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org.jaga.exampleApplications.proteinLocation
Class Locator

java.lang.Object
  extended by org.jaga.exampleApplications.proteinLocation.Locator

public class Locator
extends java.lang.Object

TODO: Complete these comments.

Project: JAGA - Java API for Genetic Algorithms.

Company: University College London and JAGA.Org (http://www.jaga.org).

Copyright: (c) 2004 by G. Paperin.
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, ONLY if you include a note of the original author(s) in any redistributed/modified copy.
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 or see http://www.gnu.org/licenses/gpl.html

Version:
JAGA public release 1.0 beta
Author:
Greg Paperin (greg@jaga.org)

Field Summary
private static int A
           
private static int B
           
private static int C
           
private  ProteinLocationClassifier[] classifiers
           
private static int D
           
private static int minOverlap
           
private  int[] totalClassifications
           
private static java.lang.String[] typeNames
           
 
Constructor Summary
Locator()
           
 
Method Summary
private  boolean align(Protein protein, ProteinLocationClassifier classif)
           
private  int analyseResults(Protein prot, boolean[] match)
           
private  int classifyProtein(Protein prot)
           
 void exec(java.lang.String fastaFile)
           
static void main(java.lang.String[] unusedArgs)
           
private  double sensitivity(int i)
           
 void setClassifiers(ProteinLocationClassifier cytosol, ProteinLocationClassifier nucleus, ProteinLocationClassifier mitochond, ProteinLocationClassifier extracell)
           
private  double specificity(int i)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

minOverlap

private static final int minOverlap
See Also:
Constant Field Values

A

private static final int A
See Also:
Constant Field Values

B

private static final int B
See Also:
Constant Field Values

C

private static final int C
See Also:
Constant Field Values

D

private static final int D
See Also:
Constant Field Values

typeNames

private static final java.lang.String[] typeNames

classifiers

private ProteinLocationClassifier[] classifiers

totalClassifications

private int[] totalClassifications
Constructor Detail

Locator

public Locator()
Method Detail

setClassifiers

public void setClassifiers(ProteinLocationClassifier cytosol,
                           ProteinLocationClassifier nucleus,
                           ProteinLocationClassifier mitochond,
                           ProteinLocationClassifier extracell)

sensitivity

private double sensitivity(int i)

specificity

private double specificity(int i)

analyseResults

private int analyseResults(Protein prot,
                           boolean[] match)

align

private boolean align(Protein protein,
                      ProteinLocationClassifier classif)

classifyProtein

private int classifyProtein(Protein prot)

exec

public void exec(java.lang.String fastaFile)

main

public static void main(java.lang.String[] unusedArgs)

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