org.rcsb.mmtf.decoder

Class ReaderUtils

java.lang.Object

org.rcsb.mmtf.decoder.ReaderUtils

public class ReaderUtils
extends Object

A class of static utility methods for reading data.

Author:

Anthony Bradley

Constructor Summary

Constructors

Constructor and Description
ReaderUtils()

Method Summary

Modifier and Type	Method and Description
static byte[]	deflateGzip(byte[] inputBytes) Deflate a gzip byte array.
static byte[]	getByteArrayFromUrl(String pdbCode) Get the GZIP compressed and messagepack serialized data from the MMTF servers
static MmtfStructure	getDataFromFile(Path filePath) A function to get MMTF data from a file path.
static MmtfStructure	getDataFromUrl(String pdbCode) Find the message pack byte array from the web using the input code and a base url.

Methods inherited from class java.lang.Object

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

Constructor Detail

ReaderUtils

public ReaderUtils()

Method Detail

getDataFromUrl

public static MmtfStructure getDataFromUrl(String pdbCode)
                                    throws IOException

Find the message pack byte array from the web using the input code and a base url. Caches the file if possible.

Parameters:

pdbCode - the pdb code for the desired structure.

Returns:

the MMTFBean of the deserialized data

Throws:

IOException - if the data cannot be read from the URL

getByteArrayFromUrl

public static byte[] getByteArrayFromUrl(String pdbCode)
                                  throws IOException

Get the GZIP compressed and messagepack serialized data from the MMTF servers

Parameters:

pdbCode - the PDB code for the data required

Returns:

the byte array (GZIP compressed) of the data from the URL

Throws:

IOException - an error reading the URL

deflateGzip

public static byte[] deflateGzip(byte[] inputBytes)
                          throws IOException

Deflate a gzip byte array.

Parameters:

inputBytes - a gzip compressed byte array

Returns:

a deflated byte array

Throws:

IOException - error in gzip input stream

getDataFromFile

public static MmtfStructure getDataFromFile(Path filePath)
                                     throws IOException

A function to get MMTF data from a file path.

Parameters:

filePath - the full path of the file to be read

Returns:

the deserialized MmtfStructure

Throws:

IOException - an error reading the file