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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.ArrayList;
import java.util.Collection;
import java.util.Iterator;
import java.util.List;
/**
* This class performs logical AND operations with two arguments for BigInteger
* plate stacks, plates, wells and well sets.
*
* Operations can be performed on stacks, plates, sets or wells of uneven length
* using standard or strict functions. Standard functions treat all values missing
* from a data set as zeroes and combine all stacks, plates, sets and wells from
* both input objects. Strict functions omit all values, stacks, plates, wells
* and sets missing from one of the input objects:
*
*
* Operation
* Output
*
*
*
*
* Standard
*
*
*
*
*
*
* Treats missing values as zeroes
*
*
* Combines stacks, plates, sets, wells and values from both input objects
*
*
*
*
*
*
*
*
* Strict
*
*
*
*
*
*
* Omits all missing values
*
*
* Combines stacks, plates, sets, wells and values present in both input objects only
*
*
*
*
*
*
* The functions within the MicroFlex library are designed to be flexible and classes
* extending the math operation binary object support operations using two stacks,
* plates, sets and well objects as input. In addition, they support operations using
* a single stack, plate, set or well object and a collection, array or constant, and
* also allow the developer to limit the operation to a subset of data:
*
*
* Input 1
* Input 2
* Beginning
Index
* Length of
Subset
* Operation
*
* Well
* Well
* +/-
* +/-
* Performs the operation using the values in the two wells
*
*
* Well
* Array
* +/-
* +/-
* Performs the operation using the values in the array and the values in the well
*
*
* Well
* Collection
* +/-
* +/-
* Performs the operation using the values in the collection and the values in the well
*
*
* Well
* Constant
* +/-
* +/-
* Performs the operation using the constant value and each value in the well
*
*
*
* Set
* Set
* +/-
* +/-
* Performs the operation on the values in each matching pair of wells in the two sets
*
*
* Set
* Array
* +/-
* +/-
* Performs the operation using the values in the array and the values in each well of the set
*
*
* Set
* Collection
* +/-
* +/-
* Performs the operation using the values in the collection and the values in each well of the set
*
*
* Set
* Constant
* +/-
* +/-
* Performs the operation using the constant and each value in each well of the set
*
*
*
* Plate
* Plate
* +/-
* +/-
* Performs the operation on the values in each matching pair of wells in the two plates
*
*
* Plate
* Array
* +/-
* +/-
* Performs the operation using the values in the array and the values in each well of the plate
*
*
* Plate
* Collection
* +/-
* +/-
* Performs the operation using the values in the collection and the values in each well of the plate
*
*
* Plate
* Constant
* +/-
* +/-
* Performs the operation using the constant and each value in each well of the plate
*
*
*
* Stack
* Stack
* +/-
* +/-
* Performs the operation on the values in each matching pair of wells in each matching plate in the stack
*
*
* Stack
* Array
* +/-
* +/-
* Performs the operation using the values in the array and the values in each well of each plate in the stack
*
*
* Stack
* Collection
* +/-
* +/-
* Performs the operation using the values in the collection and the values in each well of each plate in the stack
*
*
* Stack
* Constant
* +/-
* +/-
* Performs the operation using the constant and each value in each well of each plate in the stack
*
*
*
* @author Jesse L. Mull
* @update Updated Oct 18, 2016
* @address http://www.jessemull.com
* @email [email protected]
*/
public class AND extends MathOperationBinary {
/**
* Ands the values in the first list by the values in the second list and
* returns the result. Missing data points due to uneven list lengths are
* treated as zeroes.
* @param List list1 the first list
* @param List list2 the second list
* @return the result
* @override
*/
public List calculate(List list1, List list2) {
List largest = null;
List smallest = null;
if(list1.size() != list2.size()) {
largest = list1.size() > list2.size() ? list1 : list2;
smallest = list1.size() < list2.size() ? list1 : list2;
} else {
smallest = list1;
largest = list2;
}
List result = new ArrayList();
for(int i = 0; i < smallest.size(); i++) {
result.add(smallest.get(i).and(largest.get(i)));
}
for(int i = smallest.size(); i < largest.size(); i++) {
result.add(largest.get(i));
}
return result;
}
/**
* Ands the values in the first list by the values in the second list and
* returns the result. Missing data points due to uneven list lengths are
* omitted.
* @param List list1 the first list
* @param List list2 the second list
* @return the result
* @override
*/
public List calculateStrict(List list1, List list2) {
List smallest = list1.size() < list2.size() ? list1 : list2;
List result = new ArrayList();
for(int i = 0; i < smallest.size(); i++) {
result.add(list1.get(i).and(list2.get(i)));
}
return result;
}
/**
* Ands the values in the first list by the values in the second list and
* returns the result using the values between the indices. Missing data points
* due to uneven list lengths are treated as zeroes.
* @param List list1 the first list
* @param List list2 the second list
* @param int begin beginning index of the subset
* @param int length length of the subset
* @return the result
* @override
*/
public List calculate(List list1, List list2, int begin, int length) {
List largest = list1.size() > list2.size() ? list1 : list2;
List smallest = list1.size() < list2.size() ? list1 : list2;
List result = new ArrayList();
int end1 = begin + length;
int end2 = end1;
if(end1 > smallest.size()) {
end1 = smallest.size();
}
for(int i = begin; i < end1; i++) {
result.add(list1.get(i).and(list2.get(i)));
}
for(int i = end1; i < end2; i++) {
result.add(largest.get(i));
}
return result;
}
/**
* Ands the lists and returns the result using the values between the indices.
