Well (MicroFlex - Integer 1.0.1 API)

java.lang.Object
- com.github.jessemull.microflexinteger.plate.WellPrecursor<Integer>
- - com.github.jessemull.microflexinteger.plate.Well

All Implemented Interfaces:: Comparable<WellPrecursor<Integer>>, Iterable<Integer>

public class Well
extends WellPrecursor<Integer>
implements Iterable<Integer>

This class represents a well in a microplate. It contains the the logic to convert row letters to integers and vice-versa, enforces the correct format for well IDs and holds a list of data set values. The well object does not check for wells outside a specified range. This logic is housed within the plate object. All the classes in the microplate library are designed to be flexible in order to accommodate data in a variety of formats. The well object constructor accepts well IDs in each of the following formats:

Row	Column	Input
Integer	Integer	Row = 1 Column = 2
String	Integer	Row = "1" Column = 2
String	Integer	Row = "A" Column = 2
Integer	String	Row = 1 Column = "2"
String	String	Row = "A" Column = "2"
String	String	Row = "1" Column = "2"
String	String	"A2" Input must be [A-Za-z]+[0-9]+

The Well class also implements both hash code and equals functions in order to prevent duplicate wells within a single plate object. The well constructor is passed a flag holding the numerical data type. Once set, the numerical data type cannot be changed. This well type supports storage of integer values only. The MicroFlex library supports wells containing all primitive numerical types for input and output as well as two immutable types: BigDecimal and BigInteger.

Author:: Jesse L. Mull

Field Summary
- Fields inherited from class com.github.jessemull.microflexinteger.plate.WellPrecursor
  BIGDECIMAL, BIGINTEGER, DOUBLE, INTEGER

