org.biojava.spark.data

Class GroupDataRDD

java.lang.Object

org.biojava.spark.data.GroupDataRDD

public class GroupDataRDD
extends Object

An RDD to comprise Group level data.

Author:

Anthony Bradley

Constructor Summary

Constructors

Constructor and Description
GroupDataRDD(org.apache.spark.api.java.JavaPairRDD<String,org.biojava.nbio.structure.Group> groupRdd) Constructor of the RDD from a JavaPairRDD of Group

Method Summary

Modifier and Type	Method and Description
void	cacheData() Cache the data - for multi-processing.
Map<String,Long>	countByGroupName() Count the number of times each group name appears.
AtomData	getAtoms() Get the atoms from the groups.
org.apache.spark.api.java.JavaPairRDD<String,org.biojava.nbio.structure.Group>	getGroupRdd() Get the JavaPairRDD of Group data.

Methods inherited from class java.lang.Object

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

Constructor Detail

GroupDataRDD

public GroupDataRDD(org.apache.spark.api.java.JavaPairRDD<String,org.biojava.nbio.structure.Group> groupRdd)

Constructor of the RDD from a JavaPairRDD of Group

Parameters:

groupRdd - the input JavaPairRDD of Group

Method Detail

cacheData

public void cacheData()

Cache the data - for multi-processing.

getGroupRdd

public org.apache.spark.api.java.JavaPairRDD<String,org.biojava.nbio.structure.Group> getGroupRdd()

Get the JavaPairRDD of Group data.

Returns:

the JavaPairRDD of Group data

countByGroupName

public Map<String,Long> countByGroupName()

Count the number of times each group name appears.

Returns:

the map of group names (e.g. LYS for Lysine) and the number of times they appear in the RDD

getAtoms

public AtomData getAtoms()

Get the atoms from the groups.

Returns:

the atoms for all the groups