public class RdpNode extends OtuNodeImpl
RdpClassifier output. RDP outputs the
sequence header and taxonomy assignments for all levels in one line. Each line represents a single read. Each level
is followed by a confidence score ranging from 0-1, which can be obtained via getScore().
Sample output line from RDP classifier:
FCABK7W:1:2105:21787:12788#/1 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Clostridia class 1.0
Clostridiales order 1.0 Ruminococcaceae family 1.0 Faecalibacterium genus 1.0
CLASS_DELIM, DOMAIN_DELIM, FAMILY_DELIM, GENUS_DELIM, ORDER_DELIM, PHYLUM_DELIM, SPECIES_DELIM| Constructor and Description |
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RdpNode(String id,
String line)
Constructor called one line of RDP output.
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| Modifier and Type | Method and Description |
|---|---|
protected void |
buildRdpNode(String id,
String line)
Build the OtuNode by extracting the OTU names for each level from the line.
|
int |
getScore()
Return lowest RDP confidence percentage (0-100) above the configured threshold value.
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addTaxa, compareTo, delimToLevelMap, getCount, getLine, getOtuName, getSampleId, getTaxaMap, populateInBetweenTaxa, setCount, setLine, setSampleIdpublic RdpNode(String id, String line) throws Exception
id - Sample IDline - RDP Classifier output lineException - if propagated from buildRdpNode(String, String)public int getScore()
protected void buildRdpNode(String id, String line) throws Exception
id - Sample IDline - RDP Classifier output lineException - if required properties are invalid or undefined