Pattern Matching Pattern Matching and Grep String search. Search for given string in a large text file. Regular expression. Natural and compact way to express multiple text patterns. Quintessential programmer's tool. Grep Ex: fragile X syndrome is a common cause of mental retardation. Regular expressions Human genome contains triplet repeats of CGG or AGG, starting with Nondeterministic finite state automata GCG and ending with CTG. Number of repeats is variable, and correlated with syndrome. Use regular expression to specify pattern: GCG(CGG|AGG)*CTG. Reference: Chapter 7.1, Introduction to Computer Science, R. Sedgewick and K. Wayne. Princeton University • COS 226 • Algorithms and Data Structures • Spring 2004 • Kevin Wayne • http://www.Princeton.EDU/~cos226 2 More Pattern Matching Applications Regular Expressions: Basic Operations Test if a string matches some pattern. Regular expression. Process natural language. Compact notation to specify a set of strings. Scan for virus signatures. Core operations. Search for information using Google. Access information in digital libraries. Operation RE Yes No Find Java file containing certain string. every other Retrieve information from Lexis/Nexis. Concatenation aabaab aabaab string Search-and-replace in a word processors. babbaaa abba Filter text (SpamAssassin, NetNanny, Carnivore, AdAware). Wildcard .abba.. aabbaab abbabb Validate data-entry fields (dates, email, URL, credit card). aa every other Search for markers in human genome using PROSITE patterns. Union aa | baab baab string aa Closure ab*a Parse text files. abbbba ababa Compile a Java program. aaaab every other a(a|b)aab Crawl and index the Web. abaab string Read in data stored in some file format. Grouping a (ab)*a Automatically create Java documentation from Javadoc comments. ababa aa 3 4 Regular Expressions: Examples Using Regular Expressions Regular expression examples. Additional operations typically added for convenience. Notation is surprisingly expressive. Ex: [a-e]+ is shorthand for (a|b|c|d|e)(a|b|c|d|e)*. Regular Expression Yes No b a* | (a*ba*ba*ba*)* bbb bb Operation Regular Expression Yes No multiple of three b’s abbbaababb baabbbaa a Any single character ..oo..oo. spoonfood choochoo a | a.*a aba ab begins and ends with a abbaabba ba One or more a(bc)+de abcbcde ade abba Character classes [a-e]+ decade Upper45 .*abba.* bbabbabb abb Exactly N times [a-e]{6} decade ade contains the substring abba abbaabba bbaaba Negations [^aeiou]{6} rhythm decade 5 6 Regular Expressions in Java Regular Expressions in Java Validity checking. Is text in the set described by the pattern? Broadly applicable programmer's tool. Many other languages also support extended regular expressions. public class Validator { Built into grep, awk, emacs, Perl, PHP, Python, JavaScript. public static void main(String[] args) { String pattern = args[0]; String text = args[1]; print all lines containing NEWLINE which grep NEWLINE */*.java System.out.println(text.matches(pattern)); occurs in any file with a .java extension } } egrep '^[qwertyuiop]*[zxcvbnm]*$' dict.txt | egrep '...........' % java Validator "0*10*10*10*" 010000011 true legal Java identifier PERL. Practical Extraction and Report Language. % java Validator "[$_A-Za-z][$_A-Za-z0-9]*" ident123 true replace all occurrences of from legal email address (simplified) perl -pi -e 's|from|to|g' input.txt with to in the file input.txt % java Validator "[a-z]+@([a-z]+\.)+(edu|com)" [email protected] true Social Security numbers perl -ne 'print if /^[A-Z][A-Za-z]*$/' dict.txt % java Validator "[0-9]{3}-[0-9]{2}-[0-9]{4}" 166-11-5655 true 7 8 Regular Expression Caveats Perl RE for Valid RFC822 Email Addresses (?:(?:\r\n)?[ \t])*(?:(?:(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\".\[\]]))|"(?:[^\"\r\\]|\\.|(?:(?:\r\n)?[ \t]))*"(?:(?: Writing a RE is like writing a program. \r\n)?[ \t])*)(?:\.(?:(?:\r\n)?[ \t])*(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\".\[\]]))|"(?:[^\"\r\\]|\\.|(?:(?:\r\n)?[ \t]))*"(?:(?:\r\n)?[ \t])*))*@(?:(?:\r\n)?[ \t])*(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\".\[\]]))|\[([^\[\]\r\\]|\\.)*\ ](?:(?:\r\n)?[ \t])*)(?:\.(?:(?:\r\n)?[ \t])*(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\".\[\]]))|\[([^\[\]\r\\]|\\.)*\](?: Need to learn syntax. (?:\r\n)?[ \t])*))*|(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\".\[\]]))|"(?:[^\"\r\\]|\\.|(?:(?:\r\n)?[ \t]))*"(?:(?:\r\n) ?[ \t])*)*\<(?:(?:\r\n)?