Constructor Summary

Constructors
Constructor and Description
`Well(int row, int column)` Creates a new Well object from row and column integers.
`Well(int row, int column, Collection<Integer> data)` Creates a new Well object using the numerical type flag, row number, column number and data set.
`Well(int row, int column, Integer[] data)` Creates a new Well object using the numerical type flag, row number, column number and data set.
`Well(int row, String column)` Creates a new Well object using the numerical type flag, row number and column string.
`Well(int row, String column, Collection<Integer> data)` Creates a new Well object using the numerical type flag, row number and column string.
`Well(int row, String column, Integer[] data)` Creates a new Well object using the numerical type flag, row number and column string.
`Well(String wellID)` Creates a new Well object from a string holding the column and row values.
`Well(String wellID, Collection<Integer> data)` Creates a new Well object using the numerical type flag and a string holding the column and row values.
`Well(String row, int column)` Creates a new Well object using the numerical type flag, row string and column number.
`Well(String row, int column, Collection<Integer> data)` Creates a new Well object using the numerical type flag, row string, column number and data set.
`Well(String wellID, Integer[] data)` Creates a new Well object using the numerical type flag and a string holding the column and row values.
`Well(String row, int column, Integer[] data)` Creates a new Well object using the numerical type flag, row string, column number and data set.
`Well(String row, String column)` Creates a new Well object using the numerical type flag, row and column strings.
`Well(String row, String column, Collection<Integer> data)` Creates a new Well object using the numerical type flag, row string, column string and data set.
`Well(String row, String column, Integer[] data)` Creates a new Well object using the numerical type flag, row and column strings.
`Well(Well well)` Clones a double well without invoking clone.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`add(Collection<Integer> collection)` Adds a collection of numbers to the data set.
`void`	`add(Integer datum)` Adds a single data point to a well.
`void`	`add(Integer[] array)` Adds an array of numbers to the data set.
`void`	`add(Well well)` Adds the data from another well.
`void`	`add(WellSet set)` Adds the data from each well in the well set.
`void`	`clear()` Clears the well data.
`boolean`	`contains(Integer number)` Returns true if the well data set contains the value.
`List<Integer>`	`data()` Returns the data set.
`boolean`	`equals(Object object)` Wells are equivalent if the row, column and ALPHA_BASE fields are equivalent.
`Integer`	`get(int index)` Returns the value at the specified index.
`int`	`indexOf(Integer number)` Returns the index of the first occurrence of the specified element in this list, or -1 if this list does not contain the element.
`boolean`	`isEmpty()` Returns true if the well data set is empty and false otherwise.
`Iterator<Integer>`	`iterator()` Returns an iterator for the well data set.
`double`	`lastIndexOf(Integer number)` Returns the index of the last occurrence of the specified element in this list, or -1 if this list does not contain the element.
`void`	`remove(Collection<Integer> collection)` Removes all the values in the collection from the data set.
`void`	`remove(Integer number)` Removes the value from the data set.
`void`	`remove(Integer[] array)` Removes all the values in the array from the data set.
`void`	`removeRange(int begin, int end)` Removes all values within the indices.
`void`	`removeSet(WellSet set)` Removes the well values for each well from the data set.
`void`	`removeWell(Well well)` Removes all the well values from the data set.
`void`	`replaceData(Collection<Integer> collection)` Clears the data set and adds the collection.
`void`	`replaceData(Integer datum)` Clears the data set and adds the number.
`void`	`replaceData(Integer[] array)` Clears the data set and adds the array.
`void`	`replaceData(Well well)` Clears the data set and adds the well data set.
`void`	`replaceData(WellSet set)` Clears the data set and adds the data from each well in the set.
`void`	`retain(Collection<Integer> collection)` Retains all the values in the collection.
`void`	`retain(Integer number)` Retains the values in the data set.
`void`	`retain(Integer[] array)` Retains all the values in the array.
`void`	`retainRange(int begin, int end)` Retains all values within the indices.
`void`	`retainSet(WellSet set)` Retains all the values in each well.
`void`	`retainWell(Well well)` Retains all the values in the well.
`int`	`size()` Returns the size of the well data set.
`Well`	`subList(int begin, int length)` Returns a new well containing the values within the indices.
`List<BigDecimal>`	`toBigDecimal()` Returns the well data set as a list of big decimals.
`BigDecimal[]`	`toBigDecimalArray()` Returns the well data set as a list of big decimals.
`List<BigInteger>`	`toBigInteger()` Returns the well data set as a list of big integers.
`BigInteger[]`	`toBigIntegerArray()` Returns the well data set as an array of big integers.
`List<Byte>`	`toByte()` Returns the well data set as a list of bytes.
`byte[]`	`toByteArray()` Returns the well data set as an array of bytes.
`List<Double>`	`toDouble()` Returns the well data set as a list of doubles.
`double[]`	`toDoubleArray()` Returns the well data set as an array of doubles.
`List<Float>`	`toFloat()` Returns the well data set as a list of floats.
`float[]`	`toFloatArray()` Returns the well data set as an array of floats.
`List<Integer>`	`toInt()` Returns the well data set as an array of shorts.
`int[]`	`toIntArray()` Returns the well data set as an array of integers.
`List<Long>`	`toLong()` Returns the well data set as a list of longs.
`long[]`	`toLongArray()` Returns the well data set as an array of longs.
`List<Short>`	`toShort()` Returns the well data set as a list of shorts.
`short[]`	`toShortArray()` Returns the well data set as an array of shorts.

Methods inherited from class com.github.jessemull.microflexinteger.plate.WellPrecursor
alphaBase, column, compareTo, hashCode, index, row, rowString, toString, type, typeString

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.lang.Iterable
forEach, spliterator

- Constructor Detail
  - Well
```
public Well(int row,
            int column)
```
    Creates a new Well object from row and column integers.
    
    Parameters:
    
    int - the well row
    
    int - the well column
  - Well
```
public Well(int row,
            int column,
            Collection<Integer> data)
```
    Creates a new Well object using the numerical type flag, row number, column number and data set.
    
    Parameters:
    
    Collection - the data set
    
    int - the well row
    
    int - the well column
  - Well
```
public Well(int row,
            int column,
            Integer[] data)
```
    Creates a new Well object using the numerical type flag, row number, column number and data set.
    
    Parameters:
    
    Integer[] - the data set
    
    int - the well row
    
    int - the well column
  - Well
```
public Well(String row,
            int column)
```
    Creates a new Well object using the numerical type flag, row string and column number.
    