* Missing data points due to uneven list lengths are omitted.
* @param List list1 the first list
* @param List list2 the second list
* @param int begin beginning index of the subset
* @param int length length of the subset
* @return the result
* @override
*/
public List calculateStrict(List list1,
List list2, int begin, int length) {
List result = new ArrayList();
for(int i = begin; i < begin + length; i++) {
result.add(list1.get(i).and(list2.get(i)));
}
return result;
}
/**
* Ands the values in the list by the constant.
* @param List list the list
* @param BigInteger constant the constant value
* @return the result
* @override
*/
public List calculate(List list, BigInteger constant) {
List result = new ArrayList();
for(BigInteger bd : list) {
result.add(bd.and(constant));
}
return result;
}
/**
* Ands the list by the values within the array. Missing data points due
* to uneven list and array sizes are treated as zeroes.
* @param List list the list
* @param BigInteger[] array the array
* @return the result
* @override
*/
public List calculate(List list, BigInteger[] array) {
int index;
List result = new ArrayList();
for(index = 0; index < list.size() && index < array.length; index++) {
result.add(list.get(index).and(array[index]));
}
for(int i = index; i < list.size(); i++) {
result.add(list.get(i));
}
for(int i = index; i < array.length; i++) {
result.add(array[i]);
}
return result;
}
/**
* Ands the list by the values within the array between the indices. Missing
* data points due to uneven list and array sizes are treated as zeroes.
* @param List list the list
* @param BigInteger[] array the array
* @param int begin beginning index of the subset
* @param int length length of the subset
* @return the result
* @override
*/
public List calculate(List list, BigInteger[] array,
int begin, int length) {
int index;
List result = new ArrayList();
for(index = begin; index < list.size() && index < array.length &&
index < begin + length; index++) {
result.add(list.get(index).and(array[index]));
}
for(int i = index; i < list.size() && i < begin + length; i++) {
result.add(list.get(i));
}
for(int i = index; i < array.length && i < begin + length; i++) {
result.add(array[i]);
}
return result;
}
/**
* Ands the list values by the values within the collection. Missing
* data points due to uneven list and collection sizes are treated as zeroes.
* @param List list the list
* @param Collection collection the collection of values
* @return the result
* @override
*/
public List calculate(List list, Collection collection) {
int index;
Iterator iter = collection.iterator();
List result = new ArrayList();
for(index = 0; index < list.size() && index < collection.size(); index++) {
result.add(list.get(index).and(iter.next()));
}
for(int i = index; i < list.size(); i++) {
result.add(list.get(i));
}
while(iter.hasNext()) {
result.add(iter.next());
}
return result;
}
/**
* Ands the list values by the values within the collection. Missing
* data points due to uneven list and collection sizes are treated as zeroes.
* @param List list the list
* @param Collection collection the collection of values
* @param int begin beginning index of the subset
* @param int length length of the subset
* @return the result
* @override
*/
public List calculate(List list,
Collection collection, int begin, int length) {
int index;
Iterator iter = collection.iterator();
List result = new ArrayList();
for(int i = 0; i < begin; i++) {
iter.next();
}
for(index = begin; index < list.size() && index < collection.size() && index < begin + length; index++) {
result.add(list.get(index).and(iter.next()));
}
for(int i = index; i < list.size() && index < begin + length; i++) {
result.add(list.get(i));
}
while(iter.hasNext() && index < begin + length) {
result.add(iter.next());
index++;
}
return result;
}
/**
* Ands the list values by the values within the array. Missing data
* points due to uneven list and array sizes are omitted.
* @param List list the list
* @param BigInteger[] array the array
* @return the result
* @override
*/
public List calculateStrict(List list, BigInteger[] array) {
List result = new ArrayList();
for(int i = 0; i < list.size() && i < array.length; i++) {
result.add(list.get(i).and(array[i]));
}
return result;
}
/**
* Ands the list values by the values within the array between the indices.
* Missing data points due to uneven list and array sizes are omitted.
* @param List list the list
* @param BigInteger[] array the array
* @param int begin beginning index of the subset
* @param int length length of the subset
* @return the result
* @override
*/
public List calculateStrict(List list, BigInteger[] array,
int begin, int length) {
List result = new ArrayList();
for(int i = begin; i < list.size() && i < array.length &&
i < begin + length; i++) {
result.add(list.get(i).and(array[i]));
}
return result;
}
/**
* Ands the list values by the values within the collection. Missing data
* points due to uneven list and array sizes are omitted.
* @param List list the list
* @param Collection collection the collection
* @return the result
* @override
*/
public List calculateStrict(List list,
Collection collection) {
Iterator iter = collection.iterator();
List result = new ArrayList();
for(int i = 0; i < list.size() && i < collection.size(); i++) {
result.add(list.get(i).and(iter.next()));
}
return result;
}
/**
* Ands the list the values by the values within the collection between
* the indices. Missing data points due to uneven list and collection sizes
* are omitted.
* @param List list the list
* @param Collection collection the collection
* @param int begin beginning index of the subset
* @param int length length of the subset
* @return the result
* @override
*/
public List calculateStrict(List list,
Collection collection, int begin, int length) {
List result = new ArrayList();
Iterator iter = collection.iterator();
for(int i = 0; i < begin; i++) {
iter.next();
}
for(int i = begin; i < list.size() && iter.hasNext() &&
i < begin + length; i++) {
result.add(list.get(i).and(iter.next()));
}
return result;
}
}
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