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 Details
- CifIO
  
  public CifIO()
Method Details
- 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

Class CifIO

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

Method Details