Package 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

  • Field Details

  • Constructor Details

    • Ward

      public Ward()

  • Method Details

    • setInput

      public void setInput(ConnectionHandler conh, String querySQL) throws 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:
      SQLException
      Since:
      JChem 1.6.2

    • setInput

      public void setInput(File file) throws FileNotFoundException
      Sets input as a File.
      Parameters:
      file - the File to be used for input
      Throws:
      FileNotFoundException
      Since:
      JChem 1.6.2

    • setInput

      public void setInput(String fileName) throws FileNotFoundException
      Sets input as a file, specified by its path.
      Parameters:
      fileName - the path of File to be used for input
      Throws:
      FileNotFoundException
      Since:
      JChem 1.6.2

    • setInput

      public void setInput(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(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(File file) throws FileNotFoundException
      Directs Kelley statistics to a File.
      Parameters:
      file - the File where Kelley statistics directed to, or null,if no Kelley statistics needed.
      Throws:
      FileNotFoundException
      Since:
      JChem 1.6.2

    • setKelleyStats

      public void setKelleyStats(String fileName) throws 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:
      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 ClusteringException, IOException, SQLException, InvalidLicenseKeyException
      Starts processing.
      Throws:
      ClusteringException
      IOException
      SQLException
      InvalidLicenseKeyException
      Since:
      JChem 1.6.2

    • 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.