Package org.rcsb.cif

Class CifOptions

java.lang.Object

org.rcsb.cif.CifOptions

public class CifOptions
extends Object

Allows to set options for CIF writing. Acquire by calling builder(). Pass into CifIO functions. Use white- and blacklist functions to select a subset of categories and/or columns to write. If a value is present in both white- and blacklist, the blacklist values will trump the whitelist.

For now only writer classes will respect these options. They can be passed to reader classes as well, however there are currently no relevant options for CIF reading.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	CifOptions.CifOptionsBuilder	Internal class to handle the option building process.

Method Summary

Modifier and Type	Method	Description
static CifOptions.CifOptionsBuilder	builder()	Acquire the actual builder instance.
boolean	filterCategory(String categoryName)	Checks whether this category should be written to output files.
boolean	filterColumn(String categoryName, String columnName)	Checks whether this column should be written to output files.
String	getEncoder()	The name of the encoder which should be written to files.
Optional<EncodingStrategyHint>	getEncodingStrategyHint(String categoryName, String columnName)	Reports whether a particular encoding or floating-point precision is specified for this particular column.
String	getFetchUrl()	The URL from which files should be fetched - must follow the pattern: www.source.com/%s.cif, where %s represents the pdbId to be inserted into the URL to fetch the correct file.
CifOptions.CifOptionsBuilder.FileFormat	getFileFormat()	Reports if the input file format was specified for reading.
boolean	isGeneric()	Reading should not care about category and column types.
boolean	isGzip()	Allows for downstream GZIP operations.

Methods inherited from class java.lang.Object

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

Method Detail

isGeneric

public boolean isGeneric()

Reading should not care about category and column types.

Returns:

true if reading should be untyped

isGzip

public boolean isGzip()

Allows for downstream GZIP operations.

Returns:

true if the output should be gzipped

getEncoder

public String getEncoder()

The name of the encoder which should be written to files.

Returns:

a String representing the encoder name

getFetchUrl

public String getFetchUrl()

The URL from which files should be fetched - must follow the pattern: www.source.com/%s.cif, where %s represents the pdbId to be inserted into the URL to fetch the correct file.

Returns:

the specified fetch URL

filterCategory

public boolean filterCategory(String categoryName)

Checks whether this category should be written to output files. Specify via the white- and blacklists.

Parameters:

categoryName - the category name to check

Returns:

true if this category should be written to output files

See Also:

CifOptions.CifOptionsBuilder.categoryWhitelist(String...), CifOptions.CifOptionsBuilder.categoryBlacklist(String...)

filterColumn

public boolean filterColumn(String categoryName,
                            String columnName)

Checks whether this column should be written to output files. Specify via the white- and blacklists.

Parameters:

categoryName - the category name to check

columnName - the column name to check

Returns:

true if this column should be written to output files

See Also:

CifOptions.CifOptionsBuilder.columnWhitelist(String...), CifOptions.CifOptionsBuilder.columnBlacklist(String...)

getEncodingStrategyHint

public Optional<EncodingStrategyHint> getEncodingStrategyHint(String categoryName,
                                                              String columnName)

Reports whether a particular encoding or floating-point precision is specified for this particular column.

Parameters:

categoryName - the category name to check

columnName - the column name to check

Returns:

an optional wrapping an EncodingStrategyHint

getFileFormat

public CifOptions.CifOptionsBuilder.FileFormat getFileFormat()

Reports if the input file format was specified for reading.

Returns:

the CifOptions.CifOptionsBuilder.FileFormat if set and null otherwise

builder

public static CifOptions.CifOptionsBuilder builder()

Acquire the actual builder instance.

Returns:

a CifOptions.CifOptionsBuilder