chemaxon.clustering

Class Ward

java.lang.Object

chemaxon.clustering.Common

chemaxon.clustering.Ward

@PublicAPI
public class Ward
extends Common

Uses Ward's minimum variance method for clustering molecules based on molecular fingerprints or other descriptors.
This class can be used from command-line or from the API.
See the documentation for details.

An example for running Ward:

 ConnectionHandler ch;
 String selectString;
 ...
 Ward ward=new Ward();
 ward.setInput(ch, selectString);
 ward.setOutput(System.out);
 ward.setDimensions(0);
 ward.setFpSize(512);
 ward.setClusterCount(10);
 ward.setCentralShown(false);
 ward.setSingletonNegative(false);
 ward.setStatNeeded(true);
 ward.setOnlyStat(false);
 ward.setStatStream(System.out);
 ward.setKelleyStats("kelley_results.txt");
 ward.setMode(Ward.RNN_AND_CLUSTERING);       // execution mode
 ward.setIdGeneration(true);
 ward.run();
 

Since:

JChem 1.6.2

Author:

Andras Volford, Ferenc Csizmadia, Szilard Dorant

Field Summary

Fields

Modifier and Type	Field and Description
static int	ONLY_CLUSTERING
static int	ONLY_RNN
static int	RNN_AND_CLUSTERING

Constructor Summary

Constructors

Constructor and Description
Ward()

Method Summary

Modifier and Type	Method and Description
boolean	getCentralShown() Indicates whether central objects are displayed.
int	getClusterCount() Gets the number of clusters.
int	getMode() Gets the clustering mode.
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	setClusterCount(int count) Sets the number of clusters.
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	setKelleyStats(java.io.File file) Directs Kelley statistics to a File.
void	setKelleyStats(java.io.PrintStream ps) Directs Kelley statistics to a PrintStream.
void	setKelleyStats(java.lang.String fileName) Directs Kelley statistics to a File specified with a name.
void	setMode(int mode) Sets the clustering mode.
void	setSingletonNegative(boolean b) Specifies whether singletons get negative cluste id-s.

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

Field Detail

RNN_AND_CLUSTERING

public static final int RNN_AND_CLUSTERING

See Also:

Constant Field Values

ONLY_RNN

public static final int ONLY_RNN

See Also:

Constant Field Values

ONLY_CLUSTERING

public static final int ONLY_CLUSTERING

See Also:

Constant Field Values

Constructor Detail

Ward

public Ward()

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

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

getCentralShown

public boolean getCentralShown()

Indicates whether central objects are displayed.

Returns:

true if central objects are calculated and shown in output.

Since:

JChem 1.6.2

setKelleyStats

public void setKelleyStats(java.io.PrintStream ps)

Directs Kelley statistics to a PrintStream.

Parameters:

ps - the PrintStream where Kelley statistics directed to, or null,if no Kelley statistics needed.

Since:

JChem 1.6.2

setKelleyStats

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

Directs Kelley statistics to a File.

Parameters:

file - the File where Kelley statistics directed to, or null,if no Kelley statistics needed.

Throws:

java.io.FileNotFoundException

Since:

JChem 1.6.2

setKelleyStats

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

Directs Kelley statistics to a File specified with a name.

Parameters:

fileName - the path of the file where Kelley statistics directed to, or null,if no Kelley statistics needed.

Throws:

java.io.FileNotFoundException

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

setClusterCount

public void setClusterCount(int count)

Sets the number of clusters.

Parameters:

count - the number of clusters

Since:

JChem 1.6.2

getClusterCount

public int getClusterCount()

Gets the number of clusters.

Returns:

the number of clusters

Since:

JChem 1.6.2

setMode

public void setMode(int mode)

Sets the clustering mode.

Parameters:

mode - clustering mode constant
Selectable modes:

• RNN_AND_CLUSTERING
• ONLY_RNN
• ONLY_CLUSTERING

Since:

JChem 1.6.2

getMode

public int getMode()

Gets the clustering mode.

Returns:

one of the folloing constants:

• RNN_AND_CLUSTERING
• ONLY_RNN
• ONLY_CLUSTERING

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.