Compare (JChem Base API documentation (c) 1998-2021 ChemAxon Ltd.)

java.lang.Object
- chemaxon.clustering.Common
- - chemaxon.clustering.Compare

@PublicAPI
public class Compare
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.
See the documentation for details.

An example for running Compare:

 ConnectionHandler ch;
 String selectString1;
 String selectString2;
 ...
 Compare cp=new Compare();
 cp.setInput1(ch, selectString1 );
 cp.setInput2(ch, selectString2 );
 cp.setOutput(System.out);
 cp.setDimensions(0);
 cp.setFpSize(512);
 cp.setStatNeeded(true);
 cp.setOnlyStat(false);
 cp.setStatStream(System.out);
 cp.setIdGeneration(true);
 cp.setThreshold(0.1f);
 cp.setOnlyDissimilarListed(true);
 cp.setDifferentIdsOnly(true);
 cp.run();

Since:: JChem 1.6.2
Author:: Ferenc Csizmadia, Szilard Dorant

Constructor Summary

Constructors
Constructor and Description

Compare()

Constructors
Constructor and Description
`Compare()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`getMaxSimilar()` Gets the maximum allowed number of similar objects for a compound.
`float`	`getThreshold()` Gets the threshold value.
`boolean`	`isDifferentIdsOnly()` Indicates whether compounds with different id-s compared only.
`boolean`	`isOnlyDissimilarListed()` Indicates whether only dissimilar objects are printed.
`boolean`	`isOrderSimilarObjects()` Indicates, whether the list similar objects should be ordered by distance (closest first).
`boolean`	`isSimilarListed()` Indicates whether similar objects listed from the first set.
`static void`	`main(java.lang.String[] args)` The command line version entry point.
`void`	`run()` Starts processing.
`void`	`setDifferentIdsOnly(boolean b)` Specifies whether compounds with identical id should be compared.
`void`	`setInput1(ConnectionHandler conh, java.lang.String querySQL)` Sets the first compound library (first set) as an SQL query.
`void`	`setInput1(java.io.File file)` Sets the first compound library (first set) as a file.
`void`	`setInput1(java.io.InputStream is)` Sets the first compound library (first set) as an InputStream
`void`	`setInput1(java.lang.String fileName)` Sets the first compound library (first set) as a file, specified by the file's path.
`void`	`setInput2(ConnectionHandler conh, java.lang.String querySQL)` Sets the second compound library (second set) as an SQL query.
`void`	`setInput2(java.io.File file)` Sets the second compound library (second set) as a file.
`void`	`setInput2(java.io.InputStream is)` Sets the second compound library (second set) as an InputStream
`void`	`setInput2(java.lang.String fileName)` Sets the second compound library (second set) as a file, specified by the file's path.
`void`	`setMaxSimilar(int maxSimilar)` Sets the maximum allowed number of similar objects for a compound.
`void`	`setOnlyDissimilarListed(boolean b)` Specifies, if only dissimilar objects are to be printed.
`void`	`setOrderSimilarObjects(boolean orderSimilarObjects)` Specifies, whether the list similar objects should be ordered by distance (closest first).
`void`	`setSimilarListed(boolean b)` Specifies if similar objects are to be listed from the first set.
`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
  - Compare
```
public Compare()
```
- Method Detail
  - setInput1
```
public void setInput1(ConnectionHandler conh,
                      java.lang.String querySQL)
               throws java.sql.SQLException
```
    Sets the first compound library (first set) 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
  - setInput2
```
public void setInput2(ConnectionHandler conh,
                      java.lang.String querySQL)
               throws java.sql.SQLException
```
    Sets the second compound library (second set) 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
  - setInput1
```
public void setInput1(java.io.File file)
               throws java.io.FileNotFoundException
```
    Sets the first compound library (first set) as a file.
    
    Parameters:
    
    file - the File to be used for input
    
    Throws:
    
    java.io.FileNotFoundException
  - setInput2
```
public void setInput2(java.io.File file)
               throws java.io.FileNotFoundException
```
    Sets the second compound library (second set) as a file.
    
    Parameters:
    
    file - the File to be used for input
    
    Throws:
    
    java.io.FileNotFoundException
  - setInput1
```
public void setInput1(java.lang.String fileName)
               throws java.io.FileNotFoundException
```
    Sets the first compound library (first set) as a file, specified by the file's path.
    
