programming-for-dummies

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Sequential Text Search
Searching for the string GAG
G A T A G
A
G
A
T
Figure 3-5:
The Shift Or
algorithm
creates
a twodimensional
array.
G 0 1 1 1 0 1 0 1 1
A 1 0 1 1 1 0 1 0 1
G 1 1 1 1 1 1 0 1 1
As soon as the algorithm finds three 0s that form a diagonal line in the twodimensional
array, it can identify the exact location of the GAG string in the
much larger string. The Shift Or algorithm gets its name because the matching
string patterns look like binary numbers where the 0 constantly gets
shifted one place to the right, like this:
G → 011
A → 101
G → 110
Although the shift or algorithm takes more steps than a simple brute force
search, it’s much faster. Sometimes the simplest algorithms aren’t always the
fastest.
The finite automaton string search algorithm
First, the algorithm creates a finite state machine, which is a directed graph
(see Book III, Chapter 5) where each node represents a single character in the
target string to find. So if you wanted to find the string GAG, this algorithm
creates a finite state machine consisting of three nodes with one node representing
a starting state where the string hasn’t been found yet. The first node
represents finding the first letter G; the second node represents finding the
second letter A; and the third node represents finding the final letter G, as
shown in Figure 3-6.
After this algorithm creates a finite state machine for the target string, it next
examines each character in the search string. In this example, the search
string is GAAGGAGAA.