scores.class_scores README
Copyright (C) 2002, Columbia Genome Center
Author:       Shahmil Merchant, Paul Pavlidis, Edward Chen
Version:      0.5
Release date: January 20, 2003

The scores.class_scores is a package which enables one to study
different gene functional classes and their importance on the basis of
their pvals.These pvals are calculated using 2 algorithms using
experiment scores and correlation scores.

See web/index.html for instructions on using the software.

Contacting us
-----------
  Updates, announcements, and other information can be obtained from
  Paul Pavlidis at http://microarray.cpmc.columbia.edu/pavlidis/.

Archive Contents:
-----------
If you have downloaded the source distribution, your archive will contain
the following files. The end-user distributon does not contain all of these files:

  src/	         - source files.

  bin/               - class files.

  src/Makefile	         - makefile for Class_Scores.
  
  data/                  - data files for pvals ,genes ,classes etc.
  
  README                 - This File.	

src/ contains the following files:
 
affy_go_Parse.java       - This file parses the Affymetrix chips and their 
                           corresponding GOiD's.

class_correls.java       - Generates raw average class correlations from 
                           a matrix file and then converted to pvalues.

class_pvals.java         - Generates raw class scores from pvals and then
                           converted to pvalues.

ConstantStuff.java       - Define constant variables for Gaussian functions
                           (deprecated).

corr_class_scores.java   - Generates background distribution of class 
                           correlation scores.

exp_class_scores.java    - Generates background distribution from randomly 
                           selected individual gene scores.
 
histogram.java           - Stores histogram for each class.

Matrix.java              - Matrix handling methods for handling data.

Pval_parse.java          - Parse the Pvalue file to store respective Pvalues.

Stats.java               - Various Mathematical functions/tools.

testcomparator.java      - Overides Java compare method used in Array.sort().

Ug_Parse.java            - Parses UnigeneID file to get chips with repeats.

goName_parse.java        - Parses GoID's file with biological names.

Class_Frame.java         - Constructs the front-end GUI and event handling.

Final_Project.java       - Program that instantiates the GUI.


Building the sources:
-----------

  If you have downloaded the source distribution, you may want to build your
  own version of Class_Scores from modified sources. The makefile provides 
  build options using unix make.The make options are:

  make  	         - Rebuilds the package,
			
  make clean	         - Erases all compiled classes and files ending in ~.

  make docs	         - Builds javadocs for the Class_Scores classes.

  make run               - Runs executable.

Revision History:
-----------
none
  
How to report bugs:
-----------
Contact Paul Pavlidis(pp175@columbia.edu)

