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Microplate library for parsing wet lab data.
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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.math;
/* ------------------------------ Dependencies ------------------------------ */
import java.math.BigInteger;
import java.util.List;
import com.github.jessemull.microflexbiginteger.plate.Plate;
import com.github.jessemull.microflexbiginteger.plate.Stack;
import com.github.jessemull.microflexbiginteger.plate.Well;
import com.github.jessemull.microflexbiginteger.plate.WellSet;
/**
* This class performs mathematical operations with a single argument for BigInteger
* plate stacks, plates, wells and well sets. To create a custom mathematical
* operation extend this class and override the calculate methods using the
* appropriate operation. Unary operations can also be performed on a subset of
* data using a beginning index and subset length.
*
* MicroFlex currently supports the following unary mathematical operations
* for BigInteger objects:
*
*
* Operations
*
* Increment
*
*
* Decrement
*
*
* Compliment
*
*
*
* @author Jesse L. Mull
* @update Updated Oct 18, 2016
* @address http://www.jessemull.com
* @email [email protected]
*/
public abstract class MathOperationUnary {
/* ---------------------------- Constructors ---------------------------- */
/**
* Creates a new math operation.
*/
public MathOperationUnary() {}
/* ----------------------------- Well Methods --------------------------- */
/**
* Returns the result of the mathematical operation.
* @param Well the well
* @return result of the operation
*/
public List wells(Well well) {
if(well == null) {
throw new NullPointerException("Well is null.");
}
return calculate(well.data());
}
/**
* Returns the result of the mathematical operation. Using the values between
* the indices.
* @param Well the well
* @param int beginning index of the subset
* @param int length of the subset
* @return result of the operation
*/
public List wells(Well well, int begin, int length) {
if(well == null) {
throw new NullPointerException("Well is null.");
}
return calculate(well.data(), begin, length);
}
/* ---------------------------- Plate Methods --------------------------- */
/**
* Returns the result of the mathematical operation.
* @param Plate the plate
* @return result of the operation
*/
public Plate plates(Plate plate) {
if(plate == null) {
throw new NullPointerException("Plate is null.");
}
Plate result = new Plate(plate.rows(), plate.columns());
for(Well well : plate) {
result.addWells(new Well(well.row(), well.column(),
this.calculate(well.data())));
}
return result;
}
/**
* Returns the result of the mathematical operation using the values between
* the indices.
* @param Plate the plate
* @param int beginning index of the subset
* @param int length of the subset
* @return result of the operation
*/
public Plate plates(Plate plate, int begin, int length) {
if(plate == null) {
throw new NullPointerException("Plate is null.");
}
Plate result = new Plate(plate.rows(), plate.columns());
for(Well well : plate) {
result.addWells(new Well(well.row(), well.column(),
this.calculate(well.data(), begin, length)));
}
return result;
}
/* ----------------------------- Set Methods ---------------------------- */
/**
* Returns the result of the mathematical operation.
* @param WellSet the well set
* @return result of the operation
*/
public WellSet sets(WellSet set) {
if(set == null) {
throw new NullPointerException("Well set is null.");
}
WellSet result = new WellSet();
for(Well well : set) {
result.add(new Well(well.row(), well.column(),
this.calculate(well.data())));
}
return result;
}
/**
* Returns the result of the mathematical operation using the values between
* the indices.
* @param WellSet the well set
* @param int beginning index of the subset
* @param int length of the subset
* @return result of the operation
*/
public WellSet sets(WellSet set, int begin, int length) {
if(set == null) {
throw new NullPointerException("Well set is null.");
}
WellSet result = new WellSet();
for(Well well : set) {
result.add(new Well(well.row(), well.column(),
this.calculate(well.data(), begin, length)));
}
return result;
}
/* ---------------------------- Stack Methods --------------------------- */
/**
* Returns the result of the mathematical operation.
* @param Stack the stack
* @return the result of the operation
*/
public Stack stacks(Stack stack) {
if(stack == null) {
throw new NullPointerException("Stack is null.");
}
Stack result = new Stack(stack.rows(), stack.columns());
for(Plate plate : stack) {
result.add(this.plates(plate));
}
return result;
}
/**
* Returns the result of the mathematical operation.
* @param Stack the stack
* @param int beginning index of the sub set
* @param int length of the subset
* @return the result of the operation
*/
public Stack stacks(Stack stack, int begin, int length) {
if(stack == null) {
throw new NullPointerException("Stack is null.");
}
Stack result = new Stack(stack.rows(), stack.columns());
for(Plate plate : stack) {
result.add(this.plates(plate, begin, length));
}
return result;
}
/*------------------------ List Operation Methods ------------------------*/
/**
* Performs the mathematical operation for the list.
* @param List the list
* @return result of the mathematical operation
*/
public abstract List calculate(List list);
/**
* Performs the mathematical operation for the list using the values
* between the indices.
* @param List the list
* @return result of the mathematical operation
*/
public abstract List calculate(List list, int begin, int length);
}
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