org.expasy.jpl.commons.collection.symbol.seq
Class SymbolSequenceImpl<E>

java.lang.Object
  org.expasy.jpl.commons.collection.symbol.seq.SymbolSequenceImpl<E>

Type Parameters:

E - the element type.

All Implemented Interfaces:

Serializable, Sequence<E>, SymbolSequence<E>

public final class SymbolSequenceImpl<E>
extends Object
implements SymbolSequence<E>, Serializable

A sequence of symbol letters defined by an alphabet.

Version:

1.0

Author:

nikitin

See Also:

Serialized Form

Nested Class Summary

static class

SymbolSequenceImpl.Builder<E> This builder builds an instance of JPLAASequence given a numerous number of possible parameters.

Constructor Summary

	SymbolSequenceImpl() for serialization only
protected	SymbolSequenceImpl(SymbolSequenceImpl.Builder<E> builder) The only constructor that build an instance of JPLAASequence.

Method Summary

char	charAt(int i)
SymbolSequenceImpl<E>	clone()
boolean	equals(Object obj) Return true if 2 aa sequences are identical
SymbolSequenceImpl.Builder<E>	getBuilder()
static <E> Pattern	getSequencePattern(Symbol.SymbolType<E> type)
Symbol<E>	getSymbolAt(int i) Returns the symbol character at position i.
Symbol.SymbolType<E>	getSymbolType()
int	hashCode() Same length JPLAASequence have the same hash code.
boolean	isAmbiguous()
int	length()
SymbolSequenceImpl<E>	subSequence(int start, int end) Warning: [start, end[
String	toString()
String	toSymbolString()
E	valueAt(int i)

Methods inherited from class java.lang.Object

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

Constructor Detail

SymbolSequenceImpl

public SymbolSequenceImpl()

for serialization only

SymbolSequenceImpl

protected SymbolSequenceImpl(SymbolSequenceImpl.Builder<E> builder)
                      throws ParseException

The only constructor that build an instance of JPLAASequence.

Parameters:

builder - the builder needed to build the instance.

Throws:

ParseException

ParseException - if the sequence string is not well formatted.

JPLAAByteUndefinedException

Method Detail

getSequencePattern

public static <E> Pattern getSequencePattern(Symbol.SymbolType<E> type)

getBuilder

public SymbolSequenceImpl.Builder<E> getBuilder()

clone

public SymbolSequenceImpl<E> clone()

Overrides:

clone in class Object

equals

public boolean equals(Object obj)

Return true if 2 aa sequences are identical

Overrides:

equals in class Object

hashCode

public int hashCode()

Same length JPLAASequence have the same hash code.

Overrides:

hashCode in class Object

length

public final int length()

Specified by:

length in interface Sequence<E>

Returns:

the length of the amino-acid sequence.

isAmbiguous

public boolean isAmbiguous()

Specified by:

isAmbiguous in interface SymbolSequence<E>

Returns:

true if the sequence contains ambiguous symbols. An ambiguous symbol maps more than one T-data object.

getSymbolType

public final Symbol.SymbolType<E> getSymbolType()

Specified by:

getSymbolType in interface SymbolSequence<E>

Returns:

the type of symbol

getSymbolAt

public final Symbol<E> getSymbolAt(int i)

Returns the symbol character at position i.

Specified by:

getSymbolAt in interface SymbolSequence<E>

Returns:

the symbol character at position i.

Throws:

SequenceOutOfBoundsException - if i is out of byte array bounds.

valueAt

public final E valueAt(int i)

Specified by:

valueAt in interface Sequence<E>

Returns:

the T-typed value at the specified sequence index.

charAt

public final char charAt(int i)

Specified by:

charAt in interface SymbolSequence<E>

Returns:

the symbol character at index i

subSequence

public SymbolSequenceImpl<E> subSequence(int start,
                                         int end)

Warning: [start, end[

Specified by:

subSequence in interface Sequence<E>

Returns:

a new Sequence that is a subsequence of this sequence.

toSymbolString

public final String toSymbolString()

Specified by:

toSymbolString in interface SymbolSequence<E>

Returns:

the symbol string representation

toString

public String toString()

Overrides:

toString in class Object

Returns:

the amino acid string without the N and C terminus informations.