edu.rit.compbio.seq

Class Sequence

java.lang.Object

edu.rit.compbio.seq.Sequence

Direct Known Subclasses:

ProteinSequence

public abstract class Sequence
extends java.lang.Object

Class Sequence is the abstract base class for a biological sequence.

In a program, a sequence is represented as a byte array (type byte[]). For a sequence of length L, the byte array contains L+1 bytes. The byte at index 0 is unused and contains a value of -1. The bytes at indexes 1 through L contain the elements of the sequence. These are generally represented as small integers starting at 0, not as characters.

Constructor Summary

Constructors

Constructor and Description
Sequence() Construct a new sequence.

Method Summary

Modifier and Type	Method and Description
abstract char	charAt(int i) Returns a character version of this sequence's element at the given index.
java.lang.String	description() Get this sequence's description.
java.lang.String	elementsToString() Returns a string version of this sequence's elements.
boolean	equals(java.lang.Object obj) Determine if this sequence is equal to the given object.
int	hashCode() Returns a hash code for this sequence.
int	length() Get this sequence's length L.
byte[]	sequence() Get this sequence's elements.

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Sequence

public Sequence()

Construct a new sequence.

Method Detail

description

public java.lang.String description()

Get this sequence's description.

Returns:

Description string.

length

public int length()

Get this sequence's length L. This is the number of elements in this sequence.

Returns:

Length L.

sequence

public byte[] sequence()

Get this sequence's elements. The return value is a byte array of length L+1. The byte at index 0 is unused and contains a value of -1. The bytes at indexes 1 through L contain the elements.

Note: Do not alter the contents of the returned byte array.

Returns:

Array of elements.

equals

public boolean equals(java.lang.Object obj)

Determine if this sequence is equal to the given object. Two sequences are equal if they have the same elements.

Overrides:

equals in class java.lang.Object

Parameters:

obj - Object to test.

Returns:

True if obj is equal to this sequence, false otherwise.

hashCode

public int hashCode()

Returns a hash code for this sequence.

Overrides:

hashCode in class java.lang.Object

Returns:

Hash code.

charAt

public abstract char charAt(int i)

Returns a character version of this sequence's element at the given index.

Parameters:

i - Index in the range 1 .. L.

Returns:

Character corresponding to element i.

elementsToString

public java.lang.String elementsToString()

Returns a string version of this sequence's elements.

Returns:

String version.