edu.msu.cme.rdp.classifier.train.validation.leaveoneout

Class LeaveOneOutTester

java.lang.Object

edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTester

public class LeaveOneOutTester
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
LeaveOneOutTester(java.io.Writer writer, int numGoodBases)

Method Summary

Modifier and Type	Method and Description
java.util.ArrayList<java.util.HashMap<java.lang.String,StatusCount>>	classify(TreeFactory factory, LineageSequenceParser parser, boolean useSeed, int min_bootstrap_words, boolean hideTaxon) perform leave-one-out test.
void	displayTreeErrorRate(HierarchyTree root, int indent)
protected java.util.Map	getNum_hierLevelMap()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

LeaveOneOutTester

public LeaveOneOutTester(java.io.Writer writer,
                         int numGoodBases)
                  throws java.io.IOException

Parameters:

writer -

numGoodBases - 0 for all bases from the query, positive integer for partial length testing

Throws:

java.io.IOException

Method Detail

classify

public java.util.ArrayList<java.util.HashMap<java.lang.String,StatusCount>> classify(TreeFactory factory,
                                                                                     LineageSequenceParser parser,
                                                                                     boolean useSeed,
                                                                                     int min_bootstrap_words,
                                                                                     boolean hideTaxon)
                                                                              throws java.io.IOException

perform leave-one-out test. For each query sequence, remove it from the training set and test the classifier, put it back after each testing. The accuracy, misclassified sequences and the misclassified count for each taxon is written into the output file.

Parameters:

factory -

parser -

useSeed -

Throws:

java.io.IOException

displayTreeErrorRate

public void displayTreeErrorRate(HierarchyTree root,
                                 int indent)
                          throws java.io.IOException

Throws:

java.io.IOException

getNum_hierLevelMap

protected java.util.Map getNum_hierLevelMap()