com.chemaxon.overlap.result.impl

Class IndexedKnnResultsImpl

java.lang.Object

com.chemaxon.overlap.result.impl.IndexedKnnResultsImpl

All Implemented Interfaces:

KnnResults, NnResults, Serializable

@Beta
public final class IndexedKnnResultsImpl
extends Object
implements KnnResults, Serializable

Arrays of primitives backed implementation of KnnResults for variabl neighbor count.

Note that query and target IDs might refer to the same or different sets. If they refer to the same set the nearest neighbor list does not contain self ID.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
IndexedKnnResultsImpl(List<int[]> targets, List<double[]> dissimilarities) Construct.

Method Summary

Modifier and Type	Method and Description
int	copyNeighborsTo(int queryIndex, int[] neighbors, double[] dissimilarities) Copy neighbor data to an allocated array.
int	getAllNeighborCount() All stored neighbor count.
double[]	getDissimilarities(int queryIndex) Dissimilarity.
double	getDissimilarity(int queryIndex, int neighborIndex) Dissimilarity of a single neighbor.
int	getK() Value of k.
double	getMaxDissimilarity() Upper bound of dissimilarity values.
int	getMaxNeighborCount() Maximal neighbor count represented.
int	getMaxNeighborIndex() Upper bound of neighbor index values.
double	getMinDissimilarity() Lower bound of dissimilarity values.
int	getMinNeighborCount() Minimal neighbor count represented.
int	getMinNeighborIndex() Lower bound of neighbor index values.
double	getMostSimilarDissimilarity(int queryIndex) Dissimilarity of the most similar neighbor.
int	getMostSimilarNeighbor(int queryIndex) Index of most similar neighbor.
int	getNeighbor(int queryIndex, int neighborIndex) Index of a single neighbor.
int[]	getNeighborCountsOfAll() Neighbor count of all queries.
double	getNeighborDissimilaritiesMissingValue() Missing value for results of KnnResults.getNthNeighborDissimilaritiesOfAll(int).
int[]	getNeighbors(int queryIndex) ID of the nearest neighbors of query.
double[]	getNthNeighborDissimilaritiesOfAll(int neighborIndex) Get n-th neighbor dissimilarities for all queries.
int[]	getNthNeighborIdsOfAll(int neighborIndex) Get n-th neighbor indices for all queries.
int	getQueryCount() Number of queries stored.
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

IndexedKnnResultsImpl

public IndexedKnnResultsImpl(List<int[]> targets,
                             List<double[]> dissimilarities)

Construct.

Parameters:

targets - nearest neighbors

dissimilarities - Dissimilarities

Throws:

IllegalArgumentException - when array sizes mismatch or dissimilarities array contains NaN or INF value

Method Detail

toString

public String toString()

Overrides:

toString in class Object

getK

public int getK()

Description copied from interface: KnnResults

Value of k. Note that when thresholds are considered the neighbor count might not be constant.

Specified by:

getK in interface KnnResults

Returns:

Number of maximal neighbor count

getMinNeighborCount

public int getMinNeighborCount()

Description copied from interface: KnnResults

Minimal neighbor count represented.

Specified by:

getMinNeighborCount in interface KnnResults

Returns:

Minimal neighbor count

getMaxNeighborCount

public int getMaxNeighborCount()

Description copied from interface: KnnResults

Maximal neighbor count represented.

Specified by:

getMaxNeighborCount in interface KnnResults

Returns:

Maximal neighbor count

getAllNeighborCount

public int getAllNeighborCount()

Description copied from interface: KnnResults

All stored neighbor count.

Specified by:

getAllNeighborCount in interface KnnResults

Returns:

All neighbor count

getQueryCount

public int getQueryCount()

Description copied from interface: NnResults

Number of queries stored.

Specified by:

getQueryCount in interface NnResults

Returns:

Number of queries stored

getNeighbors

public int[] getNeighbors(int queryIndex)

Description copied from interface: KnnResults

ID of the nearest neighbors of query. Reference to the query in case of self knn is excluded. Note that upper and lower bounds returned by NnResults.getMinNeighborIndex() and NnResults.getMaxNeighborIndex() are valid for all neighbors.

First element of the returned list is the same as NnResults.getMostSimilarNeighbor(int). The length of the list might vary from query to query, but is non-empty and no longer than the value of KnnResults.getK(). The length of the list is the same as the length of KnnResults.getDissimilarities(int).

Specified by:

getNeighbors in interface KnnResults

Parameters:

queryIndex - Index

Returns:

Nearest neighbor IDs for the given query.

getDissimilarities

public double[] getDissimilarities(int queryIndex)

Description copied from interface: KnnResults

Dissimilarity. Note that upper and lower bounds returned by NnResults.getMinDissimilarity() and NnResults.getMaxDissimilarity() are valid for all neighbors.

First element of the returned list is the same as NnResults.getMostSimilarDissimilarity(int). The length of the list might vary from query to query, but is non-empty and no longer than the value of KnnResults.getK(). The length of the list is the same as the length of KnnResults.getNeighbors(int).