    Parameters:
    
    String - the well row
    
    int - the well column
  - Well
```
public Well(String row,
            int column,
            Collection<Integer> data)
```
    Creates a new Well object using the numerical type flag, row string, column number and data set.
    
    Parameters:
    
    String - the well row
    
    int - the well column
    
    Collection - the data set
  - Well
```
public Well(String row,
            int column,
            Integer[] data)
```
    Creates a new Well object using the numerical type flag, row string, column number and data set.
    
    Parameters:
    
    String - the well row
    
    int - the well column
    
    Integer[] - the data set
  - Well
```
public Well(int row,
            String column)
```
    Creates a new Well object using the numerical type flag, row number and column string.
    
    Parameters:
    
    int - the well row
    
    String - the well column
    
    Throws:
    
    IllegalArgumentException - invalid column value
  - Well
```
public Well(int row,
            String column,
            Collection<Integer> data)
```
    Creates a new Well object using the numerical type flag, row number and column string.
    
    Parameters:
    
    int - the well row
    
    String - the well column
    
    Collection - the data set
    
    Throws:
    
    IllegalArgumentException - invalid column value
  - Well
```
public Well(int row,
            String column,
            Integer[] data)
```
    Creates a new Well object using the numerical type flag, row number and column string.
    
    Parameters:
    
    int - the well row
    
    String - the well column
    
    Integer[] - the data set
    
    Throws:
    
    IllegalArgumentException - invalid column value
  - Well
```
public Well(String row,
            String column)
```
    Creates a new Well object using the numerical type flag, row and column strings.
    
    Parameters:
    
    String - the well row
    
    String - the well column
    
    Throws:
    
    IllegalArgumentException - invalid column value
  - Well
```
public Well(String row,
            String column,
            Collection<Integer> data)
```
    Creates a new Well object using the numerical type flag, row string, column string and data set.
    
    Parameters:
    
    String - the well row
    
    String - the well column
    
    Collection - the data set
    
    Throws:
    
    IllegalArgumentException - invalid column value
  - Well
```
public Well(String row,
            String column,
            Integer[] data)
```
    Creates a new Well object using the numerical type flag, row and column strings.
    
    Parameters:
    
    String - the well row
    
    String - the well column
    
    Integer[] - the data set
    
    Throws:
    
    IllegalArgumentException - invalid column value
  - Well
```
public Well(String wellID)
```
    Creates a new Well object from a string holding the column and row values. The string must be in the format [a-ZA-Z]+[0-9]+
    
    Parameters:
    
    String - the well index
  - Well
```
public Well(String wellID,
            Collection<Integer> data)
```
    Creates a new Well object using the numerical type flag and a string holding the column and row values. The string must be in the format [a-ZA-Z]+[0-9]+
    
    Parameters:
    
    String - the well index
    
    Collection - the data set
  - Well
```
public Well(String wellID,
            Integer[] data)
```
    Creates a new Well object using the numerical type flag and a string holding the column and row values. The string must be in the format [a-ZA-Z]+[0-9]+
    
    Parameters:
    
    String - the well index
    
    Integer[] - the data set
  - Well
```
public Well(Well well)
```
    Clones a double well without invoking clone.
    
    Parameters:
    
    WellPrecursor - the well to clone
- Method Detail
  - data
```
public List<Integer> data()
```
    Returns the data set.
    
    Specified by:
    
    data in class WellPrecursor<Integer>
    
    Returns:
    
    the data set
  - toDouble
```
public List<Double> toDouble()
```
    Returns the well data set as a list of doubles. Overflow results in an arithmetic exception.
    
    Returns:
    
    the data set
  - toDoubleArray
```
public double[] toDoubleArray()
```
    Returns the well data set as an array of doubles. Overflow results in an arithmetic exception.
    
    Returns:
    
    the data set
  - toByte
```
public List<Byte> toByte()
```
    Returns the well data set as a list of bytes. Overflow results in an arithmetic exception.
    
    Returns:
    
    the data set
  - toByteArray
```
public byte[] toByteArray()
```
    Returns the well data set as an array of bytes. Overflow results in an arithmetic exception.
    
    Returns:
    
    the data set
  - toShort
```
public List<Short> toShort()
```
    Returns the well data set as a list of shorts. Overflow results in an arithmetic exception.
    
