org.biojava.spark.data

Class AtomData

java.lang.Object

org.biojava.spark.data.AtomData

public class AtomData
extends Object

A wrapper around JavaRDD and Dataset of atoms.

Author:

Anthony Bradley

Constructor Summary

Constructors

Constructor and Description
AtomData(org.apache.spark.sql.Dataset<org.biojava.nbio.structure.Atom> atomDataset) Construct from a Dataset
AtomData(org.apache.spark.api.java.JavaRDD<org.biojava.nbio.structure.Atom> atomRdd) Construct from an JavaRDD

Method Summary

Modifier and Type	Method and Description
void	cacheData() Cache the data - for multi-processing.
Map<String,Long>	countByAtomName() Count the number of times each atom name appears.
Map<String,Long>	countByElement() Count the number of times each element appears.
Map<String,Long>	countByGroupAtomName() Get the unique group atom name combinations in this.
org.apache.spark.api.java.JavaRDD<org.biojava.nbio.structure.Atom>	getRdd() Get the underlying JavaRDD for this AtomDataRDD.

Methods inherited from class java.lang.Object

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

Constructor Detail

AtomData

public AtomData(org.apache.spark.api.java.JavaRDD<org.biojava.nbio.structure.Atom> atomRdd)

Construct from an JavaRDD

Parameters:

atomRdd - the input JavaRDD

AtomData

public AtomData(org.apache.spark.sql.Dataset<org.biojava.nbio.structure.Atom> atomDataset)

Construct from a Dataset

Parameters:

atomDataset - the input Dataset

Method Detail

getRdd

public org.apache.spark.api.java.JavaRDD<org.biojava.nbio.structure.Atom> getRdd()

Get the underlying JavaRDD for this AtomDataRDD.

Returns:

the underlying JavaRDD for this AtomDataRDD

cacheData

public void cacheData()

Cache the data - for multi-processing.

countByElement

public Map<String,Long> countByElement()

Count the number of times each element appears.

Returns:

the map of element names (e.g. Ca for Calcium) and the number of times they appear in the RDD

countByAtomName

public Map<String,Long> countByAtomName()

Count the number of times each atom name appears.

Returns:

the map of element names (e.g. CA for C-alpha) and the number of times they appear in the RDD

countByGroupAtomName

public Map<String,Long> countByGroupAtomName()

Get the unique group atom name combinations in this.

Returns:

the map of counts by a given atom name