Specified by:

getDissimilarities in interface KnnResults

Parameters:

queryIndex - Index of query

Returns:

Dissimilarities of the nearest neighbors of the specified query

copyNeighborsTo

public int copyNeighborsTo(int queryIndex,
                           int[] neighbors,
                           double[] dissimilarities)

Description copied from interface: KnnResults

Copy neighbor data to an allocated array.

Specified by:

copyNeighborsTo in interface KnnResults

Parameters:

queryIndex - Query index

neighbors - Array to copy neighbor indices

dissimilarities - Array to copy dissimilarities

Returns:

Number of neighbors copied

getMinNeighborIndex

public int getMinNeighborIndex()

Description copied from interface: NnResults

Lower bound of neighbor index values.

Specified by:

getMinNeighborIndex in interface NnResults

Returns:

Lower bound of neighbor index (possibly inclusive but might be broader)

getMaxNeighborIndex

public int getMaxNeighborIndex()

Description copied from interface: NnResults

Upper bound of neighbor index values.

Specified by:

getMaxNeighborIndex in interface NnResults

Returns:

Upper bound neighbor index (possibly inclusive but might be broader)

getMinDissimilarity

public double getMinDissimilarity()

Description copied from interface: NnResults

Lower bound of dissimilarity values.

Specified by:

getMinDissimilarity in interface NnResults

Returns:

Lower bound of dissimilarity values (possibly inclusive but might be broader)

getMaxDissimilarity

public double getMaxDissimilarity()

Description copied from interface: NnResults

Upper bound of dissimilarity values.

Specified by:

getMaxDissimilarity in interface NnResults

Returns:

Upper bound of dissimilarity values (possibly inclusive but might be broader)

getMostSimilarNeighbor

public int getMostSimilarNeighbor(int queryIndex)

Description copied from interface: NnResults

Index of most similar neighbor. Note that when a search implementation consider dissimilarity thresholds the returned neighbor index refers to the most similar target which conforms those thresholds.

Specified by:

getMostSimilarNeighbor in interface NnResults

Parameters:

queryIndex - Index of query

Returns:

Index of most similar neighbor conforming the thresholds

getMostSimilarDissimilarity

public double getMostSimilarDissimilarity(int queryIndex)

Description copied from interface: NnResults

Dissimilarity of the most similar neighbor. Note that when a search implementation consider dissimilarity thresholds the returned dissimilarity refers to the most similar target which conforms those thresholds.

Specified by:

getMostSimilarDissimilarity in interface NnResults

Parameters:

queryIndex - Index of query

Returns:

Dissimilarity of the most similar neighbor conforming the thresholds

getNthNeighborIdsOfAll

public int[] getNthNeighborIdsOfAll(int neighborIndex)

Description copied from interface: KnnResults

Get n-th neighbor indices for all queries.

Specified by:

getNthNeighborIdsOfAll in interface KnnResults

Parameters:

neighborIndex - 0-based neigbbor index

Returns:

n-th neighbor IDs for all queries or -1 when given neighbor is not present

getNeighborDissimilaritiesMissingValue

public double getNeighborDissimilaritiesMissingValue()

Description copied from interface: KnnResults

Missing value for results of KnnResults.getNthNeighborDissimilaritiesOfAll(int).

Specified by:

getNeighborDissimilaritiesMissingValue in interface KnnResults

Returns:

Value associated for missing items.

getNthNeighborDissimilaritiesOfAll

public double[] getNthNeighborDissimilaritiesOfAll(int neighborIndex)

Description copied from interface: KnnResults

Get n-th neighbor dissimilarities for all queries.

Specified by:

getNthNeighborDissimilaritiesOfAll in interface KnnResults

Parameters:

neighborIndex - 0-based neigbbor index

Returns:

n-th neighbor dissimilarities for all queries or KnnResults.getNeighborDissimilaritiesMissingValue() when given neighbor is not present

getNeighborCountsOfAll

public int[] getNeighborCountsOfAll()

Description copied from interface: KnnResults

Neighbor count of all queries.

Specified by:

getNeighborCountsOfAll in interface KnnResults

Returns:

Neighbor count of all queries.

getNeighbor

public int getNeighbor(int queryIndex,
                       int neighborIndex)

Description copied from interface: KnnResults

Index of a single neighbor.

Specified by:

getNeighbor in interface KnnResults

Parameters:

queryIndex - Query

neighborIndex - Neighbor index

Returns:

Neighbor ID or -1

getDissimilarity

public double getDissimilarity(int queryIndex,
                               int neighborIndex)

Description copied from interface: KnnResults

Dissimilarity of a single neighbor.

Specified by:

getDissimilarity in interface KnnResults

Parameters:

queryIndex - Query

neighborIndex - Neighbor index

Returns:

Dissimilarity or KnnResults.getNeighborDissimilaritiesMissingValue()