Often, DNA sequences are represented as a sequence of characters (String) and each character in the sequence corresponds with one of four nucleotides.
A = adenine, C = cytosine, G = guanine, T = thymine
In this homework, we will work with DNA sequences and develop a program that allows the user to input an arbitrary DNA sequence and then retrieve additional information about the sequence.
Your assignment is to implement a program that does the following:
1. Ask the user for the DNA sequence
2. Validate the sequence
a. Invalid sequences contain characters other than A,C,G, or T.
b. If it is an invalid sequence, request another
3. Display a menu containing the different things we can do with this sequence.
a. Count the number of times a specific character occurs in the DNA sequence
i. The user will input the character they are interested in.
ii. You will print out the number of occurrences for that character.
b. Count the number of a pair of characters in the DNA sequence
i. The user will input the characters they are interested in.
ii. You will print out the number of occurrences for that pair of characters.
c. Create the RNA sequence from the DNA sequence input by the user.
i. The RNA sequence is the DNA sequence with all of the T's replaced with U's.
d. Create the complement of the DNA sequence.
i. There are two steps necessary to compute the complement of a DNA sequence
1. Reverse the DNA sequence
2. Replace all A's with T's, all T's with A's, all G's with C's, and All C's replaced with G's.
e. Quit
You will lose points if you do not create any methods other than the main method. (Hint: The code for each menu item (other than Quit) should be its own method) Look at the Java String API for methods to help complete your tasks.
Sample Trace
> Please enter the DNA sequence:
GATCAGCCGC
> Please select from the following:
> 1. Count a character.
> 2. Count a pair of characters.
> 3. Convert the DNA to RNA.
> 4. Compute the complement.
> 5. Quit
1
> Please enter the character:
C
> The number of C's in the DNA sequence is 4
> Please select from the following:
> 1. Count a character.
> 2. Count a pair of characters.
> 3. Convert the DNA to RNA.
> 4. Compute the complement.
> 5. Quit
2
> Please enter the characters:
GC
> The number of GC's in the DNA sequence is 2
> Please select from the following:
> 1. Count a character.
> 2. Count a pair of characters.
> 3. Convert the DNA to RNA.
> 4. Compute the complement.
> 5. Quit
3
> The RNA sequence is GAUCAGCCGC
> Please select from the following:
> 1. Count a character.
> 2. Count a pair of characters.
> 3. Convert the DNA to RNA.
> 4. Compute the complement.
> 5. Quit
4
> The complement for the DNA sequence is GCGGCTGATC
> Please select from the following:
> 1. Count a character.
> 2. Count a pair of characters.
> 3. Convert the DNA to RNA.
> 4. Compute the complement.
> 5. Quit
5
> Goodbye!