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//******************************************************************************
//
// File: Sequence.java
// Package: edu.rit.compbio.seq
// Unit: Class edu.rit.compbio.seq.Sequence
//
// This Java source file is copyright (C) 2008 by Alan Kaminsky. All rights
// reserved. For further information, contact the author, Alan Kaminsky, at
// ark@cs.rit.edu.
//
// This Java source file is part of the Parallel Java Library ("PJ"). PJ is free
// software; you can redistribute it and/or modify it under the terms of the GNU
// General Public License as published by the Free Software Foundation; either
// version 3 of the License, or (at your option) any later version.
//
// PJ is distributed in the hope that it will be useful, but WITHOUT ANY
// WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
// A PARTICULAR PURPOSE. See the GNU General Public License for more details.
//
// Linking this library statically or dynamically with other modules is making a
// combined work based on this library. Thus, the terms and conditions of the
// GNU General Public License cover the whole combination.
//
// As a special exception, the copyright holders of this library give you
// permission to link this library with independent modules to produce an
// executable, regardless of the license terms of these independent modules, and
// to copy and distribute the resulting executable under terms of your choice,
// provided that you also meet, for each linked independent module, the terms
// and conditions of the license of that module. An independent module is a
// module which is not derived from or based on this library. If you modify this
// library, you may extend this exception to your version of the library, but
// you are not obligated to do so. If you do not wish to do so, delete this
// exception statement from your version.
//
// A copy of the GNU General Public License is provided in the file gpl.txt. You
// may also obtain a copy of the GNU General Public License on the World Wide
// Web at http://www.gnu.org/licenses/gpl.html.
//
//******************************************************************************
package edu.rit.compbio.seq;
import java.util.Arrays;
/**
* Class Sequence is the abstract base class for a biological sequence.
* <P>
* In a program, a sequence is represented as a byte array (type
* <TT>byte[]</TT>). For a sequence of length <I>L</I>, the byte array contains
* <I>L</I>+1 bytes. The byte at index 0 is unused and contains a value of -1.
* The bytes at indexes 1 through <I>L</I> contain the elements of the sequence.
* These are generally represented as small integers starting at 0, not as
* characters.
*
* @author Alan Kaminsky
* @version 01-Jul-2008
*/
public abstract class Sequence
{
// Hidden data members.
String myDescription;
byte[] mySequence;
int myLength;
// Exported constructors.
/**
* Construct a new sequence.
*/
public Sequence()
{
}
// Exported operations.
/**
* Get this sequence's description.
*
* @return Description string.
*/
public String description()
{
return myDescription;
}
/**
* Get this sequence's length <I>L</I>. This is the number of elements in
* this sequence.
*
* @return Length <I>L</I>.
*/
public int length()
{
return myLength;
}
/**
* Get this sequence's elements. The return value is a byte array of length
* <I>L</I>+1. The byte at index 0 is unused and contains a value of -1. The
* bytes at indexes 1 through <I>L</I> contain the elements.
* <P>
* <I>Note:</I> Do not alter the contents of the returned byte array.
*
* @return Array of elements.
*/
public byte[] sequence()
{
return mySequence;
}
/**
* Determine if this sequence is equal to the given object. Two sequences
* are equal if they have the same elements.
*
* @param obj Object to test.
*
* @return True if <TT>obj</TT> is equal to this sequence, false otherwise.
*/
public boolean equals
(Object obj)
{
return
(obj instanceof Sequence) &&
Arrays.equals (this.mySequence, ((Sequence) obj).mySequence);
}
/**
* Returns a hash code for this sequence.
*
* @return Hash code.
*/
public int hashCode()
{
return Arrays.hashCode (mySequence);
}
/**
* Returns a character version of this sequence's element at the given
* index.
*
* @param i Index in the range 1 .. <I>L</I>.
*
* @return Character corresponding to element <TT>i</TT>.
*/
public abstract char charAt
(int i);
/**
* Returns a string version of this sequence's elements.
*
* @return String version.
*/
public String elementsToString()
{
char[] c = new char [myLength];
for (int i = 0; i < myLength; ++ i)
{
c[i] = charAt(i+1);
}
return new String (c);
}
}
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