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/**
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
* regarding copyright ownership. The ASF licenses this file
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
* KIND, either express or implied. See the License for the
* specific language governing permissions and limitations
* under the License.
*/
/* -------------------------------- Package -------------------------------- */
package com.github.jessemull.microflexbigdecimal.stat;
/* ----------------------------- Dependencies ------------------------------ */
import java.math.BigDecimal;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.util.Map;
import java.util.TreeMap;
import com.google.common.base.Preconditions;
import com.github.jessemull.microflexbigdecimal.plate.Plate;
import com.github.jessemull.microflexbigdecimal.plate.Well;
import com.github.jessemull.microflexbigdecimal.plate.WellSet;
/**
* This class calculates percentiles for BigDecimal plate stacks, plates,
* wells and well sets using the following steps:
*
*
*
*
*
Calculate R as P/100 x (N + 1) where N is the number of values and P is the desired percentile
*
Define IR as the integer portion of R
*
Define FR as the fractional portion of R
*
Find the scores with Rank IR and with Rank IR + 1
*
Interpolate using the formula (Score IR+1 - Score IR) * FR + Score IR and return the result
*
*
*
*
* Statistical operations can be performed on stacks, plates, sets and wells using
* standard or aggregated functions. Standard functions calculate the desired
* statistic for each well in the stack, plate or set. Aggregated functions aggregate
* the values from all the wells in the stack, plate or set and perform the statistical
* operation on the aggregated values. Both standard and aggregated functions can
* be performed on a subset of data within the stack, plate, set or well.
*
*
*
* The methods within the MicroFlex library are meant to be flexible and the
* descriptive statistic object supports operations using a single stack, plate,
* set or well as well as collections and arrays of stacks, plates, sets or wells.
*
*
*
Operation
*
Beginning Index
*
Length of Subset
*
Input/Output
*
*
*
*
*
Standard
*
*
*
*
*
*
*
+/-
*
*
*
*
*
*
*
+/-
*
*
*
*
*
*
*
Accepts a single well, set, plate or stack as input
*
*
*
Calculates the statistic for each well in a well, set, plate or stack
*
*
*
*
*
*
*
*
*
Aggregated
*
*
*
*
*
*
*
+/-
*
*
*
*
*
*
*
+/-
*
*
*
*
*
*
*
Accepts a single well/set/plate/stack or a collection/array of wells/sets/plates/stacks as input
*
*
*
Aggregates the data from all the wells in a well/set/plate/stack and calculates the statistic using the aggregated data
*
*
*
*
*
*
* @author Jesse L. Mull
* @update Updated Oct 18, 2016
* @address http://www.jessemull.com
* @email [email protected]
*/
public class Percentile {
/* --------------- Well percentiles for all plate wells ----------------- */
/**
* Returns the percentile for each plate well.
* @param Plate the plate
* @param int the percentile
* @return map of wells and results
*/
public Map plate(Plate plate, int p) {
Preconditions.checkNotNull(plate, "The plate value cannot be null.");
Map result = new TreeMap();
for (Well well : plate) {
Well clone = new Well(well);
result.put(clone, well(well, p));
}
return result;
}
/**
* Returns the percentile for each plate well using the values between the
* beginning and ending indices.
* @param Plate the plate
* @param int beginning index of subset
* @param int length of subset
* @param int the percentile
* @return map of wells and results
*/
public Map plate(Plate plate, int begin, int length, int p) {
Preconditions.checkNotNull(plate, "The plate value cannot be null.");
Map result = new TreeMap();
for (Well well : plate) {
Well clone = new Well(well);
result.put(clone, well(well, begin, length, p));
}
return result;
}
/* --------------------- Aggregated plate percentiles ------------------ */
/**
* Returns the aggregated percentile for the plate.
* @param Plate the plate
* @param int the percentile
* @return the aggregated result
*/
public BigDecimal platesAggregated(Plate plate, int p) {
Preconditions.checkNotNull(plate, "The plate cannot be null.");
List aggregated = new ArrayList();
for (Well well : plate) {
aggregated.addAll(well.data());
}
return calculate(aggregated, p);
}
/**
* Returns the aggregated percentile for each plate.
* @param Collection collection of plates
* @param int the percentile
* @return map of plates and aggregated results
*/
public Map platesAggregated(Collection collection, int p) {
Preconditions.checkNotNull(collection, "The plate collection cannot be null.");
Map results = new TreeMap();
for(Plate plate : collection) {
List aggregated = new ArrayList();
Plate clone = new Plate(plate);
for (Well well : plate) {
aggregated.addAll(well.data());
}
results.put(clone, calculate(aggregated, p));
}
return results;
}
/**
* Returns the aggregated percentile for each plate.
