Class ClassifierCmd


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

      Constructors 
      Constructor Description
      ClassifierCmd()  
    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void doClassify​(java.lang.String inputFile, java.lang.String outFile, java.lang.String propfile, ClassificationResultFormatter.FORMAT format, java.lang.String gene, int min_bootstrap_words)
      It classifies query sequences from the input file.
      static void main​(java.lang.String[] args)
      This is the main method to do classification.
      static void printLicense()
      Prints the license information to std err.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • ClassifierCmd

        public ClassifierCmd()
    • Method Detail

      • doClassify

        public void doClassify​(java.lang.String inputFile,
                               java.lang.String outFile,
                               java.lang.String propfile,
                               ClassificationResultFormatter.FORMAT format,
                               java.lang.String gene,
                               int min_bootstrap_words)
                        throws java.io.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:
        java.io.IOException
        TrainingDataException
      • printLicense

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

        public static void main​(java.lang.String[] args)
                         throws java.lang.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:
        java.lang.Exception