Package org.biojava.bio.symbol

Class IntegerAlphabet.SubIntegerAlphabet

java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.symbol.AbstractAlphabet
org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
All Implemented Interfaces:
Serializable, Annotatable, Alphabet, FiniteAlphabet, Changeable
Enclosing class:
IntegerAlphabet
public static class IntegerAlphabet.SubIntegerAlphabet extends AbstractAlphabet
A class to represent a finite contiguous subset of the infinite IntegerAlphabet
Since:
1.3
Author:
Mark Schreiber, Matthew Pocock
See Also:

  • Method Details

    • getName

      public String getName()
      Description copied from interface: Alphabet
      Get the name of the alphabet.
      Returns:
      the name as a string.

    • containsImpl

      protected boolean containsImpl(AtomicSymbol sym)
      Specified by:
      containsImpl in class AbstractAlphabet

    • getTokenization

      public SymbolTokenization getTokenization(String name)
      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
      Overrides:
      getTokenization in class AbstractAlphabet
      Parameters:
      name - Currently only "token" is supported.
      Returns:
      an IntegerParser.

    • getSymbol

      public IntegerAlphabet.IntegerSymbol getSymbol(int val) throws IllegalSymbolException
      Throws:
      IllegalSymbolException

    • size

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

    • getAlphabets

      public List getAlphabets()
      Description copied from interface: Alphabet
      Return an ordered List of the alphabets which make up a compound alphabet. For simple alphabets, this will return a singleton list of itself. The returned list should be immutable.
      Returns:
      a List of alphabets

    • getSymbolImpl

      protected AtomicSymbol getSymbolImpl(List symL) throws IllegalSymbolException
      Specified by:
      getSymbolImpl in class AbstractAlphabet
      Throws:
      IllegalSymbolException

    • addSymbolImpl

      protected void addSymbolImpl(AtomicSymbol sym) throws ChangeVetoException
      Specified by:
      addSymbolImpl in class AbstractAlphabet
      Throws:
      ChangeVetoException

    • removeSymbol

      public void removeSymbol(Symbol sym) throws ChangeVetoException
      Description copied from interface: FiniteAlphabet
      Remove a symbol from this alphabet.

      If the symbol matches multiple AtomicSymbols, then each matching symbol it will be removed.

      Parameters:
      sym - the Symbol to removeintGot
      Throws:
      ChangeVetoException - if either the alphabet doesn't allow symbols to be added, or the change was vetoed

    • 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.

      Returns:
      an Iterator over the contained AtomicSymbol objects

    • getAnnotation

      public Annotation getAnnotation()
      Description copied from interface: Annotatable
      Should return the associated annotation object.
      Returns:
      an Annotation object, never null