htsjdk.samtools.util

Class Histogram<K extends java.lang.Comparable>

java.lang.Object

java.util.AbstractMap<K,V>

java.util.TreeMap<K,Histogram.Bin>

htsjdk.samtools.util.Histogram<K>

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.util.Map<K,Histogram.Bin>, java.util.NavigableMap<K,Histogram.Bin>, java.util.SortedMap<K,Histogram.Bin>

public class Histogram<K extends java.lang.Comparable>
extends java.util.TreeMap<K,Histogram.Bin>

Class for computing and accessing histogram type data. Stored internally in a sorted Map so that keys can be iterated in order.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	Histogram.Bin Represents a bin in the Histogram.

Nested classes/interfaces inherited from class java.util.AbstractMap

java.util.AbstractMap.SimpleEntry<K,V>, java.util.AbstractMap.SimpleImmutableEntry<K,V>

Constructor Summary

Constructors

Constructor and Description
Histogram() Constructs a new Histogram with default bin and value labels.
Histogram(java.util.Comparator<K> comparator) Constructs a new Histogram that'll use the supplied comparator to sort keys.
Histogram(Histogram<K> in) Copy constructor for a histogram.
Histogram(java.lang.String binLabel, java.lang.String valueLabel) Constructs a new Histogram with supplied bin and value labels.
Histogram(java.lang.String binLabel, java.lang.String valueLabel, java.util.Comparator<K> comparator) Constructor that takes labels for the bin and values and a comparator to sort the bins.

Method Summary

Methods

Modifier and Type	Method and Description
void	addHistogram(Histogram<K> addHistogram) Mutable method that allows the addition of a Histogram into the current one.
Histogram<K>	divideByHistogram(Histogram<K> divisorHistogram) Immutable method that divides the current Histogram by an input Histogram and generates a new one Throws an exception if the bins don't match up exactly
boolean	equals(java.lang.Object o) Checks that the labels and values in the two histograms are identical.
double	estimateSdViaMad() Returns a value that is intended to estimate the mean of the distribution, if the distribution is essentially normal, by using the median absolute deviation to remove the effect of erroneous massive outliers.
java.lang.String	getBinLabel()
double	getCount()
double	getCumulativeProbability(double v) Returns the cumulative probability of observing a value <= v when sampling the distribution represented by this histogram.
double	getGeometricMean() Gets the geometric mean of the distribution.
double	getMax()
double	getMean()
double	getMeanBinSize() Calculates the mean bin size
double	getMedian()
double	getMedianAbsoluteDeviation() Gets the median absolute deviation of the distribution.
double	getMedianBinSize() Calculates the median bin size
double	getMin()
double	getMode() Returns id of the Bin that's the mode of the distribution (i.e.
double	getPercentile(double percentile) Gets the bin in which the given percentile falls.
double	getStandardDeviation()
double	getStandardDeviationBinSize(double mean) Calculates the standard deviation of the bin size
double	getSum() Returns the sum of the products of the histgram bin ids and the number of entries in each bin.
double	getSumOfValues() Returns the sum of the number of entries in each bin.
java.lang.String	getValueLabel()
void	increment(K id) Increments the value in the designated bin by 1.
void	increment(K id, double increment) Increments the value in the designated bin by the supplied increment.
void	prefillBins(K... ids) Prefill the histogram with the supplied set of bins.
void	setBinLabel(java.lang.String binLabel)
void	setValueLabel(java.lang.String valueLabel)
void	trimByTailLimit(int tailLimit) Trims the histogram when the bins in the tail of the distribution contain fewer than mode/tailLimit items
void	trimByWidth(int width) Trims the histogram so that only bins <= width are kept.

Methods inherited from class java.util.TreeMap

ceilingEntry, ceilingKey, clear, clone, comparator, containsKey, containsValue, descendingKeySet, descendingMap, entrySet, firstEntry, firstKey, floorEntry, floorKey, get, headMap, headMap, higherEntry, higherKey, keySet, lastEntry, lastKey, lowerEntry, lowerKey, navigableKeySet, pollFirstEntry, pollLastEntry, put, putAll, remove, size, subMap, subMap, tailMap, tailMap, values

Methods inherited from class java.util.AbstractMap

hashCode, isEmpty, toString

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Map

hashCode, isEmpty

Constructor Detail

Histogram

public Histogram()

Constructs a new Histogram with default bin and value labels.

