should elapse before outputting a line to the logger
- Method Detail
  - setRecordsBetweenTimeChecks
```
public void setRecordsBetweenTimeChecks(long recordsBetweenTimeChecks)
```
    Set the number of records we need to process before we check the current time
    
    Parameters:
    
    recordsBetweenTimeChecks - number of records we need to process before we check the current time
  - setRecordLabel
```
public void setRecordLabel(java.lang.String label)
```
    Change the label used for records in logger messages. Default label is DEFAULT_RECORD_LABEL
    
    Parameters:
    
    label - Label to use for records in logger messages. Not null.
  - start
```
public void start()
```
    Start the progress meter and produce preliminary output such as column headings.
    
    Throws:
    
    java.lang.IllegalStateException - if the meter has been started before or has been stopped already
  - update
```
public void update(htsjdk.samtools.util.Locatable currentLocus)
```
    Signal to the progress meter that an additional record has been processed. Will output statistics to the logger roughly every secondsBetweenUpdates seconds.
    
    Parameters:
    
    currentLocus - the genomic location of the record just processed or null if the most recent record had no location.
    
    Throws:
    
    java.lang.IllegalStateException - if the meter has not been started yet or has been stopped already
  - update
```
public void update(htsjdk.samtools.util.Locatable currentLocus,
                   long recordCountIncrease)
```
    Signal to the progress meter that several additional records hav been processed. Will output statistics to the logger roughly every secondsBetweenUpdates seconds.
    
    Parameters:
    
    currentLocus - the genomic location of the last record just processed or null if the most recent record had no location.
    
    recordCountIncrease - number of new records processed.
    
    Throws:
    
    java.lang.IllegalStateException - if the meter has not been started yet or has been stopped already
  - stop
```
public void stop()
```
    Stop the progress meter and output summary statistics to the logger
    
    Throws:
    
    java.lang.IllegalStateException - if the meter has not been started yet or has been stopped already
  - started
```
public boolean started()
```
    Returns whether the meter has been started. It returns false before the call to start() and true forever after.
  - stopped
```
public boolean stopped()
```
    Returns whether the meter has been stopped. It returns false before the call to stop() and true forever after.

Class ProgressMeter

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

logger

DEFAULT_SECONDS_BETWEEN_UPDATES

DEFAULT_RECORDS_BETWEEN_TIME_CHECKS

DEFAULT_TIME_FUNCTION

MILLISECONDS_PER_SECOND

MILLISECONDS_PER_MINUTE

DEFAULT_RECORD_LABEL

Constructor Detail

ProgressMeter

ProgressMeter

Method Detail

setRecordsBetweenTimeChecks

setRecordLabel

start

update

update

stop

started

stopped