org.rcsb.mmtf.encoder

Class EncoderUtils

java.lang.Object

org.rcsb.mmtf.encoder.EncoderUtils

public class EncoderUtils
extends Object

A class of static utility functions to aid encoding of data. Convert from StructureDataInterface into a format useable by the MmtfStructure.

Author:

Anthony Bradley

Field Summary

Fields

Modifier and Type	Field and Description
static int	NULL_PARAM The Null parameter for encoding (i.e.

Constructor Summary

Constructors

Constructor and Description
EncoderUtils()

Method Summary

Modifier and Type	Method and Description
static byte[]	encodeByteArr(CharCodecs inputCodec, char[] inputData, int param) Method to prepend a byte array with a byte.
static byte[]	encodeByteArr(FloatCodecs inputCodec, float[] inputData, int param) Method to prepend a byte array with a byte.
static byte[]	encodeByteArr(IntCodecs inputCodec, int[] inputData, int param) Method to prepend a byte array with a byte.
static byte[]	encodeByteArr(StringCodecs inputCodec, String[] inputData, int param) Method to prepend a byte array with a byte.
static List<BioAssemblyData>	generateBioassemblies(StructureDataInterface structureDataInterface) Find the bioassembly information as a list from the StructureDataInterface.
static Entity[]	generateEntityList(StructureDataInterface structureDataInterface) Generate the entity level information from the StructureDataInterface.
static Group[]	generateGroupList(StructureDataInterface structureDataInterface) Regenerate a group map from the StructureDataInterface.
static String	getTypeFromChainId(StructureDataInterface structureDataInterface, int chainInd) Get the type of a given chain index.
static void	transferBioassembly(StructureDataInterface structureDataInterface, AdapterToStructureData adapterToStructureData) Transfer bioassembly data from a StructureDataInterface to an AdapterToStructureData.

Methods inherited from class java.lang.Object

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

Field Detail

NULL_PARAM

public static final int NULL_PARAM

The Null parameter for encoding (i.e. when no params are set).

See Also:

Constant Field Values

Constructor Detail

EncoderUtils

public EncoderUtils()

Method Detail

generateGroupList

public static Group[] generateGroupList(StructureDataInterface structureDataInterface)

Regenerate a group map from the StructureDataInterface.

Parameters:

structureDataInterface - the input interface

Returns:

a list of all the groups in the molecule

generateBioassemblies

public static List<BioAssemblyData> generateBioassemblies(StructureDataInterface structureDataInterface)

Find the bioassembly information as a list from the StructureDataInterface.

Parameters:

structureDataInterface - the interface from where to find the data

Returns:

a list of bioassembly information to be stored in the MMTF data structure.

generateEntityList

public static Entity[] generateEntityList(StructureDataInterface structureDataInterface)

Generate the entity level information from the StructureDataInterface.

Parameters:

structureDataInterface - the input interface

Returns:

the list of entities

getTypeFromChainId

public static String getTypeFromChainId(StructureDataInterface structureDataInterface,
                                        int chainInd)

Get the type of a given chain index.

Parameters:

structureDataInterface - the input StructureDataInterface

chainInd - the index of the relevant chain

Returns:

the String describing the chain

encodeByteArr

public static byte[] encodeByteArr(FloatCodecs inputCodec,
                                   float[] inputData,
                                   int param)

Method to prepend a byte array with a byte.

Parameters:

inputCodec - the codec to be used

inputData - the array to encode and prepend

param - the input parameter - an integer to be used in the encoding

Returns:

the updated array

encodeByteArr

public static byte[] encodeByteArr(IntCodecs inputCodec,
                                   int[] inputData,
                                   int param)

Method to prepend a byte array with a byte.

Parameters:

inputCodec - the codec to be used

inputData - the array to encode and prepend

param - the input parameter - an integer to be used in the encoding

Returns:

the updated array

encodeByteArr

public static byte[] encodeByteArr(CharCodecs inputCodec,
                                   char[] inputData,
                                   int param)

Method to prepend a byte array with a byte.

Parameters:

inputData - the array to encode and prepend

inputCodec - the codec to be used

param - the input parameter - an integer to be used in the encoding

Returns:

the updated array

encodeByteArr

public static byte[] encodeByteArr(StringCodecs inputCodec,
                                   String[] inputData,
                                   int param)

Method to prepend a byte array with a byte.

Parameters:

inputData - the array to encode and prepend

inputCodec - the codec to be used

param - the input parameter - an integer to be used in the encoding

Returns:

the updated array

transferBioassembly

public static void transferBioassembly(StructureDataInterface structureDataInterface,
                                       AdapterToStructureData adapterToStructureData)

Transfer bioassembly data from a StructureDataInterface to an AdapterToStructureData.

Parameters:

structureDataInterface - the input StructureDataInterface

adapterToStructureData - the AdapterToStructureData to pass the data to