Package de.isas.lipidomics.domain

Class ElementTable

java.lang.Object

java.util.AbstractMap<K,V>

java.util.EnumMap<Element,Integer>

de.isas.lipidomics.domain.ElementTable

All Implemented Interfaces:

Serializable, Cloneable, Map<Element,Integer>

public final class ElementTable
extends EnumMap<Element,Integer>

Accounting table for chemical element frequency. This is used to calculate sum formulas and total masses for a given chemical element distribution, e.g. in a lipid.

Author:

nils.hoffmann

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class java.util.AbstractMap

AbstractMap.SimpleEntry<K extends Object,V extends Object>, AbstractMap.SimpleImmutableEntry<K extends Object,V extends Object>

Nested classes/interfaces inherited from interface java.util.Map

Map.Entry<K extends Object,V extends Object>

Constructor Summary

Constructors

Constructor	Description
ElementTable()	Creates an empty element table.
ElementTable(String sumFormula)	Creates the element table from the provided sum formula.
ElementTable(Map<Element,? extends Integer> m)

Method Summary

Modifier and Type	Method	Description
ElementTable	add(ElementTable other)	Adds the element counts of the provided table to this one.
ElementTable	copy()	Returns an copy of all mappings in this table.
void	decrement(Element element)	Decrements the current count for element by one.
void	decrementBy(Element element, Integer decrement)	Decrement the count of the provided element by the given number.
Double	getMass()	Returns the total summed mass per number of elements.
Double	getMass(Element element)	Returns the individual total mass for the provided element.
String	getSumFormula()	Returns the sum formula for all elements in this table.
void	increment(Element element)	Increment the count of the provided element by one.
void	incrementBy(Element element, Integer increment)	Increment the count of the provided element by the given number.
void	negate(Element element)	Negates the count stored in the table.
ElementTable	subtract(ElementTable elementTable)	Subtracts all element counts in the provided element table from this table.

Methods inherited from class java.util.EnumMap

clear, clone, containsKey, containsValue, entrySet, equals, get, hashCode, keySet, put, putAll, remove, size, values

Methods inherited from class java.util.AbstractMap

isEmpty, toString

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Map

compute, computeIfAbsent, computeIfPresent, forEach, getOrDefault, merge, putIfAbsent, remove, replace, replace, replaceAll

Constructor Detail

ElementTable

public ElementTable(Map<Element,? extends Integer> m)

ElementTable

public ElementTable()

Creates an empty element table.

ElementTable

public ElementTable(String sumFormula)
             throws ParsingException

Creates the element table from the provided sum formula. If an empty string is passed in this will create an empty table.

Parameters:

sumFormula - the sum formula to parse.

Throws:

ParsingException - if the sum formula does not conform with the SumFormula grammar.

Method Detail

add

public ElementTable add(ElementTable other)

Adds the element counts of the provided table to this one.

Parameters:

other - the table to add to this one.

Returns:

a new element table.

increment

public void increment(Element element)

Increment the count of the provided element by one.

Parameters:

element - the element.

incrementBy

public void incrementBy(Element element,
                        Integer increment)

Increment the count of the provided element by the given number.

Parameters:

element - the element.

increment - the increment for the element.

decrement

public void decrement(Element element)

Decrements the current count for element by one.

Parameters:

element - the element to decrement the counts for.

decrementBy

public void decrementBy(Element element,
                        Integer decrement)

Decrement the count of the provided element by the given number.

Parameters:

element - the element.

decrement - the decrement for the element.

negate

public void negate(Element element)

Negates the count stored in the table. E.g. '5' will become '-5', '-5' would become '5'.

Parameters:

element - the element count to negate.

subtract

public ElementTable subtract(ElementTable elementTable)

Subtracts all element counts in the provided element table from this table.

Parameters:

elementTable - the element table to subtract from this.

Returns:

this element table.

getSumFormula

public String getSumFormula()

Returns the sum formula for all elements in this table.

Returns:

the sum formula. Returns an empty string if the table is empty.

getMass

public Double getMass(Element element)

Returns the individual total mass for the provided element.

Parameters:

element - the element to calculate the total mass for.

Returns:

the total mass for the given element, or 0.

getMass

public Double getMass()

Returns the total summed mass per number of elements.

Returns:

the total summed mass for this element table. Returns 0 if the table is empty.

copy

public ElementTable copy()

Returns an copy of all mappings in this table.

Returns:

the element table copy.