magpie.data.materials

Class PrototypeEntry

java.lang.Object

magpie.data.BaseEntry

magpie.data.MultiPropertyEntry

magpie.data.materials.CompositionEntry

magpie.data.materials.PrototypeEntry

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Comparable, java.util.Comparator

public class PrototypeEntry
extends CompositionEntry

Entry in a PrototypeDataset. Stores which elements are on each site, and the corresponding composition.

To Do: Improve the compare / equality to account for prototypes with equivalent sites (ex: ABC == BAC, ABC != ACB)

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected CompositionEntry[]	SiteComp Composition of each site
protected PrototypeSiteInformation	SiteInfo Link to site information from corresponding dataset

Fields inherited from class magpie.data.materials.CompositionEntry

Element, ElementNames, Fraction, HTMLFormat, NumberInCell, SortingOrder

Constructor Summary

Constructors

Constructor and Description
PrototypeEntry(PrototypeSiteInformation SiteInfo) Create a Prototype entry without specifying composition.
PrototypeEntry(PrototypeSiteInformation SiteInfo, java.lang.String Composition) Create a new PrototypeEntry.

Method Summary

Modifier and Type	Method and Description
PrototypeEntry	clone() Generates a clone of an entry.
int	compare(java.lang.Object A_obj, java.lang.Object B_obj)
boolean	equals(java.lang.Object other)
java.util.List<PrototypeEntry>	getEquivalentPrototypes() Generate a list of prototypes equivalent to this entry.
CompositionEntry	getSiteComposition(int index) Get composition of a certain site
double	getSiteGroupMean(int index, double[] lookup) Calculate the mean of an elemental property for a certain site
double	getSiteMean(int index, double[] lookup) Calculate the mean of an elemental property for a certain site
int	hashCode()
int	NSites()
void	setSiteComposition(int index, CompositionEntry composition) Set the composition of a certain site
java.lang.String	toHTMLString() Print entry in a HTML-friendly format.
org.json.JSONObject	toJSON() Print entry as a JSON object
java.lang.String	toString()

Methods inherited from class magpie.data.materials.CompositionEntry

combineCompositions, getAverageDeviation, getAverageDeviation, getElementFraction, getElementFraction, getElements, getFractions, getMaxDifference, getMaximum, getMean, getMinimum, getMost, getSortingOrder, printNumber, rectifyEntry, setComposition

Methods inherited from class magpie.data.MultiPropertyEntry

addProperty, addProperty, addProperty, clearPropertyData, deleteMeasuredClass, deletePredictedClass, getClassProbilities, getMeasuredClass, getMeasuredProperties, getMeasuredProperty, getPredictedClass, getPredictedProperty, getPropertyClassProbabilties, getTargetProperty, hasClassProbabilities, hasMeasuredProperty, hasMeasurement, hasPredictedProperty, hasPrediction, hasPropertyClassProbabilities, NProperties, setClassProbabilities, setMeasuredClass, setMeasuredProperties, setMeasuredProperty, setNProperties, setPredictedClass, setPredictedProperty, setPredictedProperty, setTargetProperty, usingPropertyAsClass

Methods inherited from class magpie.data.BaseEntry

addAttribute, addAttributes, clearAttributes, compareTo, getAttribute, getAttributes, NAttributes, reduceMemoryFootprint, setAttribute, setAttributes

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Comparator

comparing, comparing, comparingDouble, comparingInt, comparingLong, naturalOrder, nullsFirst, nullsLast, reversed, reverseOrder, thenComparing, thenComparing, thenComparing, thenComparingDouble, thenComparingInt, thenComparingLong

Field Detail

SiteInfo

protected final PrototypeSiteInformation SiteInfo

Link to site information from corresponding dataset

SiteComp

protected CompositionEntry[] SiteComp

Composition of each site

Constructor Detail

PrototypeEntry

public PrototypeEntry(PrototypeSiteInformation SiteInfo,
                      java.lang.String Composition)
               throws java.lang.Exception

Create a new PrototypeEntry. See PrototypeDataset

Parameters:

SiteInfo - Information about each site in prototype crystal

Composition - String describing elements on each site

Throws:

java.lang.Exception - If parse fails

PrototypeEntry

public PrototypeEntry(PrototypeSiteInformation SiteInfo)

Create a Prototype entry without specifying composition. These must be defined later for the entry to be usable (by using setSiteComposition(int, magpie.data.materials.CompositionEntry))

Parameters:

SiteInfo - Information about each site in prototype crystalm

Method Detail

clone

public PrototypeEntry clone()

Description copied from class: BaseEntry

Generates a clone of an entry. It creates a new list to store the attributes. So, the attribute data is preserved, but you can change the list as desired.

Overrides:

clone in class CompositionEntry

Returns:

Clone

getSiteComposition

public CompositionEntry getSiteComposition(int index)

Get composition of a certain site

Parameters:

index - Desired site index

Returns:

Composition of that site

setSiteComposition

public void setSiteComposition(int index,
                               CompositionEntry composition)

Set the composition of a certain site

Parameters:

index - Index of site in question

composition - Desired composition

equals

public boolean equals(java.lang.Object other)

Specified by:

equals in interface java.util.Comparator

Overrides:

equals in class CompositionEntry

getEquivalentPrototypes

public java.util.List<PrototypeEntry> getEquivalentPrototypes()

Generate a list of prototypes equivalent to this entry.

Returns:

List of all entries that would be equivalent to this one

hashCode

public int hashCode()

Overrides:

hashCode in class CompositionEntry

compare

public int compare(java.lang.Object A_obj,
                   java.lang.Object B_obj)

Specified by:

compare in interface java.util.Comparator

Overrides:

compare in class CompositionEntry

NSites

public int NSites()

Returns:

Number of sites in prototype crystal structure

getSiteMean

public double getSiteMean(int index,
                          double[] lookup)

Calculate the mean of an elemental property for a certain site

Parameters:

index - Desired site index

lookup - Lookup table of elemental properties

Returns:

Composition-weighted mean of supplied elemental property on that site

getSiteGroupMean

public double getSiteGroupMean(int index,
                               double[] lookup)

Calculate the mean of an elemental property for a certain site

Parameters:

index - Desired site group index

lookup - Lookup table of elemental properties

Returns:

Composition-weighted mean of supplied elemental property on that site

toHTMLString

public java.lang.String toHTMLString()

Description copied from class: BaseEntry

Print entry in a HTML-friendly format.

Overrides:

toHTMLString in class CompositionEntry

Returns:

Entry as a string

toString

public java.lang.String toString()

Overrides:

toString in class CompositionEntry

toJSON

public org.json.JSONObject toJSON()

Description copied from class: BaseEntry

Print entry as a JSON object

Overrides:

toJSON in class CompositionEntry

Returns:

JSON object