Package de.unijena.cheminf.fragment.fingerprint.performanceTest

Class PerformanceTest

java.lang.Object
de.unijena.cheminf.fragment.fingerprint.performanceTest.PerformanceTest
public class PerformanceTest extends Object
A class for testing the performance of the fragment fingerprinter. Both bit and count fingerprints are generated for this purpose.

  • Constructor Details

    • PerformanceTest

      public PerformanceTest(String[] anArgs) throws IOException, IllegalArgumentException
      Constructor. All files listed below as parameters must be located in the same directory as the application JAR file. In the constructor all necessary output files are created. There are 4 different files to document the result of the performance snapshot. One file is created that is essentially a console output and two others that contain the processing time required at each step in a structured form (CSV). Another file contains the generated bit fingerprints for each molecule. And the last file contains the generated count fingerprints for each molecule. The constructor executes the complete application. Everything the application is supposed to do is realized in the constructor, especially the generation of the bit and count fingerprints and also the shutdown at the end of the application.
      Parameters:
      anArgs - the command line arguments, anArgs[0] and anArgs[1] must be the names of the text files to load. The text files must be located in the same directory as the application's JAR file. The command line anArgs[3] must be the name of the path, where the performance test results are stored. The command line anArgs[2] must be the number of the molecules in process (bin size).
      • anArgs[0]:
        • is a semicolon separated CSV file with header
        • First column must contain unique SMILES strings. These are set as predefined fragments when the fingerprint is initialized.
        • All other columns in the file also the header are ignored.
        • The fragments read from this text file are used to initialize the fingerprint. These fragments represent the key fragments of the fingerprint.
      • anArgs[1]:
        • is a semicolon-separated CSV file with header line
        • Each row shows a molecule with its fragments
        • first column: Molecule name/ID
        • second column: unique SMILES of the molecule
        • third and following columns: alternating pairs of fragment SMILES and abundances in the respective molecule
        • In this file, the header is ignored and columns 1 and 2 are used for the correct assignment of the generated fingerprints.
        • The SMILES fragments and their frequencies from this file are matched with the key fragments to create the fingerprint.
      Throws:
      IOException - is thrown if the constructor is unable to open a text file for logging occurred exceptions.
      IllegalArgumentException - is thrown if the given arguments are invalid.