    Returns:
    
    the data set
  - toShortArray
```
public short[] toShortArray()
```
    Returns the well data set as an array of shorts. Overflow results in an arithmetic exception.
    
    Returns:
    
    the data set
  - toInt
```
public List<Integer> toInt()
```
    Returns the well data set as an array of shorts. Overflow results in an arithmetic exception.
    
    Returns:
    
    the data set
  - toIntArray
```
public int[] toIntArray()
```
    Returns the well data set as an array of integers. Overflow results in an arithmetic exception.
    
    Returns:
    
    the data set
  - toLong
```
public List<Long> toLong()
```
    Returns the well data set as a list of longs. Overflow results in an arithmetic exception.
    
    Returns:
    
    the data set
  - toLongArray
```
public long[] toLongArray()
```
    Returns the well data set as an array of longs. Overflow results in an arithmetic exception.
    
    Returns:
    
    the data set
  - toFloat
```
public List<Float> toFloat()
```
    Returns the well data set as a list of floats. Overflow results in an arithmetic exception.
    
    Returns:
    
    the data set
  - toFloatArray
```
public float[] toFloatArray()
```
    Returns the well data set as an array of floats. Overflow results in an arithmetic exception.
    
    Returns:
    
    the data set
  - toBigDecimal
```
public List<BigDecimal> toBigDecimal()
```
    Returns the well data set as a list of big decimals.
    
    Returns:
    
    the data set
  - toBigDecimalArray
```
public BigDecimal[] toBigDecimalArray()
```
    Returns the well data set as a list of big decimals.
    
    Returns:
    
    the data set
  - toBigInteger
```
public List<BigInteger> toBigInteger()
```
    Returns the well data set as a list of big integers.
    
    Returns:
    
    the data set
  - toBigIntegerArray
```
public BigInteger[] toBigIntegerArray()
```
    Returns the well data set as an array of big integers.
    
    Returns:
    
    the data set
  - add
```
public void add(Integer datum)
```
    Adds a single data point to a well.
    
    Parameters:
    
    Integer - the value to add
  - add
```
public void add(Collection<Integer> collection)
```
    Adds a collection of numbers to the data set.
    
    Parameters:
    
    Collection - the data to add
  - add
```
public void add(Integer[] array)
```
    Adds an array of numbers to the data set.
    
    Parameters:
    
    Integer[] - the data to add
  - add
```
public void add(Well well)
```
    Adds the data from another well.
    
    Parameters:
    
    WellPrecursor - the well with data set to add
  - add
```
public void add(WellSet set)
```
    Adds the data from each well in the well set.
    
    Parameters:
    
    WellSet - the well set to add
  - replaceData
```
public void replaceData(Integer datum)
```
    Clears the data set and adds the number.
    
    Parameters:
    
    Integer - replacement datum
  - replaceData
```
public void replaceData(Collection<Integer> collection)
```
    Clears the data set and adds the collection.
    
    Parameters:
    
    Collection - replacement data
  - replaceData
```
public void replaceData(Integer[] array)
```
    Clears the data set and adds the array.
    
    Parameters:
    
    Integer[] - replacement data
  - replaceData
```
public void replaceData(Well well)
```
    Clears the data set and adds the well data set.
    
    Parameters:
    
    WellPrecursor - well with replacement data
  - replaceData
```
public void replaceData(WellSet set)
```
    Clears the data set and adds the data from each well in the set.
    
    Parameters:
    
    WellSet - set of wells with replacement data
  - remove
```
public void remove(Integer number)
```
    Removes the value from the data set.
    
    Parameters:
    
    Integer - datum for removal
  - remove
```
public void remove(Collection<Integer> collection)
```
    Removes all the values in the collection from the data set.
    
    Parameters:
    
    Collection - data for removal
  - remove
```
public void remove(Integer[] array)
```
    Removes all the values in the array from the data set.
    
    Parameters:
    
    Integer[] - data for removal
  - removeWell
```
public void removeWell(Well well)
```
    Removes all the well values from the data set.
    
    Parameters:
    
    WellPrecursor - well with data for removal
  - removeSet
```
public void removeSet(WellSet set)
```
    Removes the well values for each well from the data set.
    
