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1   /*** AlamarBlueMetabolicAssayDataAnalyzer.java - part of the MirkE (say murky) application for colormetric analysis emphesizing 
2   kinetics.
3   
4   Created by: Scott Menor on 21 July, 2004.
5   
6   Copyright (c) 2004 Arizona State University - Cancer Research Institute. All rights reserved.
7   
8   MirkE is free software; you can redistribute it and/or modify
9   it under the terms of the GNU General Public License as published by
10  the Free Software Foundation; either version 2 of the License, or
11  (at your option) any later version.
12  
13  MirkE is distributed in the hope that it will be useful,
14  but WITHOUT ANY WARRANTY; without even the implied warranty of
15  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
16  GNU General Public License for more details.
17  
18  You should have received a copy of the GNU General Public License
19  along with MirkE; if not, write to the Free Software
20  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  US
21  */
22  
23  package edu.asu.cri.MirkE.util;
24  
25  import edu.asu.cri.MirkE.util.MetabolicAssayDataAnalyzer;
26  import edu.asu.cri.MirkE.exceptions.MirkEApplicationException;
27  import edu.asu.cri.MirkE.MirkE; // TODO - refactor cyclic dependency
28  
29  /***
30  
31  */ // TODO - extend JPanel and implement DataAnalyzer (perhaps all of the common stuff really belongs in a separate decorator class)
32  public abstract class AlamarBlueMetabolicAssayDataAnalyzer extends MetabolicAssayDataAnalyzer {
33  	/*** preferred constructor
34  	 * @param mirke
35  	 * @throws MirkEApplicationException
36  	 */
37  	public AlamarBlueMetabolicAssayDataAnalyzer(MirkE mirke) 
38  	throws MirkEApplicationException {
39  		super(mirke);
40  	}
41  	
42  	/***
43  	
44  	 @param categoryName the category being measured (typically a dilution like 1:256; 1:512; etc represented by the denominator)
45  	 @param strain the strain (or species/etc) being measured
46  	 
47  	 @return fractionConverted percentConverted = 100% * fractionConverted - amount of indicator converted by metabolism (relative to the growth control, if present; absolute, otherwise)
48  	 
49  	 Developers - this method should be overridden in subclasses (TODO - really need a better design and implementation for this)
50  	 
51  	 made this abstract so that subclasses can provide the implementation -- Abuayyub
52  	 */
53  	abstract double computeFractionConverted(String categoryName,
54  									String strain
55  									) ;
56  }