magpie.data.utilities.modifiers

Class CompositionSetDistanceModifier

java.lang.Object

magpie.data.utilities.modifiers.BaseDatasetModifier

magpie.data.utilities.modifiers.CompositionSetDistanceModifier

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, Options

public class CompositionSetDistanceModifier
extends BaseDatasetModifier

Compute the distance of composition from those in a user-supplied dataset, store as a property. Distance is defined as the minimum distance of a composition from the composition of any entry in another dataset.

Name of the new property is compdistance

Note: Euclidean distance is much faster than Manhattan. Weka's algorithms for fast neighbor search are not designed to work with Manhattan distance.

Usage: $<dataset> <-manhattan|-euclidean>
dataset: CompositionDataset from which to measure distance
-manhattan: Compute Manhattan distance
-euclidean: Compute Euclidean distance

See Also:

CompositionSetDistanceFilter, Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected java.util.Set<CompositionEntry>	Compositions Set of compositions to compute distance from
protected boolean	UseManhattan Whether to use Manhattan distance (vs Euclidean)

Constructor Summary

Constructors

Constructor and Description
CompositionSetDistanceModifier()

Method Summary

Modifier and Type	Method and Description
void	addComposition(CompositionEntry entry) Add a new composition to the dataset.
void	addCompositions(java.util.Collection<CompositionEntry> comps) Add a list of compositions to the set
void	clearCompositions() Clear the list of compositions in set
protected void	modifyDataset(Dataset Data) Apply changes to the Dataset.
java.lang.String	printUsage() Print out required format for options.
void	setCompositions(CompositionDataset data) Set the list of compositions to be considered
void	setOptions(java.util.List<java.lang.Object> Options) Set any options for this object.
void	setUseManhattan(boolean manhattan) Set whether to use Manhattan (vs Euclidean) distance

Methods inherited from class magpie.data.utilities.modifiers.BaseDatasetModifier

transform

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

Compositions

protected final java.util.Set<CompositionEntry> Compositions

Set of compositions to compute distance from

UseManhattan

protected boolean UseManhattan

Whether to use Manhattan distance (vs Euclidean)

Constructor Detail

CompositionSetDistanceModifier

public CompositionSetDistanceModifier()

Method Detail

setOptions

public void setOptions(java.util.List<java.lang.Object> Options)
                throws java.lang.Exception

Description copied from interface: Options

Set any options for this object. If parsing the options fails, return an Exception with the usage as its message.

Parameters:

Options - Array of options as Objects - can be null

Throws:

java.lang.Exception - if problem with inputs

printUsage

public java.lang.String printUsage()

Description copied from interface: Options

Print out required format for options. For consistency, should start with "Usage: ".

Returns:

Usage for this function

setUseManhattan

public void setUseManhattan(boolean manhattan)

Set whether to use Manhattan (vs Euclidean) distance

Parameters:

manhattan - Desired setting

clearCompositions

public void clearCompositions()

Clear the list of compositions in set

addComposition

public void addComposition(CompositionEntry entry)

Add a new composition to the dataset.

Parameters:

entry - Entry to be added

addCompositions

public void addCompositions(java.util.Collection<CompositionEntry> comps)

Add a list of compositions to the set

Parameters:

comps - Collection of compositions to be added

setCompositions

public void setCompositions(CompositionDataset data)

Set the list of compositions to be considered

Parameters:

data - Dataset containing compositions to use as dataset

modifyDataset

protected void modifyDataset(Dataset Data)

Description copied from class: BaseDatasetModifier

Apply changes to the Dataset. Should modify both each entries and the dataset as a whole.

Specified by:

modifyDataset in class BaseDatasetModifier

Parameters:

Data - Dataset to be modified