Package org.rcsb.cif.model

Interface CifFile

All Known Implementing Classes:
BinaryFile, CifCoreFile, DelegatingCifFile, MmCifFile, TextFile
public interface CifFile

The instance of a parsed CifFile. No difference between binary and text files is exposed. This class does not represent a parsed data model. Rather all source data is neatly wrapped into a type-safe hierarchy of Block, Category, and Column entities. Parsing (for text data) or decoding (for binary data) is only done, when the content of particular categories or columns is requested. Otherwise the goal is to keep interaction with the source data to a bare minimum: just enough to provide this view of the data model.

CifFiles have the following hierarchy:

  • 1 CifFile contains 1...n Blocks
  • 1 Block contains 1...n Categories
  • 1 Category contains 1...n Columns
  • 1 Column contains 1...n rows of raw values (int, double, or String)

Missing categories and columns will still be accessible, though the report being undefined and have a row count of 0. Most values in the data structure will be available, but some are missing or unknown. This property of individual values is reported by the ValueKind property of a Column.

  • Method Details

    • getBlocks

      List<? extends Block> getBlocks()
      Access to all blocks of this file.
      Returns:
      a list of present blocks

    • blocks

      default Stream<? extends Block> blocks()
      Convenience method to access all blocks as Stream.
      Returns:
      a Stream of all blocks

    • as

      default <F extends CifFile,​ B extends CifFileBuilder> F as​(SchemaProvider<F,​B> schemaProvider) throws SchemaMismatchException
      Convenience method to access this file wrapped by a given schema.
      Type Parameters:
      F - the file type
      B - the builder type
      Parameters:
      schemaProvider - the schema provider to enforce on this file
      Returns:
      this file, honoring a given schema
      Throws:
      SchemaMismatchException - if schema is mismatching

    • asButWithoutValidation

      default <F extends CifFile,​ B extends CifFileBuilder> F asButWithoutValidation​(SchemaProvider<F,​B> schemaProvider) throws SchemaMismatchException
      Convenience method to access this file wrapped by a given schema. Don't perform any checks whether the SchemaProvider is appropriate for this file.
      Type Parameters:
      F - the file type
      B - the builder type
      Parameters:
      schemaProvider - the schema provider to enforce on this file
      Returns:
      this file, honoring a given schema
      Throws:
      SchemaMismatchException