chemaxon.clustering
Class JarvisPatrick

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

public class JarvisPatrick
extends NearestNeighbors

Performs variable-length Jarvis-Patrick clustering based on binary fingerprints (bits strings) and/or other data stored in a database table or a file. It can also be used for calculating diversity measures, like average and minimum dissimilarity of a compound library.
This class can be used from command-line or from the API.
See the documentation for details.

An example for running JarvisPatrick:

 ConnectionHandler ch;
 String selectString;
 ...
 JarvisPatrick jp=new JarvisPatrick();
 jp.setInput(ch, selectString ); 
 jp.setOutput(System.out);
 jp.setDimensions(0);
 jp.setFpSize(512);
 jp.setStatNeeded(true);
 jp.setOnlyStat(false);
 jp.setStatStream(System.out);
 jp.setIdGeneration(true);
 jp.setThreshold(0.1f);
 jp.setCentralShown(true);
 jp.setMinCommonRatio(0.1f);
 jp.setSingletonNegative(true);
 jp.run();
 

Since:

JChem 1.6.2

Author:

Arpad Tamasi, Ferenc Csizmadia, Szilard Dorant

Constructor Summary

JarvisPatrick()

Method Summary

float	getMinCommonRatio() Gets the minimum ratio of common neighbors of two compounds.
boolean	isCentralShown() Indicates whether central objects are displayed.
boolean	isSingletonNegative() Indicates whether singeltons get negative cluster id-s.
static void	main(java.lang.String[] args) The command line version entry point.
void	run() Starts processing.
void	setCentralShown(boolean b) Specifies if cluster centers should be diplayed.
void	setMinCommonRatio(float ratio) Sets the minimum ratio of common neighbors of two compounds.
void	setSingletonNegative(boolean b) Specifies whether singletons get negative cluste id-s.

Methods inherited from class chemaxon.clustering.NearestNeighbors

getThreshold, setInput, setInput, setInput, setInput, setThreshold

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

JarvisPatrick

public JarvisPatrick()

Method Detail

setMinCommonRatio

public void setMinCommonRatio(float ratio)

Sets the minimum ratio of common neighbors of two compounds.

Parameters:

ratio - the ratio to be set

Since:

JChem 1.6.2

getMinCommonRatio

public float getMinCommonRatio()

Gets the minimum ratio of common neighbors of two compounds.

Returns:

the ratio

Since:

JChem 1.6.2

setSingletonNegative

public void setSingletonNegative(boolean b)

Specifies whether singletons get negative cluste id-s.

Parameters:

b - If set to true, singeltons get negative cluster id-s.

Since:

JChem 1.6.2

isSingletonNegative

public boolean isSingletonNegative()

Indicates whether singeltons get negative cluster id-s.

Returns:

true, if singeltons get negative cluster id-s.

Since:

JChem 1.6.2

setCentralShown

public void setCentralShown(boolean b)

Specifies if cluster centers should be diplayed.

Parameters:

b - if set to true, central objects are calculated and shown in output.

Since:

JChem 1.6.2

isCentralShown

public boolean isCentralShown()

Indicates whether central objects are displayed.

Returns:

true if central objects are calculated and shown in output.

Since:

JChem 1.6.2

run

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

Starts processing.

Overrides:

run in class NearestNeighbors

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.