Program 5d

COP-2250 - Java Programming  
Professor:  Michael Robinson 
e-mail   :  mrobi002@cs.fiu.edu 
Web Page :  www.cs.fiu.edu/~mrobi002/teaching 

Turn in the signed source code on paper, and email me the source code.

Make sure the program is properly documented and aligned uniformally, looking professionally,
I will take points off if it not.

Include the following header in every program:
 
/*********************************************************************
Author     : Your Name 
Course     : COP 2250 Java Programming
Professor  : Michael Robinson 
Program #  : Program Purpose/Description 
             {A brief description of the program } 
Due Date   : MM/DD/YYYY 
Certification: 
I hereby certify that this work is my own and none of it is the work of any other person. 
 ..........{ your signature }..........
*********************************************************************/

Purpose of this program:
- Implement:
  - Open, read, process, and write text files
  - Store data in an array or a String variable, your choice
  - Use many methods from the String class
  - Use for and while loops
  - Use DecimalFormat class
  - Do math computations  
  - Use if and if else statements
  - Compare characters  
  - Compare Strings
  - Use swap

How:

**** NOTE ****
Each task must be done inside its own method.
Use main ONLY to create variables and call the methods.


From main() call methods/functions passing parameters when necessary where you will implement the following:


Worth 5 points
- Download the file called 1200.dna from:
  http://users.cis.fiu.edu/~mrobi002/downloads/samples/1200.dna
  - open this file.
  - load it into a one dimension array or a String, your choice
    this file contains nueclotides/bases/letters in it such as a, c, g, t, and others.
  - Find out the total amount of neuclotides UPPER and LOWER case a, how many c, how many g, how many t and how many all others are in this file.
    Make sure to test for upper and lower cases of each a,c,g,t, and others base.
  - Print the first and the last neuclodide in the file, and using the ceil() method print the one exactly in the middle of the file
  - Print all totals in an aligned column USING the numeric format command, e.g. 1,234,567


Worth 2 points
- Download the file called pa01Probes.dna from:
  http://users.cis.fiu.edu/~mrobi002/downloads/samples/pa01Probes.dna
  - open this file.
  - this file contains sequences of length 5 each
    find out how many sequences there are
    find out which sequences have duplicates, if any
    find out if these sequences are sorted, HINT : swap


Worth 2 points
- Using the pa01Probes.dna file
  open this file and load it into a single dimension array
  write this file to a disk file called reverse.txt 
    exactly BACKWARDS e.g. last record first,....,first record last


Worth 1 points
- Create a file
- Using a while loop, write all integer numbers from 0 to 10 inclusive
- close the file
- Reopen file
- Read all data in the file adding all numbers in it.
- Print the total amount   
- close the file