-
Notifications
You must be signed in to change notification settings - Fork 368
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
2 changed files
with
151 additions
and
21 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,110 @@ | ||
| package picard.util; | ||
|
|
||
| import java.util.Map; | ||
| import java.util.SortedMap; | ||
| import java.util.TreeMap; | ||
| import java.util.concurrent.atomic.AtomicInteger; | ||
|
|
||
| public class SeriesStats { | ||
|
|
||
| // local state | ||
| private double last = Double.NaN; | ||
| private int count = 0; | ||
| private double sum = 0; | ||
| private double min = Double.NaN; | ||
| private double max = Double.NaN; | ||
| private SortedMap<Double, AtomicInteger> bins = new TreeMap<>(); | ||
|
|
||
| public void add(double v) { | ||
|
|
||
| // save in simple values | ||
| last = v; | ||
| sum += v; | ||
| if ( count > 0 ) { | ||
| min = Math.min(min, v); | ||
| max = Math.max(max, v); | ||
| } else { | ||
| min = max = v; | ||
| } | ||
| count++; | ||
|
|
||
| // save in bins | ||
| if ( bins.containsKey(v) ) { | ||
| bins.get(v).incrementAndGet(); | ||
| } else { | ||
| bins.put(v, new AtomicInteger(1)); | ||
| } | ||
| } | ||
|
|
||
| public double getLast() { | ||
| return last; | ||
| } | ||
|
|
||
| public int getCount() { | ||
| return count; | ||
| } | ||
|
|
||
| public double getMin() { | ||
| return (count != 0) ? min : Double.NaN; | ||
| } | ||
|
|
||
| public double getMax() { | ||
| return (count != 0) ? max : Double.NaN; | ||
| } | ||
|
|
||
| public int getUniq() { | ||
| return bins.size(); | ||
| } | ||
|
|
||
| public double getMean() { | ||
| return (count != 0) ? (sum / count) : Double.NaN; | ||
| } | ||
|
|
||
| public double getMedian() { | ||
| return getPercentile(50); | ||
| } | ||
|
|
||
| public double getPercentile(double precentile) { | ||
| if ( count == 0 ) { | ||
| return Double.NaN; | ||
| } else if ( count == 1 ) { | ||
| return last; | ||
| } else { | ||
|
|
||
| int percentileIndex = (int)(count * precentile / 100); | ||
| int index = 0; | ||
| for (Map.Entry<Double, AtomicInteger> entry : bins.entrySet() ) { | ||
| int binSize = entry.getValue().get(); | ||
| if ( percentileIndex >= index && (percentileIndex < (index + binSize)) ) { | ||
| return entry.getKey(); | ||
| } | ||
| index += binSize; | ||
| } | ||
|
|
||
| // if here, we need the highest entry | ||
| return bins.lastKey(); | ||
| } | ||
| } | ||
|
|
||
| public double getStd() { | ||
|
|
||
| if (count == 0) { | ||
| return Double.NaN; | ||
| } | ||
|
|
||
| // calculate mean | ||
| double mean = getMean(); | ||
|
|
||
| // calculate sum of sqr(deviations) | ||
| double vsum = 0; | ||
| for (Map.Entry<Double, AtomicInteger> entry : bins.entrySet()) { | ||
| int binSize = entry.getValue().get(); | ||
| vsum += (Math.pow(entry.getKey() - mean, 2) * binSize); | ||
| } | ||
|
|
||
| // calculate variance and std | ||
| double variance = vsum / count; | ||
| return Math.sqrt(variance); | ||
| } | ||
|
|
||
| } |