* @param PlateBigDecimal[] array of plates
* @param int the percentile
* @return map of plates and aggregated result
*/
public Map platesAggregated(Plate[] array, int p) {
Preconditions.checkNotNull(array, "The plate array cannot be null.");
Map results = new TreeMap();
for(Plate plate : array) {
List aggregated = new ArrayList();
Plate clone = new Plate(plate);
for (Well well : plate) {
aggregated.addAll(well.data());
}
results.put(clone, calculate(aggregated, p));
}
return results;
}
/**
* Returns the aggregated percentile for each plate using the values between
* the indices.
* @param Plate the plate
* @param int beginning index of subset
* @param int length of subset
* @param int the percentile
* @return the aggregated result
*/
public BigDecimal platesAggregated(
Plate plate, int begin, int length, int p) {
Preconditions.checkNotNull(plate, "The plate cannot be null.");
List aggregated = new ArrayList();
for (Well well : plate) {
aggregated.addAll(well.data().subList(begin, begin + length));
}
return calculate(aggregated, p);
}
/**
* Returns the aggregated percentile for each plate using the values between
* the indices.
* @param Collection collection of plates
* @param int beginning index of subset
* @param int length of subset
* @param int the percentile
* @return map of plates and aggregated results
*/
public Map platesAggregated(
Collection collection, int begin, int length, int p) {
Preconditions.checkNotNull(collection, "The plate collection cannot be null.");
Map results = new TreeMap();
for(Plate plate : collection) {
List aggregated = new ArrayList();
Plate clone = new Plate(plate);
for (Well well : plate) {
aggregated.addAll(well.data().subList(begin, begin + length));
}
results.put(clone, calculate(aggregated, p));
}
return results;
}
/**
* Returns the aggregated percentile for each plate using the values between
* the indices.
* @param PlateBigDecimal[] array of plates
* @param int beginning index of subset
* @param int length of subset
* @param int the percentile
* @return map of plates and aggregated results
*/
public Map platesAggregated(
Plate[] array, int begin, int length, int p) {
Preconditions.checkNotNull(array, "The plate array cannot be null.");
Map results = new TreeMap();
for(Plate plate : array) {
List aggregated = new ArrayList();
Plate clone = new Plate(plate);
for (Well well : plate) {
aggregated.addAll(well.data().subList(begin, begin + length));
}
results.put(clone, calculate(aggregated, p));
}
return results;
}
/* --------------- Well percentiles for all wells in a set ------------- */
/**
* Returns the percentile of each well in the well set.
* @param WellSet the well set
* @param int the percentile
* @return map of wells and results
*/
public Map set(WellSet set, int p) {
Preconditions.checkNotNull(set, "The set cannot be null.");
Map result = new TreeMap();
for (Well well : set) {
Well clone = new Well(well);
result.put(clone, well(well, p));
}
return result;
}
/**
* Returns the percentile of each well in the well set using the values between
* the beginning and ending indices.
* @param WellSet the well set
* @param int beginning index of subset
* @param int length of subset
* @param int the percentile
* @return map of wells and results
*/
public Map set(WellSet set, int begin, int length, int p) {
Preconditions.checkNotNull(set, "The well set cannot be null.");
Map result = new TreeMap();
for (Well well : set) {
Well clone = new Well(well);
result.put(clone, well(well, begin, length, p));
}
return result;
}
/* --------------------- Aggregated set percentiles -------------------- */
/**
* Returns the aggregated percentile for the well set.
* @param WellSet the well set
* @param int the percentile
* @return the aggregated result
*/
public BigDecimal setsAggregated(WellSet set, int p) {
Preconditions.checkNotNull(set, "The well set cannot be null.");
List aggregated = new ArrayList();
for (Well well : set) {
aggregated.addAll(well.data());
}
return calculate(aggregated, p);
}
/**
* Returns the aggregated percentile for each well set.
* @param Collection collection of well sets
* @param int the percentile
* @return map of well sets and aggregated results
*/
public Map setsAggregated(Collection collection, int p) {
Preconditions.checkNotNull(collection, "The well set collection cannot be null.");
Map results = new TreeMap();
for(WellSet set : collection) {
List aggregated = new ArrayList();
WellSet clone = new WellSet(set);
for (Well well : set) {
aggregated.addAll(well.data());
}
results.put(clone, calculate(aggregated, p));
}
return results;
}
/**
* Returns the aggregated percentile for each well set.
