chemaxon.clustering
Class Common

java.lang.Object
  chemaxon.clustering.Common

Direct Known Subclasses:

Compare, NearestNeighbors, Ward

public abstract class Common
extends java.lang.Object

Common superclass for JKlustor tools. Click here for mor information. tools.

Since:

JChem 1.6.2

Author:

Szilard Dorant

Constructor Summary

Common()

Method Summary

int	getDimensions() Gets the number of dimensions.
long	getElapsedTime() Gets the elapsed time.
int	getFpSize() Gets chemical hashed fingerprint size.
boolean	getIdGeneration() Indicates whether id-s will be generated or taken from input data.
long	getStartTime() Gets start time.
java.io.PrintStream	getStatStream() Gets the stream used to print statistics.
float[]	getWeights() Gets descriptor weights used for distance calculation.
boolean	isOnlyStat() Indicates if only statistics are produced.
boolean	isStatNeeded() Indicates whether statistics are produced.
void	setDimensions(int dim) Sets the number of dimensions.
void	setFpSize(int fpSize) Sets chemical hashed fingerprint size.
void	setIdGeneration(boolean b) Specifies if id-s will be generated or taken from input data.
void	setOnlyStat(boolean b) Specifies if only stastistics are to be generated.
void	setOutput(java.sql.Connection con, java.lang.String insertSQL) Directs output to a database table.
void	setOutput(java.io.File file) Directs output and statistics to a File.
void	setOutput(java.io.PrintStream ps) Directs output to a PrintStream.
void	setOutput(java.lang.String fileName) Directs output to a File.
void	setStatNeeded(boolean b) Enables or disables statistics generation.
void	setStatStream(java.io.PrintStream pst) Sets the stream used to print statistics.
void	setWeights(float[] weights) Sets descriptor weights used for distance calculation.

Methods inherited from class java.lang.Object

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

Constructor Detail

Common

public Common()

Method Detail

setOutput

public void setOutput(java.sql.Connection con,
                      java.lang.String insertSQL)
               throws java.sql.SQLException

Directs output to a database table.

Parameters:

con - Connection opened to the database

insertSQL - the SQL string used for inserting results into table. See the documentation for details.

Throws:

java.sql.SQLException

setOutput

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

Directs output and statistics to a File. Statisitcs can be redirected later by calling setStatStream()

Parameters:

file - the file where statistics are directed to

Throws:

java.io.FileNotFoundException

setOutput

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

Directs output to a File.

Parameters:

fileName - the path of the output file

Throws:

java.io.FileNotFoundException

setOutput

public void setOutput(java.io.PrintStream ps)

Directs output to a PrintStream.

Parameters:

ps - the PrintStream where the output will be directed to

setIdGeneration

public void setIdGeneration(boolean b)

Specifies if id-s will be generated or taken from input data.

Parameters:

b - if set to true, id will be generated for each compound. If false, the first data column will be treated as id number.

getIdGeneration

public boolean getIdGeneration()

Indicates whether id-s will be generated or taken from input data.

Returns:

true, if id will be generated for each compound, false, if the first data column will be treated as id number.

setOnlyStat

public void setOnlyStat(boolean b)

Specifies if only stastistics are to be generated.

Parameters:

b - if set to true, only statistics will be produced

isOnlyStat

public boolean isOnlyStat()

Indicates if only statistics are produced.

Returns:

true, if only statistics are to be produced , false otherwise

setStatNeeded

public void setStatNeeded(boolean b)

Enables or disables statistics generation.

Parameters:

b - true, if statistics are to be produced, false otherwise

isStatNeeded

public boolean isStatNeeded()

Indicates whether statistics are produced.

Returns:

true, if statistics are to be produced, false otherwise.

setDimensions

public void setDimensions(int dim)

Sets the number of dimensions.

Parameters:

dim - the number of dimensions (floating-point descriptors)

getDimensions

public int getDimensions()

Gets the number of dimensions.

Returns:

the number of dimensions (floating-point descriptors)

setFpSize

public void setFpSize(int fpSize)

Sets chemical hashed fingerprint size.

Parameters:

fpSize - fingerprint size in bits

getFpSize

public int getFpSize()

Gets chemical hashed fingerprint size.

Returns:

fingerprint size in bits

setWeights

public void setWeights(float[] weights)

Sets descriptor weights used for distance calculation.

Parameters:

weights - the weights of the numbers' floating-point descriptors

getWeights

public float[] getWeights()

Gets descriptor weights used for distance calculation.

Returns:

the descriptor weights, or null if not specified

getStartTime

public long getStartTime()

Gets start time.

Returns:

the start time

getElapsedTime

public long getElapsedTime()

Gets the elapsed time.

Returns:

the elapsed time in milliseconds since start time

setStatStream

public void setStatStream(java.io.PrintStream pst)

Sets the stream used to print statistics. By default statistics are printed to the standard output.

Parameters:

pst - the PrintStream, where statistics will be directed to

getStatStream

public java.io.PrintStream getStatStream()

Gets the stream used to print statistics.

Returns:

the PrintStream where statistics are directed to