    Parameters:
    
    fileName - the path of the input file
    
    Throws:
    
    java.io.FileNotFoundException
  - setInput2
```
public void setInput2(java.lang.String fileName)
               throws java.io.FileNotFoundException
```
    Sets the second compound library (second set) as a file, specified by the file's path.
    
    Parameters:
    
    fileName - the path of the input file
    
    Throws:
    
    java.io.FileNotFoundException
  - setInput1
```
public void setInput1(java.io.InputStream is)
```
    Sets the first compound library (first set) as an InputStream
    
    Parameters:
    
    is - the InputStream to be used for input
  - setInput2
```
public void setInput2(java.io.InputStream is)
```
    Sets the second compound library (second set) as an InputStream
    
    Parameters:
    
    is - the InputStream to be used for input
  - setThreshold
```
public void setThreshold(float threshold)
```
    Sets the threshold value.
    
    Parameters:
    
    threshold - the threshold value to be set
  - getThreshold
```
public float getThreshold()
```
    Gets the threshold value.
    
    Returns:
    
    the threshold value currently set
  - setOnlyDissimilarListed
```
public void setOnlyDissimilarListed(boolean b)
```
    Specifies, if only dissimilar objects are to be printed.
    
    Parameters:
    
    b - if set to true only dissimilar objects are printed, otherwise all objects are listed
  - isOnlyDissimilarListed
```
public boolean isOnlyDissimilarListed()
```
    Indicates whether only dissimilar objects are printed.
    
    Returns:
    
    true, if only dissimilar objects are printed, false otherwise
  - setSimilarListed
```
public void setSimilarListed(boolean b)
```
    Specifies if similar objects are to be listed from the first set.
    
    Parameters:
    
    b - if set to true, similar objects are printed from the first set
  - isSimilarListed
```
public boolean isSimilarListed()
```
    Indicates whether similar objects listed from the first set.
    
    Returns:
    
    true, if similar objects are printed from the first set
  - setDifferentIdsOnly
```
public void setDifferentIdsOnly(boolean b)
```
    Specifies whether compounds with identical id should be compared.
    
    Parameters:
    
    b - if set to true, compounds with different id-s compared only. Otherwise all compounds are compared.
  - isDifferentIdsOnly
```
public boolean isDifferentIdsOnly()
```
    Indicates whether compounds with different id-s compared only.
    
    Returns:
    
    true, if compunds with identical id-s are not compared
  - setMaxSimilar
```
public void setMaxSimilar(int maxSimilar)
```
    Sets the maximum allowed number of similar objects for a compound. If set to 0 (default), the number of similar objects is unlimited.
    
    Parameters:
    
    maxSimilar - the maximum number of similar neighbors
  - getMaxSimilar
```
public int getMaxSimilar()
```
    Gets the maximum allowed number of similar objects for a compound. If 0 (default), the number of similar objects is unlimited.
    
    Returns:
    
    the maximum number of similar neighbors
  - setOrderSimilarObjects
```
public void setOrderSimilarObjects(boolean orderSimilarObjects)
```
    Specifies, whether the list similar objects should be ordered by distance (closest first).
    
    Parameters:
    
    orderSimilarObjects - if set to true, the list of similar objects should be ordered by distance in the output. Default value is false.
  - isOrderSimilarObjects
```
public boolean isOrderSimilarObjects()
```
    Indicates, whether the list similar objects should be ordered by distance (closest first).
    
    Returns:
    
    true, if the list of similar objects will be ordered by distance in the output. Default value is false.
  - 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
  - main
```
public static void main(java.lang.String[] args)
```
    The command line version entry point. Parameter parsing, initialization then start.
    
    Parameters:
    
    args - the command line parameters

Class Compare

Constructor Summary

Method Summary

Methods inherited from class chemaxon.clustering.Common

Methods inherited from class java.lang.Object

Constructor Detail

Compare

Method Detail

setInput1

setInput2

setInput1

setInput2

setInput1

setInput2

setInput1

setInput2

setThreshold

getThreshold

setOnlyDissimilarListed

isOnlyDissimilarListed

setSimilarListed

isSimilarListed

setDifferentIdsOnly

isDifferentIdsOnly

setMaxSimilar

getMaxSimilar

setOrderSimilarObjects

isOrderSimilarObjects

run

main