MetricsFile

java.lang.Object
- htsjdk.samtools.metrics.MetricsFile<BEAN,HKEY>

All Implemented Interfaces:

java.io.Serializable
```
public class MetricsFile<BEAN extends MetricBase,HKEY extends java.lang.Comparable>
extends java.lang.Object
implements java.io.Serializable
```
Contains a set of metrics that can be written to a file and parsed back again. The set of metrics is composed of zero or more instances of a class, BEAN, that extends MetricBase (all instances must be of the same type) and may optionally include one or more histograms that share the same key set.

See Also:
Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`static java.lang.String`	`HISTO_HEADER`
`static java.lang.String`	`MAJOR_HEADER_PREFIX`
`static java.lang.String`	`METRIC_HEADER`
`static java.lang.String`	`MINOR_HEADER_PREFIX`
`static java.lang.String`	`SEPARATOR`

Constructor Summary

Constructors
Constructor and Description

MetricsFile()

Constructors
Constructor and Description
`MetricsFile()`

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`addAllMetrics(java.lang.Iterable<BEAN> beanz)` Add multiple metric beans at once.
`void`	`addHeader(Header h)` Adds a header to the collection of metrics.
`void`	`addHistogram(Histogram<HKEY> histogram)` Adds a histogram to the list of histograms in the metrics file.
`void`	`addMetric(BEAN bean)` Adds a bean to the collection of metrics.
`boolean`	`areHeadersEqual(MetricsFile that)`
`boolean`	`areHistogramsEqual(MetricsFile that)`
`static boolean`	`areMetricsEqual(java.io.File file1, java.io.File file2)` Compare the metrics in two files, ignoring headers and histograms.
`boolean`	`areMetricsEqual(MetricsFile that)`
`boolean`	`equals(java.lang.Object o)` Checks that the headers, metrics and histogram are all equal.
`java.util.List<Histogram<HKEY>>`	`getAllHistograms()`
`java.util.List<Header>`	`getHeaders()` Returns the list of headers.
`java.util.List<Header>`	`getHeaders(java.lang.Class<? extends Header> type)` Returns the list of headers with the specified type.
`Histogram<HKEY>`	`getHistogram()` Returns the histogram contained in the metrics file if any.
`java.util.List<BEAN>`	`getMetrics()` Returns the list of headers.
`java.util.Set<java.lang.String>`	`getMetricsColumnLabels()`
`int`	`getNumHistograms()` Returns the number of histograms added to the metrics file.
`int`	`hashCode()`
`void`	`read(java.io.Reader r)` Reads the Metrics in from the given reader.
`static java.util.List<? extends MetricBase>`	`readBeans(java.io.File file)` Convenience method to read all the Metric beans from a metrics file.
`static java.util.List<Header>`	`readHeaders(java.io.File file)` Method to read the header from a metrics file.
`void`	`setHistogram(Histogram<HKEY> histogram)` Sets the histogram contained in the metrics file.
`void`	`write(java.io.File f)` Writes out the metrics file to the supplied file.
`void`	`write(java.io.Writer w)` Writes out the metrics file to the supplied writer.

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

- Field Detail
  - MAJOR_HEADER_PREFIX
```
public static final java.lang.String MAJOR_HEADER_PREFIX
```
    See Also:
    Constant Field Values
  - MINOR_HEADER_PREFIX
```
public static final java.lang.String MINOR_HEADER_PREFIX
```
    See Also:
    Constant Field Values
  - SEPARATOR
```
public static final java.lang.String SEPARATOR
```
    See Also:
    Constant Field Values
  - HISTO_HEADER
```
public static final java.lang.String HISTO_HEADER
```
    See Also:
    Constant Field Values
  - METRIC_HEADER
```
public static final java.lang.String METRIC_HEADER
```
    See Also:
    Constant Field Values
- Constructor Detail
  - MetricsFile
```
public MetricsFile()
```
- Method Detail
  - addHeader
```
public void addHeader(Header h)
```
    Adds a header to the collection of metrics.
  - getHeaders
```
public java.util.List<Header> getHeaders()
```
    Returns the list of headers.
  - addMetric
```
public void addMetric(BEAN bean)
```
    Adds a bean to the collection of metrics.
  - addAllMetrics
```
public void addAllMetrics(java.lang.Iterable<BEAN> beanz)
```
    Add multiple metric beans at once.
  - getMetrics
```
public java.util.List<BEAN> getMetrics()
```
    Returns the list of headers.
  - getMetricsColumnLabels
```
public java.util.Set<java.lang.String> getMetricsColumnLabels()
```
  - getHistogram
```
public Histogram<HKEY> getHistogram()
```
    Returns the histogram contained in the metrics file if any.
  - setHistogram
```
public void setHistogram(Histogram<HKEY> histogram)
```
    Sets the histogram contained in the metrics file.
  - addHistogram
```
public void addHistogram(Histogram<HKEY> histogram)
```
    Adds a histogram to the list of histograms in the metrics file.
  - getAllHistograms
```
public java.util.List<Histogram<HKEY>> getAllHistograms()
```
  - getNumHistograms
```
public int getNumHistograms()
```
    Returns the number of histograms added to the metrics file.
  - getHeaders
```
public java.util.List<Header> getHeaders(java.lang.Class<? extends Header> type)
```
    Returns the list of headers with the specified type.
  - write
```
public void write(java.io.File f)
```
    Writes out the metrics file to the supplied file. The file is written out headers first, metrics second and histogram third.
    
    Parameters:
    f - a File into which to write the metrics
  - write
```
public void write(java.io.Writer w)
```
    Writes out the metrics file to the supplied writer. The file is written out headers first, metrics second and histogram third.
    
    Parameters:
    w - a Writer into which to write the metrics
  - read
```
public void read(java.io.Reader r)
```
    Reads the Metrics in from the given reader.
  - equals
```
public boolean equals(java.lang.Object o)
```
    Checks that the headers, metrics and histogram are all equal.
    
    Overrides:
    
    equals in class java.lang.Object
  - areHeadersEqual
```
public boolean areHeadersEqual(MetricsFile that)
```
  - areMetricsEqual
```
public boolean areMetricsEqual(MetricsFile that)
```
  - areHistogramsEqual
```
public boolean areHistogramsEqual(MetricsFile that)
```
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class java.lang.Object
  - readBeans
```
public static java.util.List<? extends MetricBase> readBeans(java.io.File file)
```
    Convenience method to read all the Metric beans from a metrics file.
    
    Parameters:
    file - to be read.
    
    Returns:
    list of beans from the file.
  - readHeaders
```
public static java.util.List<Header> readHeaders(java.io.File file)
```
    Method to read the header from a metrics file.
  - areMetricsEqual
```
public static boolean areMetricsEqual(java.io.File file1,
                      java.io.File file2)
```
    Compare the metrics in two files, ignoring headers and histograms.

Class MetricsFile<BEAN extends MetricBase,HKEY extends java.lang.Comparable>

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

MAJOR_HEADER_PREFIX

MINOR_HEADER_PREFIX

SEPARATOR

HISTO_HEADER

METRIC_HEADER

Constructor Detail

MetricsFile

Method Detail

addHeader

getHeaders

addMetric

addAllMetrics

getMetrics

getMetricsColumnLabels

getHistogram

setHistogram

addHistogram

getAllHistograms

getNumHistograms

getHeaders

write

write

read

equals

areHeadersEqual

areMetricsEqual

areHistogramsEqual

hashCode

readBeans

readHeaders

areMetricsEqual