* @param WellSetBigDecimal[] array of well sets
* @param int the percentile
* @return map of well sets and aggregated results
*/
public Map setsAggregated(WellSet[] array, int p) {
Preconditions.checkNotNull(array, "The well set array cannot be null.");
Map results = new TreeMap();
for(WellSet set : array) {
List aggregated = new ArrayList();
WellSet clone = new WellSet(set);
for (Well well : set) {
aggregated.addAll(well.data());
}
results.put(clone, calculate(aggregated, p));
}
return results;
}
/**
* Returns the aggregated percentile for each well set using the values between the
* indices.
* @param WellSet the well set
* @param int beginning index of subset
* @param int length of subset
* @param int the percentile
* @return the aggregated result
*/
public BigDecimal setsAggregated(
WellSet set, int begin, int length, int p) {
Preconditions.checkNotNull(set, "The well set cannot be null.");
List aggregated = new ArrayList();
for (Well well : set) {
aggregated.addAll(well.data().subList(begin, begin + length));
}
return calculate(aggregated, p);
}
/**
* Returns the aggregated percentile for each well set using the values between
* the indices.
* @param Collection collection of well sets
* @param int beginning index of subset
* @param int length of subset
* @param int the percentile
* @return map of well sets and aggregated results
*/
public Map setsAggregated(
Collection collection, int begin, int length, int p) {
Preconditions.checkNotNull(collection, "The well set collection cannot be null.");
Map results = new TreeMap();
for(WellSet set : collection) {
List aggregated = new ArrayList();
WellSet clone = new WellSet(set);
for (Well well : set) {
aggregated.addAll(well.data().subList(begin, begin + length));
}
results.put(clone, calculate(aggregated, p));
}
return results;
}
/**
* Returns the aggregated percentile for each well set using the values between
* the indices.
* @param WellSetBigDecimal[] array of well sets
* @param int beginning index of subset
* @param int length of subset
* @param int the percentile
* @return map of well sets and aggregated results
*/
public Map setsAggregated(
WellSet[] array, int begin, int length, int p) {
Preconditions.checkNotNull(array, "The well set array cannot be null.");
Map results = new TreeMap();
for(WellSet set : array) {
List aggregated = new ArrayList();
WellSet clone = new WellSet(set);
for (Well well : set) {
aggregated.addAll(well.data().subList(begin, begin + length));
}
results.put(clone, calculate(aggregated, p));
}
return results;
}
/* -------------------------- Well percentiles ------------------------- */
/**
* Returns the well percentile.
* @param Well the well
* @param int the percentile
* @return the result
*/
public BigDecimal well(Well well, int p) {
Preconditions.checkNotNull(well, "The well cannot be null.");
Preconditions.checkArgument(p <= 100 || p > 0, "Percentile is outside the valid range: %d", p);
return calculate(well.data(), p);
}
/**
* Returns the well percentile for the values between the beginning and ending
* indices.
* @param Well the well
* @param int beginning index of subset
* @param int length of the subset
* @param int the percentile
* @return the result
*/
public BigDecimal well(Well well, int begin, int length, int p) {
Preconditions.checkNotNull(well, "The well cannot be null.");
Preconditions.checkArgument(p <= 100 || p > 0, "Percentile is outside the valid range: %d", p);
Preconditions.checkArgument(begin <= well.data().size() &&
begin >= 0 &&
begin + length <= well.data().size());
return calculate(well.data(), begin, length, p);
}
/* -------- Methods for calculating the percentile of a data set ------- */
/**
* Calculates the percentile.
* @param List the list
* @param int the percentile
* @return the result
*/
public BigDecimal calculate(List list, int p) {
int n = list.size();
if(n == 1) {
return list.get(0);
}
Collections.sort(list);
double pos = (p * (n + 1)) / 100.0;
if(pos < 1) {
return list.get(0);
}
if(pos >= n) {
return list.get(list.size() - 1);
}
if(pos == Math.floor(pos) && !Double.isInfinite(pos)) {
return list.get((int) pos - 1);
}
int lowerIndex = (int) Math.floor(pos) - 1;
int upperIndex = lowerIndex + 1;
BigDecimal lower = list.get(lowerIndex);
BigDecimal upper = list.get(upperIndex);
BigDecimal d = new BigDecimal((pos - 1 - lowerIndex) + "");
return upper.subtract(lower).multiply(d).add(lower);
};
/**
* Calculates the percentile of the values between the beginning and ending
* indices.
* @param List the list
* @param int beginning index of subset
* @param int length of subset
* @param int the percentile
* @return the result
*/
public BigDecimal calculate(List list, int begin, int length, int p) {
return this.calculate(list.subList(begin, begin + length), p);
};
}
