biolockj.node.r16s

Class QiimeNode

java.lang.Object

biolockj.node.OtuNodeImpl

biolockj.node.r16s.QiimeNode

All Implemented Interfaces:

OtuNode, Comparable<OtuNode>

public class QiimeNode
extends OtuNodeImpl

This class holds the OTU assignments from one line of QiimeClassifier output.

2 sample lines (header + 1st row) from otu_table_L*.txt output by QIIME script: summarize_taxa.py
# Constructed from biom file #OTU ID 3A.1 7A.1 120A.1
7A.1 k__Bacteria;p__Actinobacteria 419.0 26.0 90.0 70.0

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	QIIME_DOMAIN_DELIM QIIME domain taxonomy level delimiter: "k__"
protected static String	SILVA_CLASS_DELIM Silva class taxonomy level delimiter: "D_2__"
protected static String	SILVA_DOMAIN_DELIM Silva domain taxonomy level delimiter: "D_0__"
protected static String	SILVA_FAMILY_DELIM Silva family taxonomy level delimiter: "D_4__"
protected static String	SILVA_GENUS_DELIM Silva genus taxonomy level delimiter: "D_5__"
protected static String	SILVA_ORDER_DELIM Silva order taxonomy level delimiter: "D_3__"
protected static String	SILVA_PHYLUM_DELIM Silva phylum taxonomy level delimiter: "D_1__"
protected static String	SILVA_SPECIES_DELIM Silva species taxonomy level delimiter: "D_6__"

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
QiimeNode(String id, String taxas, int count) Build the OtuNode by extracting the OTU names for each level from the line.

Method Summary

Modifier and Type	Method and Description
Map<String,String>	delimToLevelMap() Get a map of the ClassifierModule taxonomy delimiters to Config."report.taxonomyLevels"
protected String	getLevel(String taxa) Get the first taxonomy level delim.

Methods inherited from class biolockj.node.OtuNodeImpl

addTaxa, compareTo, 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

Field Detail

QIIME_DOMAIN_DELIM

protected static final String QIIME_DOMAIN_DELIM

QIIME domain taxonomy level delimiter: "k__"

See Also:

Constant Field Values

SILVA_CLASS_DELIM

protected static final String SILVA_CLASS_DELIM

Silva class taxonomy level delimiter: "D_2__"

See Also:

Constant Field Values

SILVA_DOMAIN_DELIM

protected static final String SILVA_DOMAIN_DELIM

Silva domain taxonomy level delimiter: "D_0__"

See Also:

Constant Field Values

SILVA_FAMILY_DELIM

protected static final String SILVA_FAMILY_DELIM

Silva family taxonomy level delimiter: "D_4__"

See Also:

Constant Field Values

SILVA_GENUS_DELIM

protected static final String SILVA_GENUS_DELIM

Silva genus taxonomy level delimiter: "D_5__"

See Also:

Constant Field Values

SILVA_ORDER_DELIM

protected static final String SILVA_ORDER_DELIM

Silva order taxonomy level delimiter: "D_3__"

See Also:

Constant Field Values

SILVA_PHYLUM_DELIM

protected static final String SILVA_PHYLUM_DELIM

Silva phylum taxonomy level delimiter: "D_1__"

See Also:

Constant Field Values

SILVA_SPECIES_DELIM

protected static final String SILVA_SPECIES_DELIM

Silva species taxonomy level delimiter: "D_6__"

See Also:

Constant Field Values

Constructor Detail

QiimeNode

public QiimeNode(String id,
                 String taxas,
                 int count)
          throws Exception

Build the OtuNode by extracting the OTU names for each level from the line.

Parameters:

id - Sample ID extracted from count column header

taxas - OTU names with level indicator prefix

count - Extracted from column of the Sample ID

Throws:

Exception - if propagated from addOtu() method

Method Detail

delimToLevelMap

public Map<String,String> delimToLevelMap()

Description copied from interface: OtuNode

Get a map of the ClassifierModule taxonomy delimiters to Config."report.taxonomyLevels"

Specified by:

delimToLevelMap in interface OtuNode

Overrides:

delimToLevelMap in class OtuNodeImpl

Returns:

Map(delim, level) map

getLevel

protected String getLevel(String taxa)
                   throws Exception

Get the first taxonomy level delim.

Parameters:

taxa - Full classifier taxonomy string

Returns:

Level delim

Throws:

Exception - if the taxa delim is undefined