Package edu.msu.cme.rdp.multicompare

Class MultiClassifier

java.lang.Object

edu.msu.cme.rdp.multicompare.MultiClassifier

public class MultiClassifier
extends java.lang.Object

Constructor Summary

Constructors

Constructor	Description
MultiClassifier(java.lang.String propfile, java.lang.String gene)
MultiClassifier(java.lang.String propfile, java.lang.String gene, java.io.File biomFile, java.io.File metadataFile)

Method Summary

Modifier and Type	Method	Description
boolean	hasCopyNumber()
MultiClassifierResult	multiClassificationParser(java.util.List<MCSample> samples, float confidence, java.io.PrintWriter assign_out, ClassificationResultFormatter.FORMAT format, java.lang.String printRank, java.util.HashSet<java.lang.String> taxonFilter)	Input files are the classification results printRank indicates which rank to filter by the confidence for the detail assignment output taxonFilter indicates which taxon to match for the detail assignment output
MultiClassifierResult	multiCompare(java.util.List<MCSample> samples)
MultiClassifierResult	multiCompare(java.util.List<MCSample> samples, float conf, int min_bootstrap_words)
MultiClassifierResult	multiCompare(java.util.List<MCSample> samples, float confidence, java.io.PrintWriter assign_out, ClassificationResultFormatter.FORMAT format, int min_bootstrap_words)	Input files are sequence files
MultiClassifierResult	multiCompare(java.util.List<MCSample> samples, int min_bootstrap_words)
MultiClassifierResult	multiCompare(java.util.List<MCSample> samples, java.io.PrintWriter assign_out, int min_bootstrap_words)

Methods inherited from class java.lang.Object

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

Constructor Detail

MultiClassifier

public MultiClassifier(java.lang.String propfile,
                       java.lang.String gene)

MultiClassifier

public MultiClassifier(java.lang.String propfile,
                       java.lang.String gene,
                       java.io.File biomFile,
                       java.io.File metadataFile)
                throws java.io.IOException

Throws:

java.io.IOException

Method Detail

hasCopyNumber

public boolean hasCopyNumber()

multiCompare

public MultiClassifierResult multiCompare(java.util.List<MCSample> samples)
                                   throws java.io.IOException

Throws:

java.io.IOException

multiCompare

public MultiClassifierResult multiCompare(java.util.List<MCSample> samples,
                                          int min_bootstrap_words)
                                   throws java.io.IOException

Throws:

java.io.IOException

multiCompare

public MultiClassifierResult multiCompare(java.util.List<MCSample> samples,
                                          float conf,
                                          int min_bootstrap_words)
                                   throws java.io.IOException

Throws:

java.io.IOException

multiCompare

public MultiClassifierResult multiCompare(java.util.List<MCSample> samples,
                                          java.io.PrintWriter assign_out,
                                          int min_bootstrap_words)
                                   throws java.io.IOException

Throws:

java.io.IOException

multiCompare

public MultiClassifierResult multiCompare(java.util.List<MCSample> samples,
                                          float confidence,
                                          java.io.PrintWriter assign_out,
                                          ClassificationResultFormatter.FORMAT format,
                                          int min_bootstrap_words)
                                   throws java.io.IOException

Input files are sequence files

Throws:

java.io.IOException

multiClassificationParser

public MultiClassifierResult multiClassificationParser(java.util.List<MCSample> samples,
                                                       float confidence,
                                                       java.io.PrintWriter assign_out,
                                                       ClassificationResultFormatter.FORMAT format,
                                                       java.lang.String printRank,
                                                       java.util.HashSet<java.lang.String> taxonFilter)
                                                throws java.io.IOException

Input files are the classification results printRank indicates which rank to filter by the confidence for the detail assignment output taxonFilter indicates which taxon to match for the detail assignment output

Throws:

java.io.IOException