Package edu.msu.cme.rdp.multicompare
Class MultiClassifier
- java.lang.Object
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- edu.msu.cme.rdp.multicompare.MultiClassifier
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public class MultiClassifier extends java.lang.Object
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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)
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Method Summary
All Methods Instance Methods Concrete Methods 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 outputMultiClassifierResult
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 filesMultiClassifierResult
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)
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Constructor Detail
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MultiClassifier
public MultiClassifier(java.lang.String propfile, java.lang.String gene)
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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
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Method Detail
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hasCopyNumber
public boolean hasCopyNumber()
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multiCompare
public MultiClassifierResult multiCompare(java.util.List<MCSample> samples) throws java.io.IOException
- Throws:
java.io.IOException
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multiCompare
public MultiClassifierResult multiCompare(java.util.List<MCSample> samples, int min_bootstrap_words) throws java.io.IOException
- Throws:
java.io.IOException
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multiCompare
public MultiClassifierResult multiCompare(java.util.List<MCSample> samples, float conf, int min_bootstrap_words) throws java.io.IOException
- Throws:
java.io.IOException
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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
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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
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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
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