Task 2: RNA class

The RNA molecule is closely related to the DNA molecule. The major difference is that RNA contains Uracil (U) rather than Thymine (T). Given a DNA strand, we can arrive at the corresponding RNA strand by replacing all occurrences of T by U.

The protein string encoded by a given RNA is computed by grouping three adjacent nucleotides (such grouping is referred to as {\em codon}) and converting them into one of the twenty amino acids. There are sixty four possible codons, so each amino acid can be encoded by multiple codons.

The mapping from the three letter RNA codons to the proteins is show in the table below, but you may prefer to use the following two arrays. (HINT: the code is much shorter if you use the arrays.) In the array the i'th row of the codons array lists all the codons that encode the i'th protein in the proteins array.

String [][] codons = {{ "AUU", "AUC", "AUA"  }, { "CUU", "CUC", "CUA", 
			   "CUG", "UUA", "UUG"  },  { "GUU", "GUC", "GUA", "GUG"  }, 
			   { "UUU", "UUC"  }, { "AUG"  }, { "UGU", "UGC"  },  
			   { "GCU", "GCC", "GCA", "GCG"  }, { "GGU", "GGC", "GGA", "GGG"  }, 
			   { "CCU", "CCC", "CCA", "CCG"  },  { "ACU", "ACC", "ACA", "ACG"  }, 
			   { "UCU", "UCC", "UCA", "UCG", "AGU", "AGC"  }, { "UAU", "UAC"  }, 
			   { "UGG"  }, { "CAA", "CAG"  }, { "AAU", "AAC"  }, { "CAU", "CAC"  }, 
			   { "GAA", "GAG"  },  { "GAU", "GAC"  }, { "AAA", "AAG"  }, 
			   { "CGU", "CGC", "CGA", "CGG", "AGA", "AGG"  },  { "UAA", "UAG", "UGA"  }};
String [] proteins = { "I", "L", "V", "F", "M", "C", 
			   "A", "G", "P", "T", "S", "Y", "W", "Q", "N", 
			   "H", "E", "D", "K", "R", "stop"}  ;		
		
		

You need to implement the `RNA` class that provides the following capabilities:

• Create an RNA object given a string representing the strand (should perform validation). This is the constructor and it should be named accordingly.
• Convert this RNA object to a string representing the protein. You will need the table of RNA to protein mapping for this. Name this method toProtein( int position ).
  This method should take as a parameter a single non-negative integer. This value indicates the position in the RNA sequence at which the conversion should start. Make sure to validate that this is a non-negative number and that it is smaller than the length of the RNA sequence.
  Your method should scan the RNA sequence until either 1) the stop codon is encountered, or 2) the end of the sequence is reached. Each codon should be converted to the corresponding amino acid and appended to the protein string that is returned. Should return null if
  • the sequence is invalid, or
  • the position is invalid (not within range of valid positions in the sequence), or
  • the length of this RNA sequence is zero, or
  • the length of the determined protein sequence is zero (because the starting codon is the "stop" codon or because the RNA sequence is too short.
• Validate the sequence (used by the constructor). This should be a private method.
• Determine if the sequence represented by this RNA object is valid or not. Name this method isValid().
• Compute the string representation of this RNA object. Should return `null` if the sequence is invalid or of zero length. Name this method toString().

In addition you need to create a TestRNA class that contains a program (read `main()` method) that

• uses DNA class to create a DNA object,
• uses toRNA() method to determine corresponding RNA sequence,
• uses that to create an RNA object,
• and finally determines the protein sequence corresponding to this RNA sequence.

This program should be interactive, i.e., the user should be prompted for the DNA sequence and the program should print out corresponding RNA sequence and the protein sequence. You should include other tests to make sure that all your methods in the RNA class are working as specified (use TestDNA class from Task 1 as a guide).