CURRENT QUESTIONS FOR JAY**************************************************************

1) Why are their two different packages under main
2) you put a dependencies in several classes.  Shouldn't this be in the pom file. Should I move them
3) Should I switch output to similar format as DNA input provider
4) when I run the program it says Failed to load Main-Class manifest attribute from
bwt-1.0-SNAPSHOT.jar.  I added manifest to main class - please check
5) BWT class why do we nee inputSeq line 47 and seq this line?
6) we never call BWTApplicationUsageExample?
7) why does the TestDNAInputProvision class not have an expected output to test.
8) DNAInputProviderSIMPLE seems like it should be a unittes not an input type
9) confused about intention of WEB dna input provided vs. refseq.
10) Why do you not use @override and extends in DNAInputProviderWEB


THING FOR MRS TO DO**************************************************************
Write unit tests for reading from website. Post on stack overflow
Look up reflection
look up override
look up abstract class
lookup class extends other class
read about java collections lists arraylists, vectors, hashmaps,


BWT PROGRAM**************************************************************
Command to run program.  >java -jar myjar.jar org.biotoolkit.algorithms.bwtx.DNAInputProviderINTERACTIVE 
Other DNAInputProvider classes could also be used to launch:
DNAInputProviderWEB.java
DNAInputProviderSIMPLE.java
DNAInputProviderINTERACTIVE.java


BWT PACKAGES, CLASSES AND FUNCTIONS**************************************************************

org.biotoolkit.algorithms package Main package containing program.
BWTApplication.java               - main class
BWTApplicaitonUsageExample.java   - example of how to call the application

org.biotoolkit.algorithmsbwtx package
RefSeqInputProvider.java
package-info.java
DNAInputProviderWEB.java
DNAInputProviderSIMPLE.java			-overides the input for the DNAInputProvider class providing a dna sequence.
DNAInputProviderINTERACTIVE.java
DNAInputProvider.java				- class that validates the the input is a correct DNA string.  Called by other classes
BWTCompressor.java   				- package compresses a bwt into a compressed string and returns to bwt.java

src/java/test package           	- Contains Junit tests for each class
TestDNAInputProvisioning.java		- Contains Junit tests for DNAInput types
TestBWTCompression.java     		- Contains Junit tests for BWT compression 
TestBWT.java						- Contains Junit tests for BWT 
AppTest.java						- Contains Junit tests that an app will run

PLANS**************************************************************
Hook up to database
Read from a website
Generate a simple UI



MAVEN**************************************************************
This is a mavenized version of the BWT project.  To run unit tests:

   mvn test

To package a jar: 

   mvn package

To add dependencies: 

   Edit the pom file. 

To set up eclipse:

1) Run "mvn test" - this ensures that the code "works"
2) Run "mvn eclipse:eclipse" - this creates eclipse project 
3) Import the project into eclipse.

GIT**************************************************************



Local path**************************************************************
    /Users/martinschiller/Desktop/SchillerDrive/Computer/Gitprojects/BWT