    Parameters:
    
    WellSet - wells with replacement data
  - removeRange
```
public void removeRange(int begin,
                        int end)
```
    Removes all values within the indices.
    
    Parameters:
    
    int - beginning index
    
    int - number of values to remove
  - retain
```
public void retain(Integer number)
```
    Retains the values in the data set.
    
    Parameters:
    
    Integer - datum for retention
  - retain
```
public void retain(Collection<Integer> collection)
```
    Retains all the values in the collection.
    
    Parameters:
    
    Collection - data for retention
  - retain
```
public void retain(Integer[] array)
```
    Retains all the values in the array.
    
    Parameters:
    
    Integer[] - data for retention
  - retainWell
```
public void retainWell(Well well)
```
    Retains all the values in the well.
    
    Parameters:
    
    WellPrecursor - well with data for retention
  - retainSet
```
public void retainSet(WellSet set)
```
    Retains all the values in each well.
    
    Parameters:
    
    WellSet - wells with retention data
  - retainRange
```
public void retainRange(int begin,
                        int end)
```
    Retains all values within the indices.
    
    Parameters:
    
    int - beginning index
    
    int - number of values to remove
  - size
```
public int size()
```
    Returns the size of the well data set.
    
    Returns:
    
    the number of values in the data set
  - clear
```
public void clear()
```
    Clears the well data.
  - isEmpty
```
public boolean isEmpty()
```
    Returns true if the well data set is empty and false otherwise.
    
    Returns:
    
    true if the data set is empty
  - subList
```
public Well subList(int begin,
                    int length)
```
    Returns a new well containing the values within the indices.
    
    Parameters:
    
    int - beginning index
    
    int - number of values to remove
    
    Returns:
    
    the new well
  - contains
```
public boolean contains(Integer number)
```
    Returns true if the well data set contains the value.
    
    Parameters:
    
    Integer - the input value
    
    Returns:
    
    true if the data set contains the value
  - indexOf
```
public int indexOf(Integer number)
```
    Returns the index of the first occurrence of the specified element in this list, or -1 if this list does not contain the element.
    
    Parameters:
    
    Integer - the input value
    
    Returns:
    
    the index
  - get
```
public Integer get(int index)
```
    Returns the value at the specified index.
    
    Parameters:
    
    int - the index
    
    Returns:
    
    the value at the index
  - lastIndexOf
```
public double lastIndexOf(Integer number)
```
    Returns the index of the last occurrence of the specified element in this list, or -1 if this list does not contain the element.
    
    Parameters:
    
    int - the index
    
    Returns:
    
    the index of the last occurrence
  - iterator
```
public Iterator<Integer> iterator()
```
    Returns an iterator for the well data set.
    
    Specified by:
    
    iterator in interface Iterable<Integer>
    
    Returns:
    
    the iterator
  - equals
```
public boolean equals(Object object)
```
    Wells are equivalent if the row, column and ALPHA_BASE fields are equivalent.
    
    Overrides:
    
    equals in class Object
    
    Parameters:
    
    Object - the object
    
    Returns:
    
    true if equal, false otherwise

Class Well

Field Summary

Fields inherited from class com.github.jessemull.microflexinteger.plate.WellPrecursor

Constructor Summary

Method Summary

Methods inherited from class com.github.jessemull.microflexinteger.plate.WellPrecursor

Methods inherited from class java.lang.Object

Methods inherited from interface java.lang.Iterable

Constructor Detail

Well

Well

Well

Well

Well

Well

Well

Well

Well

Well

Well

Well

Well

Well

Well

Well

Method Detail

data

toDouble

toDoubleArray

toByte

toByteArray

toShort

toShortArray

toInt

toIntArray

toLong

toLongArray

toFloat

toFloatArray

toBigDecimal

toBigDecimalArray

toBigInteger

toBigIntegerArray

add

add

add

add

add

replaceData

replaceData

replaceData

replaceData

replaceData

remove

remove

remove

removeWell

removeSet

removeRange

retain

retain

retain

retainWell

retainSet

retainRange

size

clear

isEmpty

subList

contains

indexOf

get

lastIndexOf

iterator

equals