Package edu.msu.cme.rdp.classifier.io
Class ClassificationResultFormatter
- java.lang.Object
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- edu.msu.cme.rdp.classifier.io.ClassificationResultFormatter
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public class ClassificationResultFormatter extends java.lang.Object
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
ClassificationResultFormatter.FORMAT
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Field Summary
Fields Modifier and Type Field Description static java.util.List<ClassificationResultFormatter.FORMAT>
fileFormats
static java.lang.String[]
RANKS
static java.lang.String[]
RANKS_WITHSPECIES
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Constructor Summary
Constructors Constructor Description ClassificationResultFormatter()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static java.lang.String
getAllRankOutput(ClassificationResult result)
static java.lang.String
getAllRankOutput(ClassificationResult result, double conf)
static java.lang.String
getBiomOutput(java.lang.String[] ranks, ClassificationResult result, float conf, char delimiter)
Output the classification result suitable to load into biom format.static java.lang.String
getDBOutput(ClassificationResult result, float conf)
static java.lang.String
getFilterByConfOutput(ClassificationResult result, float conf)
static java.lang.String
getFilterByConfOutput(java.lang.String[] ranks, ClassificationResult result, float conf)
static java.lang.String
getFixRankOutput(ClassificationResult result)
static java.lang.String
getFixRankOutput(java.lang.String[] ranks, ClassificationResult result)
static java.lang.String
getOutput(ClassificationResult result, ClassificationResultFormatter.FORMAT format)
static java.lang.String
getOutput(ClassificationResult result, ClassificationResultFormatter.FORMAT format, float conf, java.lang.String[] ranks)
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Field Detail
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RANKS
public static java.lang.String[] RANKS
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RANKS_WITHSPECIES
public static java.lang.String[] RANKS_WITHSPECIES
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fileFormats
public static final java.util.List<ClassificationResultFormatter.FORMAT> fileFormats
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Method Detail
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getOutput
public static java.lang.String getOutput(ClassificationResult result, ClassificationResultFormatter.FORMAT format)
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getOutput
public static java.lang.String getOutput(ClassificationResult result, ClassificationResultFormatter.FORMAT format, float conf, java.lang.String[] ranks)
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getAllRankOutput
public static java.lang.String getAllRankOutput(ClassificationResult result)
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getAllRankOutput
public static java.lang.String getAllRankOutput(ClassificationResult result, double conf)
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getFixRankOutput
public static java.lang.String getFixRankOutput(ClassificationResult result)
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getFixRankOutput
public static java.lang.String getFixRankOutput(java.lang.String[] ranks, ClassificationResult result)
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getFilterByConfOutput
public static java.lang.String getFilterByConfOutput(ClassificationResult result, float conf)
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getFilterByConfOutput
public static java.lang.String getFilterByConfOutput(java.lang.String[] ranks, ClassificationResult result, float conf)
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getBiomOutput
public static java.lang.String getBiomOutput(java.lang.String[] ranks, ClassificationResult result, float conf, char delimiter)
Output the classification result suitable to load into biom format. Concatenate the rank and the taxon name, remove quotes in the taxon name
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getDBOutput
public static java.lang.String getDBOutput(ClassificationResult result, float conf)
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