[ \t])*(?:@(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\".\[\]]))|\[([^\[\]\r\\]|\\.)*\](?:(?:\r\n)?[ Can be easier to write than read. \t])*)(?:\.(?:(?:\r\n)?[ \t])*(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\".\[\]]))|\[([^\[\]\r\\]|\\.)*\](?:(?:\r\n)?[ \t] )*))*(?:,@(?:(?:\r\n)?[ \t])*(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\".\[\]]))|\[([^\[\]\r\\]|\\.)*\](?:(?:\r\n)?[ \t])* )(?:\.(?:(?:\r\n)?[ \t])*(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\".\[\]]))|\[([^\[\]\r\\]|\\.)*\](?:(?:\r\n)?[ \t])*))*) *:(?:(?:\r\n)?[ \t])*)?(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\".\[\]]))|"(?:[^\"\r\\]|\\.|(?:(?:\r\n)?[ \t]))*"(?:(?:\r \n)?[ \t])*)(?:\.(?:(?:\r\n)?[ \t])*(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\".\[\]]))|"(?:[^\"\r\\]|\\.|(?:(?:\r\n)?[ \t ]))*"(?:(?:\r\n)?[ \t])*))*@(?:(?:\r\n)?[ \t])*(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\".\[\]]))|\[([^\[\]\r\\]|\\.)*\]( ?:(?:\r\n)?[ \t])*)(?:\.(?:(?:\r\n)?[ \t])*(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\".\[\]]))|\[([^\[\]\r\\]|\\.)*\](?:(? "Sometimes you have a programming problem and :\r\n)?[ \t])*))*\>(?:(?:\r\n)?[ \t])*)|(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\".\[\]]))|"(?:[^\"\r\\]|\\.|(?:(?:\r\n)? [ \t]))*"(?:(?:\r\n)?[ \t])*)*:(?:(?:\r\n)?[ \t])*(?:(?:(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\".\[\]]))|"(?:[^\"\r\\]| it seems like the best solution is to use regular \\.|(?:(?:\r\n)?[ \t]))*"(?:(?:\r\n)?[ \t])*)(?:\.(?:(?:\r\n)?[ \t])*(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\".\[\]]))|" (?:[^\"\r\\]|\\.|(?:(?:\r\n)?[ \t]))*"(?:(?:\r\n)?[ \t])*))*@(?:(?:\r\n)?[ \t])*(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\ expressions; now you have two problems." ".\[\]]))|\[([^\[\]\r\\]|\\.)*\](?:(?:\r\n)?[ \t])*)(?:\.(?:(?:\r\n)?[ \t])*(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\".\[ \]]))|\[([^\[\]\r\\]|\\.)*\](?:(?:\r\n)?[ \t])*))*|(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\".\[\]]))|"(?:[^\"\r\\]|\\.|( ?:(?:\r\n)?[ \t]))*"(?:(?:\r\n)?[ \t])*)*\<(?:(?:\r\n)?[ \t])*(?:@(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\".\[\]]))|\[([ ^\[\]\r\\]|\\.)*\](?:(?:\r\n)?[ \t])*)(?:\.(?:(?:\r\n)?[ \t])*(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\".\[\]]))|\[([^\[\ ]\r\\]|\\.)*\](?:(?:\r\n)?[ \t])*))*(?:,@(?:(?:\r\n)?[ \t])*(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\".\[\]]))|\[([^\[\]\ r\\]|\\.)*\](?:(?:\r\n)?[ \t])*)(?:\.(?:(?:\r\n)?[ \t])*(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\".\[\]]))|\[([^\[\]\r\\] |\\.)*\](?:(?:\r\n)?[ \t])*))*)*:(?:(?:\r\n)?[ \t])*)?(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\".\[\]]))|"(?:[^\"\r\\]|\\ .|(?:(?:\r\n)?[ \t]))*"(?:(?:\r\n)?[ \t])*)(?:\.(?:(?:\r\n)?[ \t])*(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\".\[\]]))|"(? :[^\"\r\\]|\\.|(?:(?:\r\n)?[ \t]))*"(?:(?:\r\n)?[ \t])*))*@(?:(?:\r\n)?[ \t])*(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\". \[\]]))|\[([^\[\]\r\\]|\\.)*\](?:(?:\r\n)?[ \t])*)(?:\.(?:(?:\r\n)?[ \t])*(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\".\[\] ]))|\[([^\[\]\r\\]|\\.)*\](?:(?:\r\n)?[ \t])*))*\>(?:(?:\r\n)?[ \t])*)(?:,\s*(?:(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\ ".\[\]]))|"(?:[^\"\r\\]|\\.|(?:(?:\r\n)?[ \t]))*"(?:(?:\r\n)?[ \t])*)(?:\.(?:(?:\r\n)?[ \t])*(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[ \["()<>@,;:\\".\[\]]))|"(?:[^\"\r\\]|\\.|(?:(?:\r\n)?[ \t]))*"(?:(?:\r\n)?[ \t])*))*@(?:(?:\r\n)?[ \t])*(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t ])+|\Z|(?=[\["()<>@,;:\\".\[\]]))|\[([^\[\]\r\\]|\\.)*\](?:(?:\r\n)?[ \t])*)(?:\.(?:(?:\r\n)?[ \t])*(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+| \Z|(?=[\["()<>@,;:\\".\[\]]))|\[([^\[\]\r\\]|\\.)*\](?:(?:\r\n)?[ \t])*))*|(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\".\[\ ]]))|"(?:[^\"\r\\]|\\.|(?:(?:\r\n)?[ \t]))*"(?:(?:\r\n)?[ \t])*)*\<(?:(?:\r\n)?[ \t])*(?:@(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\[" ()<>@,;:\\".\[\]]))|\[([^\[\]\r\\]|\\.)*\](?:(?:\r\n)?[ \t])*)(?:\.(?:(?:\r\n)?[ \t])*(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<> @,;:\\".\[\]]))|\[([^\[\]\r\\]|\\.)*\](?:(?:\r\n)?[ \t])*))*(?:,@(?:(?:\r\n)?[ \t])*(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@, ;:\\".\[\]]))|\[([^\[\]\r\\]|\\.)*\](?:(?:\r\n)?[ \t])*)(?:\.(?:(?:\r\n)?[ \t])*(?:[^()<>@,;:\\".\[\] \000-\031]+(?:(?:(?:\r\n)?[ \t])+|\Z|(?=[\["()<>@,;:\\ ".\[\]]))|\[([^\[\]\r\\]|\\.)*\](?:(?:\r\n)?[