Class SoftMaskedAlphabet

java.lang.Object
org.biojava.utils.Unchangeable
org.biojava.bio.symbol.SoftMaskedAlphabet
All Implemented Interfaces:
Annotatable, Alphabet, FiniteAlphabet, Changeable

public final class SoftMaskedAlphabet extends Unchangeable implements FiniteAlphabet
Soft masking is usually displayed by making the masked regions somehow different from the non masked regions. Typically the masked regions are lower case but other schemes could be invented. For example a softmasked DNA sequence may look like this:

 >DNA_sequence
 ATGGACGCTAGCATggtggtggtggtggtggtggtGCATAGCGAGCAAGTGGAGCGT

 
Where the lowercase regions are masked by low complexity.

SoftMaskedAlphabets come with SymbolTokenizers that understand how to read and write the softmasking. The interpretation of what constitutes a masked region is governed by an implementation of a MaskingDetector. The DEFAULT field of the MaskingDetector interface defines lower case tokens as masked.

Copyright (c) 2004 Novartis Institute for Tropical Diseases

Version:
1.0
Author:
Mark Schreiber
  • Method Details

    • getInstance

      Generates a soft masked Alphabet where lowercase tokens are assumed to be soft masked.
      Parameters:
      alphaToMask - for example the DNA alphabet.
      Returns:
      a reference to a singleton SoftMaskedAlphabet.
      Throws:
      IllegalAlphabetException - if it cannot be constructed
    • getInstance

      Creates a compound alphabet that is a hybrid of the alphabet that is to be soft masked and a binary alphabet that indicates if any Symbol is soft masked or not.
      Parameters:
      alphaToMask - for example the DNA alphabet.
      maskingDetector - to define masking behaivour
      Returns:
      a reference to a singleton SoftMaskedAlphabet.
      Throws:
      IllegalAlphabetException - if it cannot be constructed
    • getMaskedAlphabet

      Gets the Alphabet upon which masking is being applied
      Returns:
      A FiniteAlphabet
    • getDelegate

      The compound alpha that holds the symbols used by this wrapper
      Returns:
      a FiniteAlphabet
    • getAnnotation

      The SoftMaskedAlphabet has no annotation
      Specified by:
      getAnnotation in interface Annotatable
      Returns:
      Annotation.EMPTY_ANNOTATION
    • getName

      public String getName()
      The name of the Alphabet
      Specified by:
      getName in interface Alphabet
      Returns:
      a String in the form of "Softmasked {"+alphaToMask.getName()+"}"
    • getAlphabets

      public List getAlphabets()
      Gets the components of the Alphabet.
      Specified by:
      getAlphabets in interface Alphabet
      Returns:
      a List with two members, the first is the wrapped Alphabet the second is the binary SubIntegerAlphabet.
    • getSymbol

      Gets the compound symbol composed of the Symbols in the List. The Symbols in the List must be from alpha (defined in the constructor) and SUBINTEGER[0..1]
      Specified by:
      getSymbol in interface Alphabet
      Parameters:
      l - a List of Symbols
      Returns:
      A Symbol from this alphabet.
      Throws:
      IllegalSymbolException - if l is not as expected (see above)
    • getAmbiguity

      This is not supported. Ambiguity should be handled at the level of the wrapped Alphabet. Use getSymbol(List l) instead and provide it with an ambigutiy and a masking symbol.
      Specified by:
      getAmbiguity in interface Alphabet
      Parameters:
      s - a Set of Symbols
      Returns:
      a Symbol (possibly fly-weighted) for the Set of symbols in syms
      Throws:
      UnsupportedOperationException
      See Also:
    • getGapSymbol

      public Symbol getGapSymbol()
      Description copied from interface: Alphabet

      Get the 'gap' ambiguity symbol that is most appropriate for this alphabet.

      In general, this will be a BasisSymbol that represents a list of AlphabetManager.getGapSymbol() the same length as the getAlphabets list.

      Specified by:
      getGapSymbol in interface Alphabet
      Returns:
      the appropriate gap Symbol instance
    • contains

      public boolean contains(Symbol s)
      Description copied from interface: Alphabet

      Returns whether or not this Alphabet contains the symbol.

      An alphabet contains an ambiguity symbol iff the ambiguity symbol's getMatches() returns an alphabet that is a proper sub-set of this alphabet. That means that every one of the symbols that could match the ambiguity symbol is also a member of this alphabet.

      Specified by:
      contains in interface Alphabet
      Parameters:
      s - the Symbol to check
      Returns:
      boolean true if the Alphabet contains the symbol and false otherwise
    • validate

      public void validate(Symbol s) throws IllegalSymbolException
      Description copied from interface: Alphabet

      Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet.

      This function is used all over the code to validate symbols as they enter a method. Also, the code is littered with catches for IllegalSymbolException. There is a preferred style of handling this, which should be covererd in the package documentation.

      Specified by:
      validate in interface Alphabet
      Parameters:
      s - the Symbol to validate
      Throws:
      IllegalSymbolException - if r is not contained in this alphabet
    • getMaskingDetector

      Getter for the MaskingDetector
      Returns:
      the MaskingDetector
    • getTokenization

      Description copied from interface: Alphabet

      Get a SymbolTokenization by name.

      The parser returned is guaranteed to return Symbols and SymbolLists that conform to this alphabet.

      Every alphabet should have a SymbolTokenzation under the name 'token' that uses the symbol token characters to translate a string into a SymbolList. Likewise, there should be a SymbolTokenization under the name 'name' that uses symbol names to identify symbols. Any other names may also be defined, but the behavior of the returned SymbolTokenization is not defined here.

      A SymbolTokenization under the name 'default' should be defined for all sequences, that determines the behavior when printing out a sequence. Standard behavior is to define the 'token' SymbolTokenization as default if it exists, else to define the 'name' SymbolTokenization as the default, but others are possible.

      Specified by:
      getTokenization in interface Alphabet
      Parameters:
      type - the name of the parser
      Returns:
      a parser for that name
      Throws:
      BioException - if for any reason the tokenization could not be built
    • size

      public int size()
      Description copied from interface: FiniteAlphabet
      The number of symbols in the alphabet.
      Specified by:
      size in interface FiniteAlphabet
      Returns:
      the size of the alphabet
    • iterator

      public Iterator iterator()
      Description copied from interface: FiniteAlphabet
      Retrieve an Iterator over the AtomicSymbols in this FiniteAlphabet.

      Each AtomicSymbol as for which this.contains(as) is true will be returned exactly once by this iterator in no specified order.

      Specified by:
      iterator in interface FiniteAlphabet
      Returns:
      an Iterator over the contained AtomicSymbol objects
    • addSymbol

      public void addSymbol(Symbol s) throws ChangeVetoException
      SoftMaskedAlphabets cannot add new Symbols. A ChangeVetoException will be thrown.
      Specified by:
      addSymbol in interface FiniteAlphabet
      Parameters:
      s - the Symbol to add.
      Throws:
      ChangeVetoException - when called.
    • removeSymbol

      public void removeSymbol(Symbol s) throws ChangeVetoException
      SoftMaskedAlphabets cannot remove Symbols. A ChangeVetoException will be thrown.
      Specified by:
      removeSymbol in interface FiniteAlphabet
      Parameters:
      s - the Symbol to remove.
      Throws:
      ChangeVetoException - when called.
    • isMasked

      public boolean isMasked(BasisSymbol s) throws IllegalSymbolException
      Determines if a Symbol is masked.
      Parameters:
      s - the Symbol to test.
      Returns:
      true if s is masked.
      Throws:
      IllegalSymbolException