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Data Structures and Debugging

Data Structures and Debugging. Dr. Nancy Warter-Perez June 18, 2003. Overview. Programming workshop #1 solution Data Structures 2-D Arrays String Object Debugging Workshop #2. Programming Workshop #1. Write a C++ program to compute the hydrophobicity of an amino acid.

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Data Structures and Debugging

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  1. Data Structures and Debugging Dr. Nancy Warter-Perez June 18, 2003

  2. Overview • Programming workshop #1 solution • Data Structures • 2-D Arrays • String Object • Debugging • Workshop #2 Review of C++

  3. Programming Workshop #1 • Write a C++ program to compute the hydrophobicity of an amino acid • Program will prompt the user for an amino acid and will display the hydrophobicity • Program should prompt the user to continue Review of C++

  4. Programming Workshop #1 - Solution #include<iostream> using namespace std; void main () { char aa_in, aa, flag; double hydro[25] = {1.8,0,2.5,-3.5,-3.5,2.8,-0.4,-3.2,4.5,0,-3.9,3.8,1.9,-3.5,0,-1.6,-3.5,-4.5,-0.8,0.7,0,4.2,-0.9,0,-1.3}; cout << "This program will compute the hydrophobicity of an amino acid.\n" << endl; do { cout << "Please enter the amino acid: "<< flush; cin >> aa_in; // convert to upper case if necessary if((aa_in >= 'a') && (aa_in <= 'z')) aa = aa_in - 32; Review of C++

  5. Programming Workshop #1 – Solution (2) // check if valid (not required) if(((aa - 'A' >= 0) && (aa - 'A' <= 24)) && (aa != 'B') && (aa != 'J') && (aa != 'O') && (aa != 'U') && (aa != 'X')) cout << "\nThe hydrophobicity of “; cout << aa_in << " is " << hydro[aa - 'A'] << endl << endl; else cout << "\nError: " << aa_in; cout << " is not a valid amino acid.\n" << endl; cout << "Would you like to lookup another amino acid? Enter Y/N: "; cin >> flag; } while ((flag == 'y') || (flag == 'Y')); } Review of C++

  6. 2-D Arrays • int nums[2][3] = {{2,4,6},{-9,-7,-5}}; nums[0][0] == 2 nums[0][1] == 4 nums[0][2] == 6 nums[1][0] == -9 nums[1][1] == -7 nums[1][2] == -5 [0] [1] [2] 2 4 6 [0] [1] -9 -7 -5 Review of C++

  7. Nested For Loops • The following nested for loop will print the 2-D array as shown in the previous slide: int i, j, nums[2][3] = {{2,4,6},{-9,-7,-5}}; for(i=0; i < 2; i++) for(j = 0; j < 3; j++) cout << "nums[i][j] == " << nums[i][j] << endl; Review of C++

  8. Class String • Preprocessor and namespace directives • #include<string> • using namespace std; • To declare a string object • string seq; • Useful string functions • seq.c_str() and seq.data() return a pointer to the initial element of a char array whose elements are a copy of the string being represented. • seq.size() – returns the length of the string. • string1 == string2 – will test for equality of two strings. Review of C++

  9. Example Revisited: Amino Acid Search • Write a program to count the number of occurrences of an amino acid in a sequence. • The program should prompt the user for • A sequence of amino acids (seq) • The search amino acid (aa) • The program should display the number of times the search amino acid (aa) occurred in the sequence (seq) Review of C++

  10. Example Revisited: Amino Acid Search (2) // This program will find the number of occurrences of an amino acid in a sequence. // Written By: Prof. Warter-Perez // Date Created: April 16, 2002 // Last Modified: #include<string> #include<iostream> using namespacestd; voidmain () { string seq; charaa; intcount = 0, i; Review of C++

  11. Example Revisited: Amino Acid Search (3) cout << "Please enter a sequence:" << flush; cin >> seq; cout << "Enter the amino acid for comparison: "<< flush; cin >> aa; for (i = 0; i < seq.size(); i++) { if (seq.data()[i] == aa) count++; } if(count == 1) cout << "There was 1 occurence "; else cout << "There were " << count << " occurrences "; cout << "of amino acid " << aa << " in sequence " << seq << "." << endl; } Review of C++

  12. Debugging • Definition: Bug – A mistake in your program that can be one of the following • Compile-time error • Syntax error – program will not compile with syntax errors (fairly easy to fix) • Run-time error (when program is executing) • Typos – program not entered correctly, though syntax is correct (usually relatively easy to fix) • Logical error – the logic of the program/algorithm is inconsistent with the problem (much harder to find/fix) Review of C++

  13. Debugging (2) • Key Idea: • You must understand what your program is supposed to do in order to debug it • Before writing the code, create an example that can be easily verified by hand • Poor Man’s Debugger: • Print statements of program variables (cout) – allow you to see the contents of the variables as the program executes Review of C++

  14. Debugging (3) • Using a debugger it is possible to do the following: • Step through the program instruction by instruction (trace the program) • Stepping over functions F10 • Stepping into functions F11 • Stepping out of functions Shift-F11 (good if you accidentally stepped into a function) • As you step through the program, you can look at the contents of variables and track their changes. • If you expect a variable to change to a specific value and it does not – you have found your bug! Review of C++

  15. Debugging (4) • Sometimes stepping through a program is too time consuming. In this case, set breakpoints and run (go) until you reach the next breakpoint • In Visual C++ Debugger – breakpoints are set by putting cursor on the line where you want to stop and clicking on the hand (or F9). You should see a stop sign on the left scroll bar. To remove a breakpoint, repeat the process and the stop sign should go away. Review of C++

  16. Debugging (5) • To start debugging or continue to the next breakpoint, click on the Go button (text with a down arrow next to it) or use F5 • To stop debugging, click on the Stop Debugging button (text with down arrow and red x) or use Shift-F5 • While there are many other functions available in the debugger, these few key concepts are a good start Review of C++

  17. Debugging (6) • Convert the nested for loop example into a simple C++ program • Debug this simple program tracing the values of • i • j • nums[i][j], as they are displayed Review of C++

  18. Other debugging and development tips • Write your program in small incremental steps (functions) and test each step thoroughly • In case you don’t follow tip 1: if there are many errors (compile-time or run-time), comment out large portions of the code and test incrementally Review of C++

  19. Programming Workshop #2 • Write a sliding window program to compute the hydrophobicity of an amino acid sequence. • The program should prompt the user for • The amino acid sequence • The window size (assume the window increment is 1) • Use the Kyte and Doolittle scale from programming workshop #1. • Obtain the SWISSPROT entry of bacteriorhodopsin and compute the hydrophobicity. • Plot your result in EXCEL and compare your plot to the one given in yesterday afternoon’s workshop. Review of C++

  20. Extension to Programming Workshop #2 (optional) • Modify your program to compute the %GC in a sequence of nucleotides. • The program should prompt the user for • The DNA sequence • The window size (assume the window increment is 1) • Test your program using the data for yesterday afternoon’s workshop. Review of C++

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