OtuNode

All Known Implementing Classes:

Kraken2Node, KrakenNode, MetaphlanNode, OtuNodeImpl, QiimeNode, RdpNode
```
public interface OtuNode
```
Classes that implement this interface store taxonomy assignment info for one sequence, as output by a classifier. ParserModules read ClassifierModule output to build standardized OTU abundance tables. Each line of classifier output is parsed for the OTU name, OTU count, and sample ID. Note that if data is demultiplexed, the Sample ID is extracted from the file name instead of the sequence header.

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method and Description
`void`	`addTaxa(String taxa, String levelDelim)` Add `OtuNode` taxa names for the `Config`."report.taxonomyLevels" level mapped by the classifier specific levelDelim parameter: .
`Map<String,String>`	`delimToLevelMap()` Get a map of the `ClassifierModule` taxonomy delimiters to `Config`."report.taxonomyLevels"
`int`	`getCount()` Gets the OTU count.
`String`	`getLine()` Get the line from classifier output file used to create this OtuNode.
`String`	`getOtuName()` Build the OTU name from the taxaMap.
`String`	`getSampleId()` Gets the sample ID to which the read belongs
`Map<String,String>`	`getTaxaMap()` Gets the map holding level-specific OTU names
`void`	`setCount(int count)` Set the number of reads for a sample ID that have this OTU assignment.
`void`	`setLine(String line)` Set the classifier report line parsed to build this OTU node.
`void`	`setSampleId(String sampleId)` Set the sample ID, parsed from file name or sequence header, to which this taxonomy assignment belongs.

- Method Detail
  - addTaxa
```
void addTaxa(String taxa,
             String levelDelim)
      throws Exception
```
    Add OtuNode taxa names for the Config."report.taxonomyLevels" level mapped by the classifier specific levelDelim parameter: .
    
    Parameters:
    
    taxa - Classifier Taxa name
    
    levelDelim - Classifier specific taxonomy level indicator
    
    Throws:
    
    Exception - if errors occur adding the taxa
  - delimToLevelMap
```
Map<String,String> delimToLevelMap()
```
    Get a map of the ClassifierModule taxonomy delimiters to Config."report.taxonomyLevels"
    
    Returns:
    
    Map(delim, level) map
  - getCount
```
int getCount()
```
    Gets the OTU count.
    
    Returns:
    
    Number of reads in node sampleId with node OTU assignment
  - getLine
```
String getLine()
```
    Get the line from classifier output file used to create this OtuNode.
    
    Returns:
    
    Line of classifier output
  - getOtuName
```
String getOtuName()
```
    Build the OTU name from the taxaMap.
    
    Returns:
    
    OTU name
  - getSampleId
```
String getSampleId()
```
    Gets the sample ID to which the read belongs
    
    Returns:
    
    Sample ID
  - getTaxaMap
```
Map<String,String> getTaxaMap()
                       throws Exception
```
    Gets the map holding level-specific OTU names
    
    Returns:
    
    OTU map (key=level, value=OTU)
    
    Throws:
    
    Exception - if errors occur building map
  - setCount
```
void setCount(int count)
```
    Set the number of reads for a sample ID that have this OTU assignment.
    
    Parameters:
    
    count - Number of reads having this OTU assignment
  - setLine
```
void setLine(String line)
```
    Set the classifier report line parsed to build this OTU node.
    
    Parameters:
    
    line - Classifier report line
  - setSampleId
```
void setSampleId(String sampleId)
```
    Set the sample ID, parsed from file name or sequence header, to which this taxonomy assignment belongs.
    
    Parameters:
    
    sampleId - ID of sample to which this taxonomy assignment belongs

Interface OtuNode

Method Summary

Method Detail

addTaxa

delimToLevelMap

getCount

getLine

getOtuName

getSampleId

getTaxaMap

setCount

setLine

setSampleId