Package edu.msu.cme.rdp.classifier
Class ClassifierCmd
- java.lang.Object
-
- edu.msu.cme.rdp.classifier.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.
-
-
-
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
-
-