biolockj.node.wgs

Class KrakenNode

java.lang.Object

biolockj.node.OtuNodeImpl

biolockj.node.wgs.KrakenNode

All Implemented Interfaces:

OtuNode, Comparable<OtuNode>

public class KrakenNode
extends OtuNodeImpl

This class represents one line of KrakenClassifier output. Kraken outputs the sequence header and taxonomy assignments for all levels in one line. Each line represents a single read.

Sample mpa-output line from Kraken:
FCC6MMAACXX:8:1101:1968:2100#GTATTCTC/1 d__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_vulgatus

Field Summary

Fields inherited from class biolockj.node.OtuNodeImpl

CLASS_DELIM, DOMAIN_DELIM, FAMILY_DELIM, GENUS_DELIM, ORDER_DELIM, PHYLUM_DELIM, SPECIES_DELIM

Constructor Summary

Constructors

Constructor and Description
KrakenNode(String id, String line) Constructor called for each line of Kraken output. Builds the OtuNode by extracting the OTU names for each taxonomy level found in the line.

Method Summary

Methods inherited from class biolockj.node.OtuNodeImpl

addTaxa, compareTo, delimToLevelMap, getCount, getLine, getOtuName, getSampleId, getTaxaMap, populateInBetweenTaxa, setCount, setLine, setSampleId

Methods inherited from class java.lang.Object

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

Constructor Detail

KrakenNode

public KrakenNode(String id,
                  String line)
           throws Exception

Constructor called for each line of Kraken output.
Builds the OtuNode by extracting the OTU names for each taxonomy level found in the line.

Parameters:

id - Sample ID

line - Kraken mpa-output line

Throws:

Exception - if required properties are invalid or undefined