com.milaboratory.core.sequence

Class Alphabet<S extends Sequence<S>>

java.lang.Object

com.milaboratory.core.sequence.Alphabet<S>

Type Parameters:

S - corresponding type of sequence

All Implemented Interfaces:

Serializable

Direct Known Subclasses:

AminoAcidAlphabet, NucleotideAlphabet

public abstract class Alphabet<S extends Sequence<S>>
extends Object
implements Serializable

Interface for sequence letters alphabet (amino acid, nucleotide, etc.). Alphabet is responsible for conversion between char representation of letters (e.g. 'A', 'T', 'G', 'C' in case of NucleotideAlphabet) and their internal byte representation.

Alphabet also responsible for storing information about symbols wildcards.

All alphabets letters grouped in two sets: pure letters and wildcards. Pure letters has codes less than basicSize(), wildcards has codes greater or equals to basicSize().

Implementation note: all alphabets should be singletons.

Author:

Dmitriy Bolotin (bolotin.dmitriy@gmail.com), Stanislav Poslavsky (stvlpos@mail.ru), Mikhail Shugay (mikhail.shugay@gmail.com)

See Also:

Sequence, SequenceBuilder, NucleotideAlphabet, NucleotideSequence, Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static class	Alphabet.AlphabetSerialization

Method Summary

Methods

Modifier and Type	Method and Description
int	basicSize() Gets number of letters in this alphabet without wildcard letters
char	codeToSymbol(byte code) Gets a char symbol for an alphabet code of the letter
Wildcard	codeToWildcard(byte code) Returns wildcard defined by specified code (letter).
abstract SequenceBuilder<S>	createBuilder() Returns a sequence builder for corresponding sequence type.
boolean	equals(Object obj) Checks that in is the same object (this points to the same address as obj) All Alphabet implementations must be singletons.
List<Wildcard>	getAllWildcards() Returns a collection of all wildcards defined for this.
String	getAlphabetName() Returns the human readable name of this alphabet.
S	getEmptySequence() Returns empty sequence singleton
byte	getId() Returns byte id of this alphabet
Wildcard	getWildcardForAnyLetter() Returns wildcard for any letter (e.g.
int	hashCode() Returns "address in memory" (hash code as specified by Object.hashCode().
boolean	isWildcard(byte code) Returns true if this code represents wildcard symbol
Wildcard	maskToWildcard(long basicMask) Converts wildcard basicMask to Wildcard object.
S	parse(String string) Parses string representation of sequence.
int	size() Gets number of letters in this alphabet including wildcard letters
byte	symbolToCode(char symbol) Gets the binary code representing given symbol (case insensitive) or -1 if there is no such symbol in this alphabet
byte	symbolToCodeWithException(char symbol) Gets the binary code corresponding to given symbol (case insensitive) or throws IllegalArgumentException if there is no such symbol in this alphabet
Wildcard	symbolToWildcard(char symbol) Returns a wildcard object for specified letter.
String	toString() Convert alphabet to a readable string.
protected Object	writeReplace()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Method Detail

size

public final int size()

Gets number of letters in this alphabet including wildcard letters

Returns:

number of letters in this alphabet including wildcard letters

basicSize

public final int basicSize()

Gets number of letters in this alphabet without wildcard letters

Returns:

number of letters in this alphabet without wildcard letters

isWildcard

public final boolean isWildcard(byte code)

Returns true if this code represents wildcard symbol

Parameters:

code - code of letter

Returns:

true if this code represents wildcard symbol

codeToWildcard

public final Wildcard codeToWildcard(byte code)

Returns wildcard defined by specified code (letter).

Parameters:

code - code

Returns:

wildcard defined by specified code (letter)

symbolToWildcard

public final Wildcard symbolToWildcard(char symbol)

Returns a wildcard object for specified letter.

Parameters:

symbol - symbol

Returns:

wildcard object for specified letter

getAllWildcards

public final List<Wildcard> getAllWildcards()

Returns a collection of all wildcards defined for this.

Returns:

a collection of all wildcards defined for this.

getWildcardForAnyLetter

public final Wildcard getWildcardForAnyLetter()

Returns wildcard for any letter (e.g. N for nucleotides, X for amino acids).

Returns:

wildcard for any letter (e.g. N for nucleotides, X for amino acids)

maskToWildcard

public Wildcard maskToWildcard(long basicMask)

Converts wildcard basicMask to Wildcard object.

Parameters:

basicMask - bit represenatation of wildcard

Returns:

wildcard object; null if there is no such wildcard in the alphabet

codeToSymbol

public final char codeToSymbol(byte code)

Gets a char symbol for an alphabet code of the letter

Parameters:

code - alphabet code of segment

Returns:

char symbol for an alphabet code of the letter

symbolToCode

public byte symbolToCode(char symbol)

Gets the binary code representing given symbol (case insensitive) or -1 if there is no such symbol in this alphabet

Parameters:

symbol - symbol to convert

Returns:

binary code of the symbol (case insensitive) or -1 if there is no such symbol in the alphabet

symbolToCodeWithException

public final byte symbolToCodeWithException(char symbol)

Gets the binary code corresponding to given symbol (case insensitive) or throws IllegalArgumentException if there is no such symbol in this alphabet

Parameters:

symbol - symbol to convert

Returns:

binary code of the symbol (case insensitive)

Throws:

IllegalArgumentException - if there is no such symbol in the alphabet

createBuilder

public abstract SequenceBuilder<S> createBuilder()

Returns a sequence builder for corresponding sequence type.

Returns:

sequence builder for corresponding sequence type

getEmptySequence

public S getEmptySequence()

Returns empty sequence singleton

Returns:

empty sequence singleton

getAlphabetName

public final String getAlphabetName()

Returns the human readable name of this alphabet.

This name can be then used to obtain the instance of this alphabet using Alphabets.getByName(String) method if it is registered (see Alphabets.register(Alphabet)).

getId

public final byte getId()

Returns byte id of this alphabet

This name can be then used to obtain the instance of this alphabet using Alphabets.getById(byte) method if it is registered (see Alphabets.register(Alphabet)).

parse

public final S parse(String string)

Parses string representation of sequence.

Parameters:

string - string representation of sequence

Returns:

sequence

toString

public final String toString()

Convert alphabet to a readable string.

Overrides:

toString in class Object

Returns:

alphabet as a readable string

hashCode

public final int hashCode()

Returns "address in memory" (hash code as specified by Object.hashCode(). All Alphabet implementations must be singletons.

Overrides:

hashCode in class Object

equals

public final boolean equals(Object obj)

Checks that in is the same object (this points to the same address as obj) All Alphabet implementations must be singletons.

Overrides:

equals in class Object

Parameters:

obj - alphabet to check for equality with

Returns:

true if alphabets are the same

writeReplace

protected Object writeReplace()
                       throws ObjectStreamException

Throws:

ObjectStreamException