biolockj.node

Class ParsedSample

java.lang.Object

biolockj.node.ParsedSample

All Implemented Interfaces:

Serializable, Comparable<ParsedSample>

public class ParsedSample
extends Object
implements Serializable, Comparable<ParsedSample>

ParserModules create and store one ParsedSample, with OTU assignments and counts, for each sample. Only the samples that contain one or more reads used by ClassifierModule to generate a valid taxonomic assignment are used.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
ParsedSample(OtuNode node) Construct a new ParsedSample with it's 1st OtuNode.

Method Summary

Modifier and Type	Method and Description
void	addNode(OtuNode node) Add the OtuNode to the ParsedSample.
int	compareTo(ParsedSample o)
boolean	equals(Object o)
TreeMap<String,Integer>	getOtuCounts() Get the streamlined taxonomy tree with counts, each OTU listed only 1 time with num occurrences in the sample. Example: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides_vulgatus 87342
String	getSampleId() Getter for sampleId.

Methods inherited from class java.lang.Object

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

Constructor Detail

ParsedSample

public ParsedSample(OtuNode node)

Construct a new ParsedSample with it's 1st OtuNode.

Parameters:

node - OtuNode

Method Detail

addNode

public void addNode(OtuNode node)

Add the OtuNode to the ParsedSample.

Parameters:

node - OtuNode

compareTo

public int compareTo(ParsedSample o)

Specified by:

compareTo in interface Comparable<ParsedSample>

equals

public boolean equals(Object o)

Overrides:

equals in class Object

getOtuCounts

public TreeMap<String,Integer> getOtuCounts()
                                     throws Exception

Get the streamlined taxonomy tree with counts, each OTU listed only 1 time with num occurrences in the sample.
Example: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides_vulgatus 87342

Returns:

map OTU-count

Throws:

Exception - if errors occur

getSampleId

public String getSampleId()

Getter for sampleId.

Returns:

Sample ID.