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Exact Pattern Matching: the brute force approach

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• The Exact String Matching problem
  • Exact String Matching:

    Given: A text string T = t0 t1 t2 ... tn-1                   length(T) = n A pattern string P = p0 p1 p2 ... pm-1          length(P) = m Problem: Determine all the occurences of the pattern P in the text T Example: T = acgttagatactaggatacca P = gata Solution: acgttagatactaggatacca

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• The brute force approach
  • Reminder: the Brute Force method

    Generate every possible outcome           For each outcome, test if the outcome is a valid solution

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  • Example:

    T = acgttagatactaggatgcca P = gata Try: acgttagatactaggatacca gata acgttagatactaggatacca gata acgttagatactaggatacca gata acgttagatactaggatacca gata and so on...

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  • What are the possible positions to try:

    Positions: 0123456789..... T = xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ppppp ^^^^^ pattern P may be found here pattern P may be found starting at position 0 of text string T pattern P may be found starting at position 1 of text string T ....

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  • Where do we start looking:

    0123456789..... T = xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ppppp ^^^^^ First position that P could be found So: start looking for P at position: 0

  • Where do we stop looking:

    0123456789..... T = xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ppppp ^^^^^ | Last position that P could be found What is this position: 0 T.length()-1 | | v v T = xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx |ppppp |^^^^^ | P.length() V position of x = T.length()-1-P.length() So: Last position to look for P = T.length()-P.length()

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  • Psuedo code for the brute force pattern matching algorithm:

    T = text; P = pattern; for ( pos = 0; pos <= T.length()-P.length(); pos++ ) do { if ( P is found starting at position pos ) { print pos; } }

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  • Refined Psuedo code:

    T = text; P = pattern; for ( pos = 0; pos <= T.length()-P.length(); pos++ ) do { cand = T.substring( pos, pos+P.length() ); // Try to match this... if ( P equal to cand ) { print pos; } }

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• Comparing if 2 Strings are equal
  • Recall that: (See: click here)

    String is not a primitive type in Java String is a class (user defined type) provided by the Java library ( click here ) java.lang.String Operations on String variables are implemented with methods

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  • The method used to compare whether 2 Strings are equal ( click here ):

    String1.equals( String2 ) returns: true if String1 and String2 contains the same characters in the same order false otherwise

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  • Example: check if the strings P and cand are equal

    if ( P.equals(cand) ) { .... }

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• Reading a line from the input
  • Recall:

    Scanner input = new Scanner( System.in ); String s; s = input.next(); // Read a word (ended by a space)

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  • Line (of text):

    Input line = a text that is ended by a new line (return) character (A line is a string, but it can contain space characters.)

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  • How to read a line from the input:

    Scanner input = new Scanner( System.in ); String s; s = input.nextLine(); // Read a line (ended by RETURN)

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• The exact string matching algorithm in Java

  • Java code:

    import java.util.Scanner; public class StringMatching1 { public static void main(String[] args) { Scanner in = new Scanner(System.in); String T, P, cand; int pos; System.out.print("Enter a text string T: "); T = in.nextLine(); System.out.print("Enter a pattern string P: "); P = in.next(); for ( pos = 0; pos <= T.length() - P.length(); pos++ ) { cand = T.substring( pos, pos+P.length() ); // Try to match this... if ( P.equals(cand) ) { System.out.println("Found pattern at posistion: " + pos); // Found } } } }

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  • Example Program: (Demo above code)                                                
    • Prog file: click here

    How to run the program:

    Right click on link and save in a scratch directory To compile:   javac StringMatching1.java To run:          java StringMatching1

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  • Example output:

    UNIX>> java StringMatching1 Enter a text string T: acgttagatactaggatacca Enter a pattern string P: gata 6 14

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• You can make the output prettier after you've done the hard work...
  • Nice looking output:

    import java.util.Scanner; public class StringMatching2 { public static void main(String[] args) { Scanner in = new Scanner(System.in); String T, P, cand; int pos, i; System.out.print("Enter a text string T: "); T = in.nextLine(); System.out.print("Enter a pattern string P: "); P = in.next(); System.out.println(); for ( pos = 0; pos <= T.length() - P.length(); pos++ ) { cand = T.substring( pos, pos+P.length() ); // Try to match this... if ( P.equals(cand) ) { System.out.println(T); // Print the text for ( i = 0 ; i < pos; i++ ) // Indent to found position System.out.print(" "); System.out.println(P); // Print the pattern below System.out.println(); } } } }

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  • Example Program: (Demo above code)                                                
    • Prog file: click here

    How to run the program:

    Right click on link and save in a scratch directory To compile:   javac StringMatching2.java To run:          java StringMatching2

    Sample output:

    UNIX>> java StringMatching2 Enter a text string T: acgttagatactaggatacca Enter a pattern string P: gata acgttagatactaggatacca gata acgttagatactaggatacca gata