com.chemaxon.overlap.wui.resources

Class KnnResource

java.lang.Object

com.chemaxon.overlap.wui.resources.KnnResource

@Path(value="knn-results")
public final class KnnResource
extends Object

KNN analysis results JAX-RS resource.

Constructor Summary

Constructors

Constructor and Description
KnnResource()

Method Summary

Modifier and Type	Method and Description
KnnsInfo	get() Description of available KNN results.
KnnData	getKnnData(String res) Knn data.
KnnInfo	getKnnInfo(String res) Description of a knn result.
MoleculePropRange	getNeighborCounts(KnnRes res) Stored neighbor count for each record.
MoleculePropRange	getNeighborDissimilarities(KnnRes res, int k, String missing) Dissimilarities of the k-th most similar neighbors.
MoleculePropRange	getNeighborIndices(KnnRes res, int k, String missing) Indices of the k-th most similar neighbors.
byte[]	getNeighborPngOrPlaceholder(KnnRes res, int queryIndex, int neighborIndex, int w, int h, String aromatize, String hydrogenize) Get molecule image for a specific neighbor in PNG format or a placeholder image for absent molecules.
MoleculePropRange	getNeighborProps(KnnRes res, int k, String propname, String missing) Additional stored property of the k-th most similar neighbors for all queries.
MoleculePropRange	getQueryIndices(KnnRes res, String missing) Indices of the queries.
byte[]	getQueryPngOrPlaceholder(KnnRes res, int queryIndex, int w, int h, String aromatize, String hydrogenize) Get molecule image for a query in PNG format or a placeholder image for absent molecules.
SizeInfoDto	getSizeinfo(KnnRes res, SizeInfoMethod method) Experimental endpoint to estimate allocated size.
KnnTableLabels	getTableLabels(KnnRes res, List<Integer> queries, List<Integer> neighbors, String missing) Get labels to be displayed in a k-NN view table.

Methods inherited from class java.lang.Object

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

Constructor Detail

KnnResource

public KnnResource()

Method Detail

get

@GET
 @Produces(value="application/json")
public KnnsInfo get()

Description of available KNN results.

Returns:

Available knn results.

getKnnInfo

@GET
 @Path(value="{res}")
 @Produces(value="application/json")
public KnnInfo getKnnInfo(@PathParam(value="res")
                                                                                          String res)

Description of a knn result.

Parameters:

res - Knn results name

Returns:

Description of a knn result.

getKnnData

@GET
 @Path(value="{res}/knndata")
 @Produces(value="application/json")
public KnnData getKnnData(@PathParam(value="res")
                                                                                                  String res)

Knn data.

Parameters:

res - Knn results name

Returns:

Knn data.

getQueryIndices

@GET
 @Path(value="{res}/queryindices")
 @Produces(value="application/json")
public MoleculePropRange getQueryIndices(@PathParam(value="res")
                                                                                                                      KnnRes res,
                                                                                                                      @QueryParam(value="missing") @DefaultValue(value="????")
                                                                                                                      String missing)

Indices of the queries.

Parameters:

res - Knn results name

missing - Missing value marker; not used.

Returns:

Indices of the specified neighbor for each query

getNeighborCounts

@GET
 @Path(value="{res}/neighborcounts")
 @Produces(value="application/json")
public MoleculePropRange getNeighborCounts(@PathParam(value="res")
                                                                                                                          KnnRes res)

Stored neighbor count for each record.

Parameters:

res - Knn results name

Returns:

Neighbor count for all queries

getNeighborPngOrPlaceholder

@GET
 @Path(value="{res}/neighbor-png-or-placeholder")
 @Produces(value="image/png")
public byte[] getNeighborPngOrPlaceholder(@PathParam(value="res")
                                                                                                                               KnnRes res,
                                                                                                                               @QueryParam(value="query")
                                                                                                                               int queryIndex,
                                                                                                                               @QueryParam(value="neighbor")
                                                                                                                               int neighborIndex,
                                                                                                                               @QueryParam(value="w") @DefaultValue(value="100")
                                                                                                                               int w,
                                                                                                                               @QueryParam(value="h") @DefaultValue(value="100")
                                                                                                                               int h,
                                                                                                                               @QueryParam(value="aromatize") @DefaultValue(value="source")
                                                                                                                               String aromatize,
                                                                                                                               @QueryParam(value="hydrogenize") @DefaultValue(value="source")
                                                                                                                               String hydrogenize)
                                                                                                                        throws IOException,
                                                                                                                               WuiNotFoundException

Get molecule image for a specific neighbor in PNG format or a placeholder image for absent molecules. When the given molecule is absent then a placeholder image is generated. This call delegates to the target molecule sets MoleculesResource.getPngOrPlaceholder(com.chemaxon.overlap.wui.res.MolsRes, int, int, int, java.lang.String, java.lang.String) with translation to the actual neighbor target.

Parameters:

res - Knn results name

queryIndex - Qurery index

neighborIndex - Neighbor index

w - Image width in pixels

h - Image height in pixels

aromatize - Aromatize options, use source, aromatize or dearomatize

hydrogenize - Hydrogenize options. use source, hydrogenize or dehydrogenize

Returns:

Molecule in SDF format with ID set to SDF property "id".

