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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.microflexbiginteger.stat;
/* ----------------------------- Dependencies ------------------------------ */
import java.math.BigDecimal;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.Map;
import java.util.TreeMap;
import com.google.common.base.Preconditions;
import com.github.jessemull.microflexbiginteger.plate.Plate;
import com.github.jessemull.microflexbiginteger.plate.Well;
import com.github.jessemull.microflexbiginteger.plate.WellSet;
/**
* This class performs statistical operations for BigInteger plate stacks, plates,
* wells and well sets. To create a custom statistical operation extend this class
* and override the calculate methods using the appropriate statistical operation.
*
*
*
* 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 abstract class DescriptiveStatistic {
/* ---------------- Well statistics for all plate wells ----------------- */
/**
* Returns the statistic for each plate well.
* @param Plate the plate
* @return map of wells and results
*/
public Map plate(Plate plate) {
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));
}
return result;
}
/**
* Returns the statistic 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
* @return map of wells and results
*/
public Map plate(Plate plate, int begin, int length) {
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));
}
return result;
}
/* --------------------- Aggregated plate statistics ------------------- */
/**
* Returns the aggregated statistic for the plate.
* @param Plate the plate
* @return the aggregated result
*/
public BigDecimal platesAggregated(Plate plate) {
Preconditions.checkNotNull(plate, "The plate cannot be null.");
List aggregated = new ArrayList();
for (Well well : plate) {
aggregated.addAll(well.toBigDecimal());
}
return calculate(aggregated);
}
/**
* Returns the aggregated statistic for each plate.
* @param Collection collection of plates
* @return map of plates and aggregated results
*/
public Map platesAggregated(Collection collection) {
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.toBigDecimal());
}
results.put(clone, calculate(aggregated));
}
return results;
}
/**
* Returns the aggregated statistic for each plate.
* @param PlateBigInteger[] array of plates
* @return map of plates and aggregated result
*/
public Map platesAggregated(Plate[] array) {
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.toBigDecimal());
}
results.put(clone, calculate(aggregated));
}
return results;
}
/**
* Returns the aggregated statistic for each plate using the values between the
* indices.
* @param Plate the plate
* @param int beginning index of subset
* @param int length of subset
* @return the aggregated result
*/
public BigDecimal platesAggregated(
Plate plate, int begin, int length) {
Preconditions.checkNotNull(plate, "The plate cannot be null.");
List aggregated = new ArrayList();
for (Well well : plate) {
aggregated.addAll(well.toBigDecimal().subList(begin, begin + length));
}
return calculate(aggregated);
}
/**
* Returns the aggregated statistic 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
* @return map of plates and aggregated results
*/
public Map platesAggregated(
Collection collection, int begin, int length) {
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.toBigDecimal().subList(begin, begin + length));
}
results.put(clone, calculate(aggregated));
}
return results;
}
/**
* Returns the aggregated statistic for each plate using the values between
* the indices.
* @param PlateBigInteger[] array of plates
* @param int beginning index of subset
* @param int length of subset
* @return map of plates and aggregated results
*/
public Map platesAggregated(
Plate[] array, int begin, int length) {
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.toBigDecimal().subList(begin, begin + length));
}
results.put(clone, calculate(aggregated));
}
return results;
}
/* --------------- Well statistics for all wells in a set -------------- */
/**
* Returns the statistic of each well in the well set.
* @param WellSet the well set
* @return map of wells and results
*/
public Map set(WellSet set) {
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));
}
return result;
}
/**
* Returns the statistic 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
* @return map of wells and results
*/
public Map set(WellSet set, int begin, int length) {
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));
}
return result;
}
/* --------------------- Aggregated set statistics --------------------- */
/**
* Returns the aggregated statistic for the well set.
* @param WellSet the well set
* @return the aggregated result
*/
public BigDecimal setsAggregated(WellSet set) {
Preconditions.checkNotNull(set, "The well set cannot be null.");
List aggregated = new ArrayList();
for (Well well : set) {
aggregated.addAll(well.toBigDecimal());
}
return calculate(aggregated);
}
/**
* Returns the aggregated statistic for each well set.
* @param Collection collection of well sets
* @return map of well sets and aggregated results
*/
public Map setsAggregated(Collection collection) {
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.toBigDecimal());
}
results.put(clone, calculate(aggregated));
}
return results;
}
/**
* Returns the aggregated statistic for each well set.
* @param WellSetBigInteger[] array of well sets
* @return map of well sets and aggregated results
*/
public Map setsAggregated(WellSet[] array) {
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.toBigDecimal());
}
results.put(clone, calculate(aggregated));
}
return results;
}
/**
* Returns the aggregated statistic 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
* @return the aggregated result
*/
public BigDecimal setsAggregated(
WellSet set, int begin, int length) {
Preconditions.checkNotNull(set, "The well set cannot be null.");
List aggregated = new ArrayList();
for (Well well : set) {
aggregated.addAll(well.toBigDecimal().subList(begin, begin + length));
}
return calculate(aggregated);
}
/**
* Returns the aggregated statistic 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
* @return map of well sets and aggregated results
*/
public Map setsAggregated(
Collection collection, int begin, int length) {
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.toBigDecimal().subList(begin, begin + length));
}
results.put(clone, calculate(aggregated));
}
return results;
}
/**
* Returns the aggregated statistic for each well set using the values between
* the indices.
* @param WellSetBigInteger[] array of well sets
* @param int beginning index of subset
* @param int length of subset
* @return map of well sets and aggregated results
*/
public Map setsAggregated(
WellSet[] array, int begin, int length) {
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.toBigDecimal().subList(begin, begin + length));
}
results.put(clone, calculate(aggregated));
}
return results;
}
/* -------------------------- Well statistics -------------------------- */
/**
* Returns the well statistic.
* @param Well the well
* @return the result
*/
public BigDecimal well(Well well) {
Preconditions.checkNotNull(well, "The well cannot be null.");
return calculate(well.toBigDecimal());
}
/**
* Returns the well statistic 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
* @return the result
*/
public BigDecimal well(Well well, int begin, int length) {
Preconditions.checkNotNull(well, "The well cannot be null.");
Preconditions.checkArgument(begin <= well.toBigDecimal().size() &&
begin >= 0 &&
begin + length <= well.toBigDecimal().size());
return calculate(well.toBigDecimal(), begin, length);
}
/* -------- Methods for calculating the statistic of a data set -------- */
/**
* Calculates the statistic.
* @param List the list
* @return the result
*/
public abstract BigDecimal calculate(List list);
/**
* Calculates the statistic of the values between the beginning and ending indices.
* @param List the list
* @param int beginning index of subset
* @param int length of subset
* @return the result
*/
public abstract BigDecimal calculate(List list, int begin, int length);
}
