Package org.rcsb.cif

Class CifOptions.CifOptionsBuilder

java.lang.Object
org.rcsb.cif.CifOptions.CifOptionsBuilder
Enclosing class:
CifOptions
public static class CifOptions.CifOptionsBuilder
extends Object
Internal class to handle the option building process.

  • Constructor Details

  • Method Details

    • gzip

      public CifOptions.CifOptionsBuilder gzip​(boolean gzip)
      Allows for downstream GZIP operations.
      Parameters:
      gzip - true if the output should be gzipped
      Returns:
      this builder instance

    • encoder

      public CifOptions.CifOptionsBuilder encoder​(String encoder)
      The name of the encoder which should be written to files.
      Parameters:
      encoder - String representing the encoder name
      Returns:
      this builder instance

    • fetchUrl

      public CifOptions.CifOptionsBuilder fetchUrl​(String fetchUrl)
      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.
      Parameters:
      fetchUrl - the specified fetch URL
      Returns:
      this builder instance

    • categoryWhitelist

      public CifOptions.CifOptionsBuilder categoryWhitelist​(String... categoryWhitelist)
      Add entries to the category whitelist. If the whitelist has any entries, the category must be explicitly contained for the category to appear in the output.
      Parameters:
      categoryWhitelist - a collection of String values to explicitly include in the output, all other possible entries will be implicitly excluded
      Returns:
      this builder instance

    • categoryWhitelist

      public CifOptions.CifOptionsBuilder categoryWhitelist​(List<String> categoryWhitelist)
      Add entries to the category whitelist. If the whitelist has any entries, the category must be explicitly contained for the category to appear in the output.
      Parameters:
      categoryWhitelist - a collection of String values to explicitly include in the output, all other possible entries will be implicitly excluded
      Returns:
      this builder instance

    • categoryBlacklist

      public CifOptions.CifOptionsBuilder categoryBlacklist​(String... categoryBlacklist)
      Add entries to the category blacklist. Any entries will be ignored when composing the output.
      Parameters:
      categoryBlacklist - a collection of String values to explicitly exclude from the output, all other possible entries will be implicitly included
      Returns:
      this builder instance

    • categoryBlacklist

      public CifOptions.CifOptionsBuilder categoryBlacklist​(List<String> categoryBlacklist)
      Add entries to the category blacklist. Any entries will be ignored when composing the output.
      Parameters:
      categoryBlacklist - a collection of String values to explicitly exclude from the output, all other possible entries will be implicitly included
      Returns:
      this builder instance

    • columnWhitelist

      public CifOptions.CifOptionsBuilder columnWhitelist​(String... columnWhitelist)
      Add entries to the column whitelist. If the whitelist has any entries, the column must be explicitly contained for the column to appear in the output. Names follow the pattern category_name.column_name.
      Parameters:
      columnWhitelist - a collection of String values to explicitly include in the output, all other possible entries will be implicitly excluded
      Returns:
      this builder instance

    • columnWhitelist

      public CifOptions.CifOptionsBuilder columnWhitelist​(List<String> columnWhitelist)
      Add entries to the column whitelist. If the whitelist has any entries, the column must be explicitly contained for the column to appear in the output. Names follow the pattern category_name.column_name.
      Parameters:
      columnWhitelist - a collection of String values to explicitly include in the output, all other possible entries will be implicitly excluded
      Returns:
      this builder instance

    • columnBlacklist

      public CifOptions.CifOptionsBuilder columnBlacklist​(String... columnBlacklist)
      Add entries to the column blacklist. Any entries will be ignored when composing the output. Names follow the pattern category_name.column_name.
      Parameters:
      columnBlacklist - a collection of String values to explicitly exclude from the output, all other possible entries will be implicitly included
      Returns:
      this builder instance

    • columnBlacklist

      public CifOptions.CifOptionsBuilder columnBlacklist​(List<String> columnBlacklist)
      Add entries to the column blacklist. Any entries will be ignored when composing the output. Names follow the pattern category_name.column_name.
      Parameters:
      columnBlacklist - a collection of String values to explicitly exclude from the output, all other possible entries will be implicitly included
      Returns:
      this builder instance

    • encodingStrategyHint

      public CifOptions.CifOptionsBuilder encodingStrategyHint​(Path path)
      Read EncodingStrategyHint data from a JSON file.
      Parameters:
      path - the file to read
      Returns:
      this builder instance

    • encodingStrategyHint

      public CifOptions.CifOptionsBuilder encodingStrategyHint​(String json)
      Read EncodingStrategyHint data from a JSON string.
      Parameters:
      json - the string to read
      Returns:
      this builder instance

    • encodingStrategyHint

      public CifOptions.CifOptionsBuilder encodingStrategyHint​(String categoryName, String columnName, String encoding, int precision)
      Manually specify encoding strategy and precision for a column.
      Parameters:
      categoryName - the category name
      columnName - the column name
      encoding - the encoding to employ: "pack" | "rle" | "delta" | "delta-rle"
      precision - the number of decimal places to keep during FixedPointEncoding
      Returns:
      this builder instance

    • encodingStrategyHint

      public CifOptions.CifOptionsBuilder encodingStrategyHint​(EncodingStrategyHint... encodingStrategyHints)
      Manually specify encoding strategy and precision for a column.
      Parameters:
      encodingStrategyHints - the hints to process
      Returns:
      this builder instance

    • encodingStrategyHint

      public CifOptions.CifOptionsBuilder encodingStrategyHint​(List<EncodingStrategyHint> encodingStrategyHints)
      Manually specify encoding strategy and precision for a column.
      Parameters:
      encodingStrategyHints - the hints to process
      Returns:
      this builder instance

    • fileFormatHint

      public CifOptions.CifOptionsBuilder fileFormatHint​(CifOptions.CifOptionsBuilder.FileFormat fileFormat)
      The library can automatically detect compression and file format. This involves some guessing and can be omitted by specifying the format explicitly. This may increase performance and will improve safety when malformed or unexpected files are handled.
      Parameters:
      fileFormat - an instance of the supported file formats
      Returns:
      this builder instance

    • build

      public CifOptions build()
      Exit this builder and retrieve the actual, immutable CifOptions instance.
      Returns:
      a CifOptions instance