com.chemaxon.overlap.result

Interface KnnResults

All Superinterfaces:

NnResults, Serializable

All Known Implementing Classes:

FixedKnnResultsImpl, IndexedKnnResultsImpl

@Beta
public interface KnnResults
extends NnResults

Results of at most K nearest neighbors calculations. Queries are indexed from 0 to NnResults.getQueryCount()-1. For at least one neighbor index (NnResults.getMostSimilarNeighbor(int)) with a dissimilarity value (NnResults.getMostSimilarDissimilarity(int)) is stored. Interpretation of the query and target indices is implementation dependent. Note that some search implementation might accept dissimilarity threshold values which might result in no hits for certain queries. Such queries are not represented by an instance of this interface and the index mapping must be provided outside.

Note that the stored neighbor count might not be constant for implementations providing such thresholds.

This result object holds ordered target-query-dissimilarity triplets. Self and inter-set nearest neighbor list can be represented by this type. When self knn is represented reference to the actual query is not part of the resulted nearest neighbor lists.

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() Deprecated. Use getMinNeighborCount() and getMaxNeighborCount()
int	getMaxNeighborCount() Maximal neighbor count represented.
int	getMinNeighborCount() Minimal neighbor count represented.
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 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.

Methods inherited from interface com.chemaxon.overlap.result.NnResults

getMaxDissimilarity, getMaxNeighborIndex, getMinDissimilarity, getMinNeighborIndex, getMostSimilarDissimilarity, getMostSimilarNeighbor, getQueryCount

Method Detail

getK

@Deprecated
int getK()

Deprecated. Use getMinNeighborCount() and getMaxNeighborCount()

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

Returns:

Number of maximal neighbor count

getMaxNeighborCount

int getMaxNeighborCount()

Maximal neighbor count represented.

Returns:

Maximal neighbor count

getMinNeighborCount

int getMinNeighborCount()

Minimal neighbor count represented.

Returns:

Minimal neighbor count

getAllNeighborCount

int getAllNeighborCount()

All stored neighbor count.

Returns:

All neighbor count

getNeighbors

int[] getNeighbors(int queryIndex)

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 getK(). The length of the list is the same as the length of getDissimilarities(int).

Parameters:

queryIndex - Index

Returns:

Nearest neighbor IDs for the given query.

getNeighborCountsOfAll

int[] getNeighborCountsOfAll()

Neighbor count of all queries.

Returns:

Neighbor count of all queries.

getNeighbor

int getNeighbor(int queryIndex,
                int neighborIndex)

Index of a single neighbor.

Parameters:

queryIndex - Query

neighborIndex - Neighbor index

Returns:

Neighbor ID or -1

getNthNeighborIdsOfAll

int[] getNthNeighborIdsOfAll(int neighborIndex)

Get n-th neighbor indices for all queries.

Parameters:

neighborIndex - 0-based neigbbor index

Returns:

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

Throws:

IllegalArgumentException - when neighborIndex is less than 0 or more or equal to the getMaxNeighborCount()

getDissimilarities

double[] getDissimilarities(int queryIndex)

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 getK(). The length of the list is the same as the length of getNeighbors(int).

Parameters:

queryIndex - Index of query

Returns:

Dissimilarities of the nearest neighbors of the specified query

getDissimilarity

double getDissimilarity(int queryIndex,
                        int neighborIndex)

Dissimilarity of a single neighbor.

Parameters:

queryIndex - Query

neighborIndex - Neighbor index

Returns:

Dissimilarity or getNeighborDissimilaritiesMissingValue()

getNeighborDissimilaritiesMissingValue

double getNeighborDissimilaritiesMissingValue()

Missing value for results of getNthNeighborDissimilaritiesOfAll(int).

Returns:

Value associated for missing items.

getNthNeighborDissimilaritiesOfAll

double[] getNthNeighborDissimilaritiesOfAll(int neighborIndex)

Get n-th neighbor dissimilarities for all queries.

Parameters:

neighborIndex - 0-based neigbbor index

Returns:

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

Throws:

IllegalArgumentException - when neighborIndex is less than 0

copyNeighborsTo

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

Copy neighbor data to an allocated array.

Parameters:

queryIndex - Query index

neighbors - Array to copy neighbor indices

dissimilarities - Array to copy dissimilarities

Returns:

Number of neighbors copied

Throws:

IllegalArgumentException - when array size is small to store neighbor data