字符串处理技术 Algorithms on Strings,Trees and Sequences(1)

生物信息科学中,作者把DNA看作是以$\Sigma=\{A,C,G,T\}$为字符集的序列,或者(以计算机专业词汇所称呼的)字符串.
本书讲述了很多$\text{string technique}$,尤其是$\text{inperfect data}$的处理,等等,故闲余之下以心拜读.

$\S$1 Exact Matchting .完全匹配

1.1.1 一些简单的定义

Given a string P called pattern and long string T called text, the exact matching problem is to find all occurences, if any, of pattern P in text T.

例如$P=\text{“aba”},T=\text{“cabac”}$,那么$T$能匹配到$P$.

Definition (string) A string $S$ is an ordered list of characters written continguously from left to right.

字符串定义

Definition (substring) For any string $S$, $S[i...j]$ is the (contingurous) substring of $S$ that starts at position $i$ and ends at position $j$ of $S$.

子串定义

Definition (prefix/suffix) In particular, $S[1...i]$ is the prefix of string $S$ that ends at position $i$, and $S[j...|S|]$ is the suffix of string $S$ that begins at position $j$, where $|S|$ denotes the number of characters in string $S$.

前缀后缀定义

Definition (empty string) S[i…j] is the empty string if $i>j$.

空串定义

Definition (proper prefix/proper suffix/proper substring) A proper prefix/suffix/substring is repectively,a prefix/suffix/substring that is neither the entire of the string $S$, nor the empty string.

真前缀/后缀/子串定义

Definition (i-th character) For any string $S, S(i)$ denotes the i-th character of string $S$.

$S(i)$函数定义

符号习惯:
我就不讲了…应该都是很朴素且通用的符号,如果有人需要我解释,我就把一些符号的含义贴在这吧…

1.1.2 暴力匹配

显然如果$|P|=n$,$|T|=m$,那么下面暴力匹配的方法的复杂度将会是$\Theta(nm)$.

SUBSTRING(string P,string T)
    p ← 1
    t ← 1
    for t from 1 to |T|-|P|+1
        for p from 1 to |P| or until pattern false
            if T(t+p-1) ≠ P(p) then pattern false
        if patterned then return true
    return false

bool substring(string &P,string &T){
    int endRef=T.length()-P.length();
    for(int i=0,matched;i<=endRef;i++){
        matched=1;
        for(int j=0;matched&&j<P.length();j++){
            if(P[j]!=T[i+j])matched=0;
        }
        if(matched)return true;
    }
    return false;
}

于是我们需要尝试使用更优秀的算法去完成完全匹配的任务

1.1.3 Z-Algorithm

点我查看Z-Algorithm算法介绍及内容

definition Zi(S)(i>1) Z