org.biojava.spark.mappers

Class MapperUtils

java.lang.Object

org.biojava.spark.mappers.MapperUtils

All Implemented Interfaces:

Serializable

public class MapperUtils
extends Object
implements Serializable

A class to preserve the log if the functions in mappers. Mappers should not contain logic - as they are hard to test.

Author:

Anthony Bradley

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
MapperUtils()

Method Summary

Modifier and Type	Method and Description
static org.biojava.nbio.structure.Structure	byteArrToBiojavaStruct(String pdbCodePlus, byte[] inputByteArr) Converts a byte array of the messagepack (mmtf) to a Biojava structure.
static org.apache.spark.api.java.JavaPairRDD<org.apache.hadoop.io.Text,org.apache.hadoop.io.BytesWritable>	generateRdd(List<String> inputList, String ccdUrl) PDB RDD generator.
static scala.Tuple2<String,byte[]>	getByteArray(String pdbId) Get the available data as a byte array from an input PDB id.
static scala.Tuple2<String,byte[]>	getByteArray(String pdbId, String producer) Get the available data as a byte array from an input PDB id.

Methods inherited from class java.lang.Object

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

Constructor Detail

MapperUtils

public MapperUtils()

Method Detail

byteArrToBiojavaStruct

public static org.biojava.nbio.structure.Structure byteArrToBiojavaStruct(String pdbCodePlus,
                                                                          byte[] inputByteArr)
                                                                   throws IOException

Converts a byte array of the messagepack (mmtf) to a Biojava structure.

Parameters:

pdbCodePlus - The pdb code is the first four characters. Additional characters can be used.

inputByteArr - The message pack bytre array to be decoded.

Returns:

the decoded and inflated structure

Throws:

IOException

generateRdd

public static org.apache.spark.api.java.JavaPairRDD<org.apache.hadoop.io.Text,org.apache.hadoop.io.BytesWritable> generateRdd(List<String> inputList,
                                                                                                                              String ccdUrl)

PDB RDD generator. Converts a list of pdb ids to a JavaPairRDD with key Text and value BytesWritable.

Parameters:

sparkContext - the input JavaSparkContext

inputList - a List of Strings of the input PDB ids

Returns:

a JavaPairRDD with key Text and value BytesWritable

getByteArray

public static scala.Tuple2<String,byte[]> getByteArray(String pdbId)
                                                throws IOException,
                                                       org.biojava.nbio.structure.StructureException

Get the available data as a byte array from an input PDB id.

Parameters:

pdbId - the input PDB id

Returns:

the data as a byte array

Throws:

org.biojava.nbio.structure.StructureException - an error parsing the Structure using Biojava

IOException - an error accessing the file

getByteArray

public static scala.Tuple2<String,byte[]> getByteArray(String pdbId,
                                                       String producer)
                                                throws IOException,
                                                       org.biojava.nbio.structure.StructureException

Get the available data as a byte array from an input PDB id.

Parameters:

pdbId - the input PDB id

Returns:

the data as a byte array

Throws:

org.biojava.nbio.structure.StructureException - an error parsing the Structure using Biojava

IOException - an error accessing the file