chemaxon.clustering
Class NearestNeighbors

java.lang.Object
  chemaxon.clustering.Common
      chemaxon.clustering.NearestNeighbors

Direct Known Subclasses:

JarvisPatrick

public class NearestNeighbors

extends Common

Compares two sets of objects (like compound libraries) using diversity and dissimilarity calculations.
This class can be used from command-line or from the API.

• Comparing all individual compounds of a set with a library.
• Comparing two libraries.
• Library self-dissimilarity test: comparing all individual compounds of a set with the rest of the compounds.

An example for running NearestNeighbours:

 ConnectionHandler ch;
 String selectString;
 ...
 NearestNeighbors nn=new NearestNeighbors();
 nn.setInput(ch, selectString);
 nn.setOutput(System.out);
 nn.setDimensions(0);
 nn.setFpSize(0);
 nn.setIdGeneration(true);
 nn.setThreshold(0.1f);
 nn.run();
 

Since:

JChem 1.6.2

Author:

Ferenc Csizmadia, Szilard Dorant

Constructor Summary

NearestNeighbors()

Method Summary

float	getThreshold() Gets the threshold value.
static void	main(java.lang.String[] args) The command line version entry point.
void	run() Starts processing.
void	setInput(ConnectionHandler conh, java.lang.String querySQL) Sets input as an SQL query.
void	setInput(java.io.File file) Sets input as a File.
void	setInput(java.io.InputStream is) Sets input as an InputStream
void	setInput(java.lang.String fileName) Sets input as a file, specified by its path.
void	setThreshold(float threshold) Sets the threshold value.

Methods inherited from class chemaxon.clustering.Common

getDimensions, getElapsedTime, getFpSize, getIdGeneration, getStartTime, getStatStream, getWeights, isOnlyStat, isStatNeeded, setDimensions, setFpSize, setIdGeneration, setOnlyStat, setOutput, setOutput, setOutput, setOutput, setStatNeeded, setStatStream, setWeights

Methods inherited from class java.lang.Object

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

Constructor Detail

NearestNeighbors

public NearestNeighbors()

Method Detail

setInput

public void setInput(ConnectionHandler conh,
                     java.lang.String querySQL)
              throws java.sql.SQLException

Sets input as an SQL query.

Parameters:

conh - ConnectionHandler object opened to the database

querySQL - an SQL SELECT statement used as data source

Throws:

java.sql.SQLException

Since:

JChem 1.6.2

setInput

public void setInput(java.io.File file)
              throws java.io.FileNotFoundException

Sets input as a File.

Parameters:

file - the File to be used for input

Throws:

java.io.FileNotFoundException

Since:

JChem 1.6.2

setInput

public void setInput(java.lang.String fileName)
              throws java.io.FileNotFoundException

Sets input as a file, specified by its path.

Parameters:

fileName - the path of File to be used for input

Throws:

java.io.FileNotFoundException

Since:

JChem 1.6.2

setInput

public void setInput(java.io.InputStream is)

Sets input as an InputStream

Parameters:

is - the InputStream to be used for input

Since:

JChem 1.6.2

setThreshold

public void setThreshold(float threshold)

Sets the threshold value.

Parameters:

threshold - the threshold value to be used

Since:

JChem 1.6.2

getThreshold

public float getThreshold()

Gets the threshold value.

Returns:

the current threshold value

Since:

JChem 1.6.2

run

public void run()
         throws chemaxon.clustering.ClusteringException,
                java.io.IOException,
                java.sql.SQLException,
                chemaxon.clustering.InvalidLicenseKeyException

Starts processing.

Throws:

chemaxon.clustering.ClusteringException

java.io.IOException

java.sql.SQLException

chemaxon.clustering.InvalidLicenseKeyException

Since:

JChem 1.6.2

main

public static void main(java.lang.String[] args)

The command line version entry point. Parameter parsing, initialization then start.