Help in bioinformatic | Biology homework help

I have a Bioinformatic assignment, my doctor gave us a code in Ruby language. This code is to do a global alignment, and the doctor wants semi-global alignment. So we have to modify the code of global alignment to be semi-global alignment. I will attached the code for you. Second add numbers to make longer alignments more readable
 
That what I want
 
I attached Five files.
 
1. The code of global alignment with the output to use it to make the change on it to be semi global alignment.
 
2. I attached the question file that has the two questions with details
 
3. It has class-note link (Here is doctors explanations, examples, etc) This assignment is number 3. So when you open the class-note link, make sure that you look at assignment 3 because this link represent the whole chapters, and Assignment 3 start from:
 
Chapter 3 St. Clair Visick, continued
Tuesday, October 21 to Thursday, October 30 
 
4. chapter 3 from the book.
 
5. Data used in homework assignment 3
 
 
Please this assignment is very important to me if you dont know how to do it let me know, please do not try to do it if 100% that you do it.