Class ClassifierCmd

java.lang.Object
edu.msu.cme.rdp.classifier.ClassifierCmd

public class ClassifierCmd extends Object
This is the legacy command line class to do the classification. See edu.msu.cme.rdp.multicompare.main
  • Constructor Details

    • ClassifierCmd

      public ClassifierCmd()
  • Method Details

    • doClassify

      public void doClassify(String inputFile, String outFile, String propfile, ClassificationResultFormatter.FORMAT format, String gene, int min_bootstrap_words) throws IOException, TrainingDataException
      It classifies query sequences from the input file. If the property file of the mapping of the training files is not null, the default property file will be override. The classification results will be writen to the output file.
      Throws:
      IOException
      TrainingDataException
    • printLicense

      public static void printLicense()
      Prints the license information to std err.
    • main

      public static void main(String[] args) throws Exception
      This is the main method to do classification.

      Usage: java ClassifierCmd queryFile outputFile [property file].
      queryFile can be one of the following formats: Fasta, Genbank and EMBL.
      outputFile will be used to save the classification output.
      property file contains the mapping of the training files.
      Note: the training files and the property file should be in the same directory. The default property file is set to data/classifier/16srrna/rRNAClassifier.properties.

      Throws:
      Exception