Package org.rcsb.cif

Class CifIO

java.lang.Object

org.rcsb.cif.CifIO

public class CifIO
extends Object

Collection of IO operations to retrieve, process, and write CIF files. All read and write operations are thread-safe. The data model (i.e. CifFile, Block, Category, and Column) is immutable to the user but maintains some internal state to improve performance. Therefore, multi-threaded access to data of one CifFile is not safe and should be avoided.

Constructor Summary

Constructors

Constructor	Description
CifIO()

Method Summary

Modifier and Type	Method	Description
static CifFile	readById(String pdbId)	Read a CifFile from web.
static CifFile	readById(String pdbId, CifOptions options)	Read a CifFile from web.
static CifFile	readFromInputStream(InputStream inputStream)	Read a CifFile from a given InputStream.
static CifFile	readFromInputStream(InputStream inputStream, CifOptions options)	Read a CifFile from a given InputStream.
static CifFile	readFromPath(Path path)	Read a CifFile from a given Path.
static CifFile	readFromPath(Path path, CifOptions options)	Read a CifFile from a given Path.
static CifFile	readFromURL(URL url)	Read a CifFile from a given URL.
static CifFile	readFromURL(URL url, CifOptions options)	Read a CifFile from a given URL.
static byte[]	writeBinary(CifFile cifFile)	Convert a CifFile to its binary byte[] representation.
static void	writeBinary(CifFile cifFile, Path outputFile)	Write a binary CifFile to a given Path.
static void	writeBinary(CifFile cifFile, Path outputFile, CifOptions options)	Write a binary CifFile to a given Path.
static byte[]	writeBinary(CifFile cifFile, CifOptions options)	Convert a CifFile to its binary byte[] representation.
static byte[]	writeText(CifFile cifFile)	Convert a CifFile to its text byte[] representation.
static void	writeText(CifFile cifFile, Path outputFile)	Write a text CifFile to a given Path.
static void	writeText(CifFile cifFile, Path outputFile, CifOptions options)	Write a text CifFile to a given Path.
static byte[]	writeText(CifFile cifFile, CifOptions options)	Convert a CifFile to its text byte[] representation.

Methods inherited from class java.lang.Object

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

Constructor Detail

CifIO

public CifIO()

Method Detail

readById

public static CifFile readById(String pdbId)
                        throws IOException

Read a CifFile from web. Refine the address via CifOptions.CifOptionsBuilder.fetchUrl(String). Otherwise binaryCIF will be loaded.

Parameters:

pdbId - the pdbId which should be fetched from the web - the library will determine whether the file is gzipped or plain information and whether it is in binary format (after resolving GZIP if needed) or text the appropriate reader will be chosen automatically

Returns:

a CifFile instance

Throws:

IOException - thrown when reading fails

readById

public static CifFile readById(String pdbId,
                               CifOptions options)
                        throws IOException

Read a CifFile from web. Refine the address via CifOptions.CifOptionsBuilder.fetchUrl(String). Otherwise binaryCIF will be loaded.

Parameters:

pdbId - the pdbId which should be fetched from the web - the library will determine whether the file is gzipped or plain information and whether it is in binary format (after resolving GZIP if needed) or text the appropriate reader will be chosen automatically

options - CifOptions for the reading process

Returns:

a CifFile instance

Throws:

IOException - thrown when reading fails

readFromURL

public static CifFile readFromURL(URL url)
                           throws IOException

Read a CifFile from a given URL.

Parameters:

url - the URL from which to read - the library will determine whether the file is gzipped or plain information and whether it is in binary format (after resolving GZIP if needed) or text the appropriate reader will be chosen automatically

Returns:

a CifFile instance

Throws:

IOException - thrown when reading fails

readFromURL

public static CifFile readFromURL(URL url,
                                  CifOptions options)
                           throws IOException

Read a CifFile from a given URL.

Parameters:

url - the URL from which to read - the library will determine whether the file is gzipped or plain information and whether it is in binary format (after resolving GZIP if needed) or text the appropriate reader will be chosen automatically

options - CifOptions for the reading process

Returns:

a CifFile instance

Throws:

IOException - thrown when reading fails

readFromPath

public static CifFile readFromPath(Path path)
                            throws IOException

Read a CifFile from a given Path.

