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/* BaseAlgorithm.java
*
* created: Wed Dec 16 1998
*
* This file is part of Artemis
*
* Copyright (C) 1998,1999,2000 Genome Research Limited
*
* This program 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.
*
* This program 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 this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
* $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/plot/BaseAlgorithm.java,v 1.1 2004-06-09 09:51:16 tjc Exp $
*/
package uk.ac.sanger.artemis.plot;
import uk.ac.sanger.artemis.sequence.*;
/**
* The BaseAlgorithm class is the base class for algorithms that work
* directly on bases. A BaseAlgorithm has a name and is specific to one
* Strand of DNA, meaning the algorithm can't change strand part way along.
*
* @author Kim Rutherford
* @version $Id: BaseAlgorithm.java,v 1.1 2004-06-09 09:51:16 tjc Exp $
**/
public abstract class BaseAlgorithm extends Algorithm {
/**
* Create a new BaseAlgorithm object.
* @param strand The strand to do the calculation on.
* @param algorithm_name A String used to identify this algorithm to the
* user.
* @param algorithm_short_name A String used to identify this algorithm
* internally. See the Algorithm constructor for more details.
**/
public BaseAlgorithm (final Strand strand, final String algorithm_name,
final String algorithm_short_name) {
super (algorithm_name, algorithm_short_name);
this.bases = strand.getBases ();
if (strand.isForwardStrand ()) {
forward_flag = true;
} else {
forward_flag = false;
}
}
/**
* Return the Bases object of the Strand that was passed to the
* constructor.
**/
public Bases getBases () {
return bases;
}
/**
* Returns the strand we will do the calculation on.
**/
public Strand getStrand () {
if (forward_flag ^ rev_comp_display) {
return getBases ().getForwardStrand ();
} else {
return getBases ().getReverseStrand ();
}
}
/**
* If rev_comp_display is true all calculations will be performs on the
* opposite Strand to the strand that was passed to the constructor.
**/
public void setRevCompDisplay (final boolean rev_comp_display) {
this.rev_comp_display = rev_comp_display;
}
/**
* Returns true if the FeatureDisplay is reverse complemented. All
* calculations should be performed on the opposite Strand to the strand
* that was passed to the constructor.
**/
public boolean isRevCompDisplay () {
return rev_comp_display;
}
/**
* Return the value of the function between a pair of bases.
* @param start The start base (included in the range).
* @param end The end base (included in the range).
* @param values The results are returned in this array, hence it should be
* allocated at the size given by getValueCount ().
**/
public abstract void getValues (int start, int end, final float [] values);
/**
* Return the number of values a call to getValues () will return.
**/
public abstract int getValueCount ();
/**
* The Bases we will do the calculation on.
**/
private Bases bases;
/**
* If rev_comp_display is true all calculations will be performed on the
* opposite Strand to the strand that was passed to the constructor.
**/
private boolean rev_comp_display = false;
/**
* true if and only if the calculations should be done on the forward
* Strand.
**/
private boolean forward_flag;
}