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/*
* OutMatrix.java
*
* Copyright 2003 Sergio Anibal de Carvalho Junior
*
* This file is part of NeoBio.
*
* NeoBio 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 2 of the License, or (at your option) any later version.
*
* NeoBio 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.
*
* You should have received a copy of the GNU General Public License along with NeoBio;
* if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330,
* Boston, MA 02111-1307, USA.
*
* Proper attribution of the author as the source of the software would be appreciated.
*
* Sergio Anibal de Carvalho Junior mailto:[email protected]
* Department of Computer Science http://www.dcs.kcl.ac.uk
* King's College London, UK http://www.kcl.ac.uk
*
* Please visit http://neobio.sourceforge.net
*
* This project was supervised by Professor Maxime Crochemore.
*
*/
package net.maizegenetics.analysis.gbs.neobio;
/**
* Implements an interface to the OUT matrix of a block. This class is used by the
* {@linkplain CrochemoreLandauZivUkelson} and subclasses to enconde the OUT matrix
* from the input border and DIST matrix of an {@linkplain AlignmentBlock}.
*
* The OUT matrix defined as OUT[i,j] = I[i] + DIST[i,j] where I is the
* input border array and DIST is the DIST matrix.
*
* The output border of a block is computed from the OUT matrix by taking the maximum
* value of each column. Note that this class does not compute the OUT matrix, it
* just stores the necessary information to retrieve a value at any position of the
* matrix.
*
* It implements the Matrix interface so that the SMAWK algorithm can be used to
* compute its column maxima.
*
* For more information on how this class is used, please refer to the specification
* of the CrochemoreLandauZivUkelson and its subclasses.
*
* @author Sergio A. de Carvalho Jr.
* @see CrochemoreLandauZivUkelson
* @see CrochemoreLandauZivUkelsonGlobalAlignment
* @see CrochemoreLandauZivUkelsonLocalAlignment
* @see AlignmentBlock
* @see Smawk
*/
public class OutMatrix implements Matrix
{
/**
* The length of the longest sequence (number of characters) being aligned. It needs
* to be set only once per alignment.
*/
protected int max_length;
/**
* The maximum absolute score that the current scoring scheme can return. It needs
* to be set only once per alignment.
*/
protected int max_score;
/**
* The DIST matrix of a block.
*/
protected int[][] dist;
/**
* The input border of a block.
*/
protected int[] input_border;
/**
* The dimension of the OUT matrix.
*/
protected int dim;
/**
* The number of columns of the block.
*/
protected int lc;
/**
* Initialised this OUT matrix interface. This method needs to be executed only once
* per alignment.
*
* @param max_length the length of the longest sequence (number of characters) being
* aligned
* @param max_score the maximum absolute score that the current scoring scheme can
* return
*/
public void init (int max_length, int max_score)
{
this.max_length = max_length;
this.max_score = max_score;
}
/**
* Sets this interface's data to represent an OUT matrix for a block. This method
* is typically executed once for each block being aligned.
*
* @param dist the DIST matrix
* @param input_border the input border
* @param dim the dimension of the OUT matrix
* @param lc the number of columns of the block
*/
public void setData (int[][] dist, int[] input_border, int dim, int lc)
{
this.dist = dist;
this.input_border = input_border;
this.dim = dim;
this.lc = lc;
}
/**
* Returns the value at a given position of the matrix. In general it returns the
* value of DIST[col][row] + input_border[row]. However, special cases
* occur for its upper right and lower left triangular parts.
*
* @param row row index
* @param col column index
* @return the value at row row, column col of this OUT
* matrix
*/
public int valueAt (int row, int col)
{
// The DIST matrix is indexed by [column][row]
if (col < lc)
{
if (row < dim - (lc - col))
return dist[col][row] + input_border[row];
else
// lower left triangle entries
return - (max_length + row + 1) * max_score;
}
else if (col == lc)
{
return dist[col][row] + input_border[row];
}
else
{
if (row < (col - lc))
// upper right triangle entries
return Integer.MIN_VALUE + row;
else
return dist[col][row - (col - lc)] + input_border[row];
}
}
/**
* Returns the number of rows of this OUT matrix.
*
* @return the number of rows of this OUT matrix
*/
public int numRows ()
{
return dim;
}
/**
* Returns the number of columns of this OUT matrix.
*
* @return the number of columns of this OUT matrix
*/
public int numColumns ()
{
return dim;
}
}