jbil.sequence
Class Sequence

java.lang.Object
  jbil.sequence.Sequence

Direct Known Subclasses:

ByteArraySequence, SymbolArraySequence

public abstract class Sequence
extends java.lang.Object

Abstract class representing a sequence of symbols from a fixed alphabet. A sequence can be associated to a name.

Author:

Paulo G. S. da Fonseca

Constructor Summary

Sequence()

Method Summary

abstract void	append(Sequence sequence) Appends a sequence to this sequence.
abstract void	append(Symbol symbol) Appends a symbol to this sequence.
abstract Sequence	clone()
abstract void	delete(int beginIndex, int endIndex) Deletes a subsequence of this sequence.
boolean	endsWith(Sequence subSequence) Checks if this sequence ends with a given suffix.
abstract Alphabet	getAlphabet()
java.lang.String	getName()
int	indexAt(int index) Gets the position in the base alphabet of the symbol at a given position in the sequence.
abstract void	insert(int index, Sequence sequence) Inserts a sequence at a given position in this sequence.
abstract void	insert(int index, Symbol symbol) Inserts a new symbol at a given position in this sequence.
abstract int	length()
boolean	occursAt(Sequence subSequence, int beginIndex) Checks if a sequence occurs at a specified position of this sequence.
abstract void	prepend(Sequence sequence) Prepends a sequence to this sequence.
abstract void	prepend(Symbol symbol) Prepends a symbol to this sequence.
void	setName(java.lang.String name) Sets the name of the sequence.
abstract void	setSymbolAt(int index, Symbol symbol) Sets the symbol at a given position in this sequence.
boolean	startsWith(Sequence subSequence) Checks if this sequence begins with a given prefix.
abstract Sequence	subSequence(int beginIndex) Gets a new sequence that is a suffix of this sequence.
abstract Sequence	subSequence(int beginIndex, int endIndex) Gets a new sequence that is a subsequence of this sequence.
abstract Symbol	symbolAt(int index) Gets the symbol at a given position in the sequence.
java.lang.String	toString()
abstract java.lang.String	toString(int beginIndex, int endIndex) Returns the srting representation of a subsequence of this sequence.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Sequence

public Sequence()

Method Detail

getName

public java.lang.String getName()

Returns:

The name of the sequence.

setName

public void setName(java.lang.String name)

Sets the name of the sequence.

getAlphabet

public abstract Alphabet getAlphabet()

Returns:

The base alphabet.

clone

public abstract Sequence clone()

Overrides:

clone in class java.lang.Object

Returns:

A clone of this sequence.

length

public abstract int length()

Returns:

The length of this sequence.

symbolAt

public abstract Symbol symbolAt(int index)

Gets the symbol at a given position in the sequence.

Parameters:

index - A position in the sequence.

Returns:

The symbol at the given position.

indexAt

public int indexAt(int index)

Gets the position in the base alphabet of the symbol at a given position in the sequence.

Parameters:

index - A position in the sequence.

Returns:

The position in the base alphabet of the symbol at the given position.

setSymbolAt

public abstract void setSymbolAt(int index,
                                 Symbol symbol)

Sets the symbol at a given position in this sequence.

Parameters:

index - The position to be set.

symbol - The new symbol.

subSequence

public abstract Sequence subSequence(int beginIndex)

Gets a new sequence that is a suffix of this sequence.

Parameters:

beginIndex - The start position of the suffix.

Returns:

The suffix starting at the given position.

subSequence

public abstract Sequence subSequence(int beginIndex,
                                     int endIndex)

Gets a new sequence that is a subsequence of this sequence.

Parameters:

beginIndex - The start position of the subsequence.

endIndex - The end position of the subsequence.

Returns:

The subsequence starting at beginIndex and ending at endIndex-1.

append

public abstract void append(Symbol symbol)

Appends a symbol to this sequence.

Parameters:

symbol - The symbol to be appended.

append

public abstract void append(Sequence sequence)

Appends a sequence to this sequence.

Parameters:

sequence - The sequence to be appended.

prepend

public abstract void prepend(Symbol symbol)

Prepends a symbol to this sequence.

Parameters:

symbol - The symbol to be prepended.

prepend

public abstract void prepend(Sequence sequence)

Prepends a sequence to this sequence.

Parameters:

sequence - The sequence to be prepended.

insert

public abstract void insert(int index,
                            Symbol symbol)

Inserts a new symbol at a given position in this sequence.

Parameters:

index - The position at which the symbol is inserted.

symbol - The symbol to be inserted.

insert

public abstract void insert(int index,
                            Sequence sequence)

Inserts a sequence at a given position in this sequence.

Parameters:

index - The position at which the sequence is inserted.

sequence - The sequence to be inserted.

delete

public abstract void delete(int beginIndex,
                            int endIndex)

Deletes a subsequence of this sequence.

Parameters:

beginIndex - The start position of the subsequence to be deleted.

endIndex - The end position (not inclusive) of the subsequence to be deleted.

occursAt

public boolean occursAt(Sequence subSequence,
                        int beginIndex)

Checks if a sequence occurs at a specified position of this sequence.

Parameters:

subSequence - The subsequence.

beginIndex - The start position of the match.

Returns:

True if the subsequence occurs at the specified position, or false, otherwise.

startsWith

public boolean startsWith(Sequence subSequence)

Checks if this sequence begins with a given prefix.

Parameters:

subSequence - The prefix.

Returns:

True if this sequence begins with the given prefix, or false, otherwise.

endsWith

public boolean endsWith(Sequence subSequence)

Checks if this sequence ends with a given suffix.

Parameters:

subSequence - The suffix.

Returns:

True if this sequence ends with the given suffix, or false, otherwise.

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

toString

public abstract java.lang.String toString(int beginIndex,
                                          int endIndex)

Returns the srting representation of a subsequence of this sequence.

Parameters:

beginIndex - The start position of the subsequence.

endIndex - The end position of the subsequence.

Returns:

The string representation of the subsequence starting at beginIndex and ending at endIndex-1.