Package chemaxon.clustering

Class Compare

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

  • Constructor Details

    • Compare

      public Compare()

  • Method Details

    • setInput1

      public void setInput1(ConnectionHandler conh, String querySQL) throws 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:
      SQLException

    • setInput2

      public void setInput2(ConnectionHandler conh, String querySQL) throws 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:
      SQLException

    • setInput1

      public void setInput1(File file) throws FileNotFoundException
      Sets the first compound library (first set) as a file.
      Parameters:
      file - the File to be used for input
      Throws:
      FileNotFoundException

    • setInput2

      public void setInput2(File file) throws FileNotFoundException
      Sets the second compound library (second set) as a file.
      Parameters:
      file - the File to be used for input
      Throws:
      FileNotFoundException

    • setInput1

      public void setInput1(String fileName) throws 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:
      FileNotFoundException

    • setInput2

      public void setInput2(String fileName) throws 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:
      FileNotFoundException

    • setInput1

      public void setInput1(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(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, IOException, SQLException, chemaxon.clustering.InvalidLicenseKeyException
      Starts processing.
      Throws:
      chemaxon.clustering.ClusteringException
      IOException
      SQLException
      chemaxon.clustering.InvalidLicenseKeyException

    • main

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JAN_01_2025) public static void main(String[] args)
      Deprecated, for removal: This API element is subject to removal in a future version.
      This main method will be removed, CLI interfaces should not be used directly from Java code.
      The command line version entry point. Parameter parsing, initialization then start.
      Parameters:
      args - the command line parameters