Parameters:

path - the Path from which to read - the library will determine whether the file is gzipped or plain information and whether it is in binary format (after resolving GZIP if needed) or text the appropriate reader will be chosen automatically

Returns:

a CifFile instance

Throws:

IOException - thrown when reading fails

readFromPath

public static CifFile readFromPath(Path path,
                                   CifOptions options)
                            throws IOException

Read a CifFile from a given Path.

Parameters:

path - the Path from which to read - the library will determine whether the file is gzipped or plain information and whether it is in binary format (after resolving GZIP if needed) or text the appropriate reader will be chosen automatically

options - CifOptions for the reading process

Returns:

a CifFile instance

Throws:

IOException - thrown when reading fails

readFromInputStream

public static CifFile readFromInputStream(InputStream inputStream)
                                   throws IOException

Read a CifFile from a given InputStream.

Parameters:

inputStream - the InputStream to process - the library will determine whether the file is gzipped or plain information and whether it is in binary format (after resolving GZIP if needed) or text - the appropriate reader will be chosen automatically

Returns:

a CifFile instance

Throws:

IOException - thrown when reading fails

readFromInputStream

public static CifFile readFromInputStream(InputStream inputStream,
                                          CifOptions options)
                                   throws IOException

Read a CifFile from a given InputStream.

Parameters:

inputStream - the InputStream to process - the library will determine whether the file is gzipped or plain information and whether it is in binary format (after resolving GZIP if needed) or text - the appropriate reader will be chosen automatically

options - CifOptions for the reading process

Returns:

a CifFile instance

Throws:

IOException - thrown when reading fails

writeBinary

public static void writeBinary(CifFile cifFile,
                               Path outputFile)
                        throws IOException

Write a binary CifFile to a given Path.

Parameters:

cifFile - the CifFile to process

outputFile - the Path where the content should be written

Throws:

IOException - thrown when writing fails

writeBinary

public static void writeBinary(CifFile cifFile,
                               Path outputFile,
                               CifOptions options)
                        throws IOException

Write a binary CifFile to a given Path.

Parameters:

cifFile - the CifFile to process

outputFile - the Path where the content should be written

options - CifOptions for the writing process

Throws:

IOException - thrown when writing fails

writeBinary

public static byte[] writeBinary(CifFile cifFile)
                          throws IOException

Convert a CifFile to its binary byte[] representation.

Parameters:

cifFile - the CifFile to process

Returns:

a byte[] representing the information to write

Throws:

IOException - thrown when writing fails

writeBinary

public static byte[] writeBinary(CifFile cifFile,
                                 CifOptions options)
                          throws IOException

Convert a CifFile to its binary byte[] representation.

Parameters:

cifFile - the CifFile to process

options - CifOptions for the writing process

Returns:

a byte[] representing the information to write

Throws:

IOException - thrown when writing fails

writeText

public static void writeText(CifFile cifFile,
                             Path outputFile)
                      throws IOException

Write a text CifFile to a given Path.

Parameters:

cifFile - the CifFile to process

outputFile - the Path where the content should be written

Throws:

IOException - thrown when writing fails

writeText

public static void writeText(CifFile cifFile,
                             Path outputFile,
                             CifOptions options)
                      throws IOException

Write a text CifFile to a given Path.

Parameters:

cifFile - the CifFile to process

outputFile - the Path where the content should be written

options - CifOptions for the writing process

Throws:

IOException - thrown when writing fails

writeText

public static byte[] writeText(CifFile cifFile)
                        throws IOException

Convert a CifFile to its text byte[] representation.

Parameters:

cifFile - the CifFile to process

Returns:

a byte[] representing the information to write

Throws:

IOException - thrown when conversion fails

writeText

public static byte[] writeText(CifFile cifFile,
                               CifOptions options)
                        throws IOException

Convert a CifFile to its text byte[] representation.

Parameters:

cifFile - the CifFile to process

options - CifOptions for the writing process

Returns:

a byte[] representing the information to write

Throws:

IOException - thrown when conversion fails