org.biojava.spark.utils

Class ClusterSequences

java.lang.Object

org.biojava.spark.utils.ClusterSequences

All Implemented Interfaces:

Serializable

public class ClusterSequences
extends Object
implements Serializable

Cluster protein sequences using SmithWaterman algorithm

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
ClusterSequences(int nrFractions, Float minOverlap1, Float minOverlap2, Float minPercentageId)

Method Summary

Modifier and Type	Method and Description
org.apache.spark.api.java.JavaPairRDD<String,Iterable<String>>	clusterSequences(org.apache.spark.api.java.JavaSparkContext sc, org.apache.spark.api.java.JavaPairRDD<String,String> sequences, int nrIterations) passes in a JavaPairRDD where the first element is the ID of a sequence, the second one the string representation

Methods inherited from class java.lang.Object

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

Constructor Detail

ClusterSequences

public ClusterSequences(int nrFractions,
                        Float minOverlap1,
                        Float minOverlap2,
                        Float minPercentageId)

Method Detail

clusterSequences

public org.apache.spark.api.java.JavaPairRDD<String,Iterable<String>> clusterSequences(org.apache.spark.api.java.JavaSparkContext sc,
                                                                                       org.apache.spark.api.java.JavaPairRDD<String,String> sequences,
                                                                                       int nrIterations)

passes in a JavaPairRDD where the first element is the ID of a sequence, the second one the string representation

Parameters:

sc - Java spark context

sequences - the sequences represented as sequence ID and sequence string..

nrIterations - how many iterations of clustering should be performed. if < 1 nothing will get run.

Returns:

a pair with the first being the representative name, second is a list of all members of the cluster