with Ada.Text_IO; with Ada.Integer_Text_IO; with Ada.IO_Exceptions; procedure Assign11 is

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1 with Ada.Text_IO; with Ada.Integer_Text_IO; with Ada.IO_Exceptions; procedure Assign11 is DNA pattern matcher written by John McCormick, April 2013 This program counts the number of times a pattern of nucleotides occurs in a text file and the number of lines in that file. A pattern may NOT extend over multiple lines. Valid nucleotide symbols are A, C, G, and T (or their lowercase equivalents) Invalid nucleotide symbols in the data file and in the pattern entered at the keyboard are ignored. Assumptions Pattern contains at least one nucleotide and no more than 10,000 nucleotides The name of the data file contains no more than 80 characters No line in the data file contains more than 10,000 nucleotides Input From Keyboard Name of data file Pattern of nucleotides From Data file Lines of nucleotides Output (to screen) Number of lines processed The pattern Number of pattern matches detected Types for arrays of nucleotides type Nucleotide is (A, C, G, T); type Nucleotide_Array is array (Positive range <>) of Nucleotide; subtype Index_Range is Integer range _000; subtype Length_Range is Integer range 0.. Index_Range'Last; subtype Line_Array is Nucleotide_Array (Index_Range); package Nucleotide_IO is new Ada.Text_IO.Enumeration_IO (Enum => Nucleotide);

2 procedure Prepare_Input_File (Prompt : in String; File : out Ada.Text_IO.File_Type) is This procedure prompts the user for a file name and opens that file for input Preconditions : File is not open Postconditins : File is open for input Keyboard reading marker is advanced to the next line subtype File_Name_String is String (1.. 80); File_Name : File_Name_String; The input file name Last : Natural; Number of characters in File_Name Get a valid input file name Each iteration, get one name Validation_Loop : Ada.Text_IO.Put_Line (Prompt); Ada.Text_IO.Get_Line (Item => File_Name, Last => Last); Advance reading marker if necessary if Last = File_Name'Last then Ada.Text_IO.Skip_Line; Validation_Block : Handles case of non-existent file Ada.Text_IO.Open (File => File, Mode => Ada.Text_IO.In_File, Name => File_Name (1.. Last)); exit Validation_Loop; exception when Ada.IO_Exceptions.Name_Error => Ada.Text_IO.Put ("Cannot find a file called """ & File_Name (1.. Last)); Ada.Text_IO.Put_Line (""", please try again"); end Validation_Block; end Validation_Loop;

3 end Prepare_Input_File; procedure Get_Nucleotides (File : in Ada.Text_IO.File_Type; Item : out Nucleotide_Array; Last : out Natural) is Reads one line of nucleotides from File. Any invalid nucleotides are ignored Preconditions : File is open for input Postconditions : Item contains the nucleotides from the current line Last contains the index of the last nucleotide in array Item If there are no nucleotides in Item, Last is set to Item'First - 1 The reading marker is left on the line terminator Char : Character; One character from the input Last := Item'First - 1; Initialize array index Get all the nucleotides on a line Each iteration, get one nucleotide Input_Loop : exit Input_Loop when Ada.Text_IO.End_Of_Line (File); Ada.Text_IO.Get (File => File, Item => Char); case Char is when 'A' 'a' => Item (Last) := A; when 'C' 'c' => Item (Last) := C; when 'G' 'g' => Item (Last) := G; when 'T' 't' => Item (Last) := T; when others =>

4 null; end case; end Input_Loop; end Get_Nucleotides; function Count_Matches (Pattern : in Nucleotide_Array; Line : in Nucleotide_Array) return Natural is Preconditions : Pattern'Length > 0 Postconditions : Returns the number of times Pattern occurs in Line Result : Natural; The answer First : Positive; Line slice Last : Positive; indices Result := 0; Check for all occurrences of Pattern in Line Each iteration, check the pattern against one part of the Line The part is Line (First.. Last) First := Line'First; Last := First + Pattern'Length - 1; exit when Last > Line'Last; Check if the pattern matches at the current position if Line (First.. Last) = Pattern then Result := Result + 1; Move on to the next part of Line First := First + 1; end ; return Result; end Count_Matches;

5 procedure Search_File (File : in Ada.Text_IO.File_Type; Pattern : in Nucleotide_Array; Lines : out Natural; Matches : out Natural) is Searches for occurrences of Pattern in File Preconditions : File is open Pattern'Length > 0 Postconditions : Lines is the number of lines in File Matches is the number of pattern matches found in File Line (data and length) Line : Line_Array; Line_Length : Length_Range; Initialize counters Lines := 0; Matches := 0; Process all of the lines in the input file Each iteration, search for the pattern in one line Line_Loop : exit Line_Loop when Ada.Text_IO.End_Of_File (File); Get one line of nucleotides Get_Nucleotides (File => File, Item => Line, Last => Line_Length); Advance reading marker to next line if not Ada.Text_IO.End_Of_File (File) then Ada.Text_IO.Skip_Line (File); Update the two counters Lines := Lines + 1; Matches := Matches + Count_Matches (Pattern => Pattern, end Line_Loop; end Search_File; Line => Line (1.. Line_Length));

6 procedure Display_Results (Lines : in Natural; Matches : in Natural; Pattern : in Nucleotide_Array) is Display the number of lines processed, the pattern, and the number of pattern matches found, Preconditions : None Postconditions : All parameter values are displayed Ada.Integer_Text_IO.Put (Item => Lines, Width => 1); Ada.Text_IO.Put_Line (" lines processed."); Ada.Text_IO.Put ("The pattern "); Display the pattern Each iteration, display one nucleotide of the pattern for Index in Pattern'Range Nucleotide_IO.Put (Item => Pattern (Index), Width => 1); end ; Ada.Text_IO.Put (" was found "); Ada.Integer_Text_IO.Put (Item => Matches, Width => 1); if Matches = 1 then Ada.Text_IO.Put_Line (" time."); else Ada.Text_IO.Put_Line (" times."); end Display_Results; - Nucleotide_File : Ada.Text_IO.File_Type; Input file Pattern : Line_Array; Pattern (data and length) Pattern_Length : Length_Range; Lines_Processed : Natural; Matches_Found : Natural; Counters (results)

7 Prepare the file for input Prepare_Input_File (Prompt => "Please enter the name of the file of nucleotides", File => Nucleotide_File); Get the Pattern Each iteration, get one line from the user Ada.Text_IO.Put_Line ("Please enter a pattern of nucleotides on a single line"); Get_Nucleotides (File => Ada.Text_IO.Standard_Input, Item => Pattern, Last => Pattern_Length); exit when Pattern_Length > 0; Ada.Text_IO.Put_Line ("You must enter at least one valid nucleotide"); Ada.Text_IO.Skip_Line; end ; Search the File for pattern Matches Search_File (File => Nucleotide_File, Pattern => Pattern (1.. Pattern_Length), Lines => Lines_Processed, Matches => Matches_Found); Done with file Ada.Text_IO.Close (Nucleotide_File); Display the results Display_Results (Lines => Lines_Processed, Matches => Matches_Found, Pattern => Pattern (1.. Pattern_Length)); end Assign11;

In the case above, only the x:= x+1 statement is executed and the result is 4;

C-10 1. For X = 3 Case 1. IF x >= 0 THEN x:= x+1; ELSIF x >=1 THEN x := x + 2; END IF; In the case above, only the x:= x+1 statement is executed and the result is 4; Case 2. IF x >= 0 THEN x := x + 1;