CSE 142: Computer Programming I, Autumn 2011

Homework 7 (DNA) FAQ

Q: Where do I start?

A: Try to break the problem into pieces. First try to read a record (a name and its sequence of nucleotides) from the file. Then try to count the nucleotides. Look at the diagram of the arrays on the HW7 spec for inspiration. If you aren't very familiar with arrays, perhaps try looking at practice problems about them first until you feel comfortable.

Q: How do I read two lines at a time?

A: Well, the thing that you do to read one line at a time.... do that twice in a row.

Q: How do I examine the letters of the line to see which nucleotide they are (A, C, G, or T)?

A: Look at section 4.4 in the textbook about Text Processing, and look over section 7 problems about text processing. The String class's charAt method is useful.

Q: How do I place the nucleotide into the right element of the array, when counting the occurrences of nucleotides?

A: Look at the lecture example on section attendance. It's okay to use if/else statements to express the mapping between the characters and the array indexes, as long as you avoid redundancy as much as possible.

Q: Why are my mass percentages way off?

A: Are you sure that you are weighting each nucleotide by its mass as listed in the handout? For example, adenine has a molar mass of 135.128.

Q: Why are my mass percentages SLIGHTLY off (0.1 or so)?

A: Usually that's because you didn't round correctly or used the wrong type somewhere (int vs double).

Q: I have a lot of repetitive code. How do I make it less redundant?

A: You must work especially hard on this assignment to eliminate redundancy. Use techniques we've practiced in the past, such as factoring common code out of an if/else statement, or creating a helping method to hold common code. Look at the "Sections" program from lecture or at Chapter 7's case study to learn how to write good methods that use arrays as parameters/returns.