Histogram

public Histogram(java.lang.String binLabel,
         java.lang.String valueLabel)

Constructs a new Histogram with supplied bin and value labels.

Histogram

public Histogram(java.util.Comparator<K> comparator)

Constructs a new Histogram that'll use the supplied comparator to sort keys.

Histogram

public Histogram(java.lang.String binLabel,
         java.lang.String valueLabel,
         java.util.Comparator<K> comparator)

Constructor that takes labels for the bin and values and a comparator to sort the bins.

Histogram

public Histogram(Histogram<K> in)

Copy constructor for a histogram.

Method Detail

prefillBins

public void prefillBins(K... ids)

Prefill the histogram with the supplied set of bins.

increment

public void increment(K id)

Increments the value in the designated bin by 1.

increment

public void increment(K id,
             double increment)

Increments the value in the designated bin by the supplied increment.

getBinLabel

public java.lang.String getBinLabel()

setBinLabel

public void setBinLabel(java.lang.String binLabel)

getValueLabel

public java.lang.String getValueLabel()

setValueLabel

public void setValueLabel(java.lang.String valueLabel)

equals

public boolean equals(java.lang.Object o)

Checks that the labels and values in the two histograms are identical.

Specified by:

equals in interface java.util.Map<K extends java.lang.Comparable,Histogram.Bin>

Overrides:

equals in class java.util.AbstractMap<K extends java.lang.Comparable,Histogram.Bin>

getMean

public double getMean()

getSum

public double getSum()

Returns the sum of the products of the histgram bin ids and the number of entries in each bin.

getSumOfValues

public double getSumOfValues()

Returns the sum of the number of entries in each bin.

getStandardDeviation

public double getStandardDeviation()

getMeanBinSize

public double getMeanBinSize()

Calculates the mean bin size

getMedianBinSize

public double getMedianBinSize()

Calculates the median bin size

getStandardDeviationBinSize

public double getStandardDeviationBinSize(double mean)

Calculates the standard deviation of the bin size

getPercentile

public double getPercentile(double percentile)

Gets the bin in which the given percentile falls.

Parameters:

percentile - a value between 0 and 1

Returns:

the bin value in which the percentile falls

getCumulativeProbability

public double getCumulativeProbability(double v)

Returns the cumulative probability of observing a value <= v when sampling the distribution represented by this histogram.

getMedian

public double getMedian()

getMedianAbsoluteDeviation

public double getMedianAbsoluteDeviation()

Gets the median absolute deviation of the distribution.

estimateSdViaMad

public double estimateSdViaMad()

Returns a value that is intended to estimate the mean of the distribution, if the distribution is essentially normal, by using the median absolute deviation to remove the effect of erroneous massive outliers.

getMode

public double getMode()

Returns id of the Bin that's the mode of the distribution (i.e. the largest bin).

getMin

public double getMin()

getMax

public double getMax()

getCount

public double getCount()

getGeometricMean

public double getGeometricMean()

Gets the geometric mean of the distribution.

trimByTailLimit

public void trimByTailLimit(int tailLimit)

Trims the histogram when the bins in the tail of the distribution contain fewer than mode/tailLimit items

trimByWidth

public void trimByWidth(int width)

Trims the histogram so that only bins <= width are kept.

divideByHistogram

public Histogram<K> divideByHistogram(Histogram<K> divisorHistogram)
                                                            throws java.lang.IllegalArgumentException

Immutable method that divides the current Histogram by an input Histogram and generates a new one Throws an exception if the bins don't match up exactly

Parameters:

divisorHistogram -

Returns:

Throws:

java.lang.IllegalArgumentException

addHistogram

public void addHistogram(Histogram<K> addHistogram)

Mutable method that allows the addition of a Histogram into the current one.

Parameters:

addHistogram -