biolockj.node

Class OtuNodeImpl

java.lang.Object

biolockj.node.OtuNodeImpl

All Implemented Interfaces:

OtuNode, Comparable<OtuNode>

Direct Known Subclasses:

Kraken2Node, KrakenNode, MetaphlanNode, QiimeNode, RdpNode

public abstract class OtuNodeImpl
extends Object
implements OtuNode, Comparable<OtuNode>

The default implementation of OtuNode is also the superclass for all WGS and 16S OtuNode classes. OtuNodes hold taxonomy assignment info, represents one line of ClassifierModule output. The assignment is stored in a local taxaMap, which holds one taxa name per taxonomy level.

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	CLASS_DELIM Standard classifier output level delimiter for CLASS
protected static String	DOMAIN_DELIM Standard classifier output level delimiter for DOMAIN
protected static String	FAMILY_DELIM Standard classifier output level delimiter for FAMILY
protected static String	GENUS_DELIM Standard classifier output level delimiter for GENUS
protected static String	ORDER_DELIM Standard classifier output level delimiter for ORDER
protected static String	PHYLUM_DELIM Standard classifier output level delimiter for PHYLUM
protected static String	SPECIES_DELIM Standard classifier output level delimiter for SPECIES

Constructor Summary

Constructors

Constructor and Description
OtuNodeImpl()

Method Summary

Modifier and Type	Method and Description
void	addTaxa(String taxa, String level) If called for level not included in Config."report.taxonomyLevels", check if the top level taxonomy level is already assigned.
int	compareTo(OtuNode node) The sort order of the TreeSet(OtuNode) is absolutely required for proper processing in addTaxa(String, String) and getTaxaMap().
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() This implementation ensures all levels between top and bottom taxonomy levels are complete.
protected void	populateInBetweenTaxa() Populate missing OTUs if top level taxa is defined and there is a level gap between the top level and the bottom level.
void	setCount(int count) Set the number of reads for a sample ID that have this OTU assignment.
void	setLine(String line) Set line only if in DEBUG mode, so we can print OtuNode constructor inputs.
void	setSampleId(String sampleId) Set the sample ID, parsed from file name or sequence header, to which this taxonomy assignment belongs.

Methods inherited from class java.lang.Object

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

Field Detail

CLASS_DELIM

protected static String CLASS_DELIM

Standard classifier output level delimiter for CLASS

DOMAIN_DELIM

protected static String DOMAIN_DELIM

Standard classifier output level delimiter for DOMAIN

FAMILY_DELIM

protected static String FAMILY_DELIM

Standard classifier output level delimiter for FAMILY

GENUS_DELIM

protected static String GENUS_DELIM

Standard classifier output level delimiter for GENUS

ORDER_DELIM

protected static String ORDER_DELIM

Standard classifier output level delimiter for ORDER

PHYLUM_DELIM

protected static String PHYLUM_DELIM

Standard classifier output level delimiter for PHYLUM

SPECIES_DELIM

protected static String SPECIES_DELIM

Standard classifier output level delimiter for SPECIES

Constructor Detail

OtuNodeImpl

public OtuNodeImpl()

Method Detail

addTaxa

public void addTaxa(String taxa,
                    String level)
             throws Exception

If called for level not included in Config."report.taxonomyLevels", check if the top level taxonomy level is already assigned. If so, populate missing levels by passing the parent taxa to TaxaUtil.buildUnclassifiedTaxa(String) until the given in level is assigned.

This method assumes it is called repeatedly for each OTU (once/level) and that each subsequent call passes a lower taxonomy level than the previous.

Specified by:

addTaxa in interface OtuNode

Parameters:

taxa - Taxa name

level - Taxonomy level

Throws:

Exception - if errors occur

compareTo

public int compareTo(OtuNode node)

The sort order of the TreeSet(OtuNode) is absolutely required for proper processing in addTaxa(String, String) and getTaxaMap(). We sort alphabetically by otuName, however if one otuName is a substring of the compared otuName, the longer name is ordered before the shorter name.
Because of this, when iterating through a sorted list of OtuNodes we can be sure we add nodes in the taxonomy hierarchy from the bottom-up.

Specified by:

compareTo in interface Comparable<OtuNode>

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

Returns:

Map(delim, level) map

getCount

public int getCount()

Description copied from interface: OtuNode

Gets the OTU count.

Specified by:

getCount in interface OtuNode

Returns:

Number of reads in node sampleId with node OTU assignment

getLine

public String getLine()

Description copied from interface: OtuNode

Get the line from classifier output file used to create this OtuNode.

Specified by:

getLine in interface OtuNode

Returns:

Line of classifier output

getOtuName

public String getOtuName()

Description copied from interface: OtuNode

Build the OTU name from the taxaMap.

Specified by:

getOtuName in interface OtuNode

Returns:

OTU name

getSampleId

public String getSampleId()

Description copied from interface: OtuNode

Gets the sample ID to which the read belongs

Specified by:

getSampleId in interface OtuNode

Returns:

Sample ID

getTaxaMap

public Map<String,String> getTaxaMap()
                              throws Exception

This implementation ensures all levels between top and bottom taxonomy levels are complete. If missing middle levels are found, they inherit their parent taxa.

Specified by:

getTaxaMap in interface OtuNode

Returns:

OTU map (key=level, value=OTU)

Throws:

Exception - if errors occur building map

setCount

public void setCount(int count)

Description copied from interface: OtuNode

Set the number of reads for a sample ID that have this OTU assignment.

Specified by:

setCount in interface OtuNode

Parameters:

count - Number of reads having this OTU assignment

setLine

public void setLine(String line)

Set line only if in DEBUG mode, so we can print OtuNode constructor inputs.

Specified by:

setLine in interface OtuNode

Parameters:

line - Classifier report line

setSampleId

public void setSampleId(String sampleId)

Description copied from interface: OtuNode

Set the sample ID, parsed from file name or sequence header, to which this taxonomy assignment belongs.

Specified by:

setSampleId in interface OtuNode

Parameters:

sampleId - ID of sample to which this taxonomy assignment belongs

populateInBetweenTaxa

protected void populateInBetweenTaxa()

Populate missing OTUs if top level taxa is defined and there is a level gap between the top level and the bottom level. Missing levels inherit the parent name as "Unclassified (parent-name) OTU".