Throws:

IOException - Propagated from MolExporter

WuiNotFoundException

getQueryPngOrPlaceholder

@GET
 @Path(value="{res}/query-png-or-placeholder")
 @Produces(value="image/png")
public byte[] getQueryPngOrPlaceholder(@PathParam(value="res")
                                                                                                                         KnnRes res,
                                                                                                                         @QueryParam(value="query")
                                                                                                                         int queryIndex,
                                                                                                                         @QueryParam(value="w") @DefaultValue(value="100")
                                                                                                                         int w,
                                                                                                                         @QueryParam(value="h") @DefaultValue(value="100")
                                                                                                                         int h,
                                                                                                                         @QueryParam(value="aromatize") @DefaultValue(value="source")
                                                                                                                         String aromatize,
                                                                                                                         @QueryParam(value="hydrogenize") @DefaultValue(value="source")
                                                                                                                         String hydrogenize)
                                                                                                                  throws IOException,
                                                                                                                         WuiNotFoundException

Get molecule image for a query in PNG format or a placeholder image for absent molecules. When the given molecule is absent then a placeholder image is generated. This call delegates to the query molecule sets MoleculesResource.getPngOrPlaceholder(com.chemaxon.overlap.wui.res.MolsRes, int, int, int, java.lang.String, java.lang.String) with translation to the actual query master index.

Parameters:

res - Knn results name

queryIndex - Qurery index in the knn resuls

w - Image width in pixels

h - Image height in pixels

aromatize - Aromatize options, use source, aromatize or dearomatize

hydrogenize - Hydrogenize options. use source, hydrogenize or dehydrogenize

Returns:

Molecule in SDF format with ID set to SDF property "id".

Throws:

IOException - Propagated from MolExporter

WuiNotFoundException

getNeighborIndices

@GET
 @Path(value="{res}/neighbors/{k}/indices")
 @Produces(value="application/json")
public MoleculePropRange getNeighborIndices(@PathParam(value="res")
                                                                                                                                  KnnRes res,
                                                                                                                                  @PathParam(value="k")
                                                                                                                                  int k,
                                                                                                                                  @QueryParam(value="missing") @DefaultValue(value="????")
                                                                                                                                  String missing)

Indices of the k-th most similar neighbors.

Parameters:

res - Knn results name

k - Neighbor index (0-based)

missing - Value to use for missing k-th neighbors.

Returns:

Indices of the specified neighbor for each query

getNeighborDissimilarities

@GET
 @Path(value="{res}/neighbors/{k}/dissimilarities")
 @Produces(value="application/json")
public MoleculePropRange getNeighborDissimilarities(@PathParam(value="res")
                                                                                                                                                  KnnRes res,
                                                                                                                                                  @PathParam(value="k")
                                                                                                                                                  int k,
                                                                                                                                                  @QueryParam(value="missing") @DefaultValue(value="????")
                                                                                                                                                  String missing)

Dissimilarities of the k-th most similar neighbors.

Parameters:

res - Knn results name

k - Neighbor index (0-based)

missing - Value to use for missing k-th neighbors.

Returns:

Dissimilarities of the specified neighbor for each query

getNeighborProps

@GET
 @Path(value="{res}/neighbors/{k}/props/{propname}")
 @Produces(value="application/json")
public MoleculePropRange getNeighborProps(@PathParam(value="res")
                                                                                                                                         KnnRes res,
                                                                                                                                         @PathParam(value="k")
                                                                                                                                         int k,
                                                                                                                                         @PathParam(value="propname")
                                                                                                                                         String propname,
                                                                                                                                         @QueryParam(value="missing") @DefaultValue(value="????")
                                                                                                                                         String missing)

Additional stored property of the k-th most similar neighbors for all queries.

Parameters:

res - Knn results name

k - Neighbor index (0-based)

propname - Property name

missing - Value to use for missing values. Note that a property value is considered missing when the specified neighbor is not stored or when the specified neighbor is stored but its specified property value is not available.

Returns:

Property for k-th nearest neighbor of all queries

getTableLabels

@POST
 @Path(value="{res}/table-labels")
 @Consumes(value="application/x-www-form-urlencoded")
 @Produces(value="application/json")
public KnnTableLabels getTableLabels(@PathParam(value="res")
                                                                                                                                                                         KnnRes res,
                                                                                                                                                                         @FormParam(value="queries[]")
                                                                                                                                                                         List<Integer> queries,
                                                                                                                                                                         @FormParam(value="neighbors[]")
                                                                                                                                                                         List<Integer> neighbors,
                                                                                                                                                                         @QueryParam(value="missing") @DefaultValue(value="????")
                                                                                                                                                                         String missing)

Get labels to be displayed in a k-NN view table. A typical visualization use case is to display some of the neighbors of some of the queries along with IDs.

Parameters:

res - Knn results name

queries - Query indices in the kNN table

neighbors - Neighbors to retrieve

missing - Value to use for missing values.

Returns:

Collected labels

getSizeinfo

@Beta
 @GET
 @Produces(value="application/json")
 @Path(value="{res}/get-sizeinfo")
public SizeInfoDto getSizeinfo(@PathParam(value="res")
                                                                                                                   KnnRes res,
                                                                                                                   @QueryParam(value="method")
                                                                                                                   SizeInfoMethod method)

Experimental endpoint to estimate allocated size. Please note that this endpoint is under construction, use with caution: execution might fail and execution might have significant memory/cpu impact. The availability/functionality of this endpoint might change in any of the subsequent releases.

Parameters:

res - Knn results name

method - Size info method to use.

Returns:

Size info description