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## org.biojava.bio.symbol
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.

`SoftMaskedAlphabet`s 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

Nested Class Summary
`class` | `SoftMaskedAlphabet.CaseSensitiveTokenization` This `SymbolTokenizer` works with a delegate to softmask symbol tokenization as appropriate.
`static interface` | `SoftMaskedAlphabet.MaskingDetector` Implementations will define how soft masking looks.

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
`Annotatable.AnnotationForwarder`

Field Summary

Fields inherited from interface org.biojava.bio.symbol.Alphabet
`EMPTY_ALPHABET, PARSERS, SYMBOLS`

Fields inherited from interface org.biojava.bio.Annotatable
`ANNOTATION`

Method Summary
`void` | `addSymbol(Symbol s)` `SoftMaskedAlphabet`s cannot add new `Symbol`s.
`boolean` | `contains(Symbol s)` Returns whether or not this Alphabet contains the symbol.
`List` | `getAlphabets()` Gets the components of the `Alphabet`.
`Symbol` | `getAmbiguity(Set s)` This is not supported.
`Annotation` | `getAnnotation()` The SoftMaskedAlphabet has no annotation
`protected FiniteAlphabet` | `getDelegate()` The compound alpha that holds the symbols used by this wrapper
`Symbol` | `getGapSymbol()` Get the 'gap' ambiguity symbol that is most appropriate for this alphabet.
`static SoftMaskedAlphabet` | `getInstance(FiniteAlphabet alphaToMask)` Generates a soft masked Alphabet where lowercase tokens are assumed to be soft masked.
`static SoftMaskedAlphabet` | `getInstance(FiniteAlphabet alphaToMask, SoftMaskedAlphabet.MaskingDetector maskingDetector)` 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.
`FiniteAlphabet` | `getMaskedAlphabet()` Gets the `Alphabet` upon which masking is being applied
`SoftMaskedAlphabet.MaskingDetector` | `getMaskingDetector()` Getter for the `MaskingDetector```
`String` | `getName()` The name of the Alphabet
`Symbol` | `getSymbol(List l)` Gets the compound symbol composed of the `Symbols` in the List.
`SymbolTokenization` | `getTokenization(String type)` Get a SymbolTokenization by name.
`boolean` | `isMasked(BasisSymbol s)` Determines if a `Symbol` is masked.
`Iterator` | `iterator()` Retrieve an Iterator over the AtomicSymbols in this FiniteAlphabet.
`void` | `removeSymbol(Symbol s)` `SoftMaskedAlphabet`s cannot remove `Symbol`s.
`int` | `size()` The number of symbols in the alphabet.
`void` | `validate(Symbol s)` Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet.

Methods inherited from class org.biojava.utils.Unchangeable
`addChangeListener, addChangeListener, addForwarder, getForwarders, getListeners, isUnchanging, removeChangeListener, removeChangeListener, removeForwarder`

Methods inherited from class java.lang.Object
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Methods inherited from interface org.biojava.utils.Changeable
`addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener`

Method Detail

### getInstance

    public static SoftMaskedAlphabet getInstance(FiniteAlphabet alphaToMask)
                                          throws IllegalAlphabetException

  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

    public static SoftMaskedAlphabet getInstance(FiniteAlphabet alphaToMask,
                                                 SoftMaskedAlphabet.MaskingDetector maskingDetector)
                                          throws IllegalAlphabetException

  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

    public FiniteAlphabet getMaskedAlphabet()

  Gets the `Alphabet` upon which masking is being applied

  Returns:
    A `FiniteAlphabet`

### getDelegate

    protected FiniteAlphabet getDelegate()

  The compound alpha that holds the symbols used by this wrapper

  Returns:
    a `FiniteAlphabet`

### getAnnotation

    public Annotation 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

    public Symbol getSymbol(List l)
                     throws IllegalSymbolException

  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

    public Symbol getAmbiguity(Set s)
                        throws UnsupportedOperationException

  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:
    `getSymbol(List l)`

### 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

    public SoftMaskedAlphabet.MaskingDetector getMaskingDetector()

  Getter for the `MaskingDetector`

  ``
  Returns:
    the `MaskingDetector```

### getTokenization

    public SymbolTokenization getTokenization(String type)
                                       throws BioException

  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 behaviour 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

  `SoftMaskedAlphabet`s cannot add new `Symbol`s. 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

  `SoftMaskedAlphabet`s cannot remove `Symbol`s. 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`

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