找出两个字符串中，连续相同的字符个数最少为min的字符串

找出两个字符串中，连续相同的字符个数最少为min的字符串

（具体涉及一些不能公布的，还是不说了，有更好的算法，请拍砖讨论）

主要是这个函数--Compare2Str(String str1, String str2, int min)，其他不用管

-----------------------------似乎还有点问题！等待明天继续调试

package com.ssj.test;

import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;

public class CompareString {

	/**
	 * @param args
	 */
	public static void main(String[] args) {
		// TODO Auto-generated method stub

		String contig1 = "AAGAAACGTATCCGTGTTTACATGGATGGATGTTTCGATCTCATGCATTATGGACACGCA"+
						"AATGCTTTAAGACAAGCTAAAGCTTTAGGAGATGAACTAGTAGTTGGAATTGTAAGTGAT"
					+"GAAGAAATCATCAAGAACAAAGGTCCTCCTGTTTTATCAATGGAGGAAAGATTGGCACTT"
					+"GTTAGTGGATTGAAGTGGGTTGATGAAGTTATTGCTAATGCACCATATGCTATTACCGAA"
					+"GACTTCATGAACAGTCTATTTAAAGAACATAAGATTGATTATATCATTCATGGAGATGAT"
					+"CCTTGTTTGCTTCCTGATGGAAGTGATGCATATGCTTTAGCAAAAAAAGTCGGTCGTTAC"
					+"AAGCAAATTAAACGTACAGAAGGCGTATCAAGCACCGACATTGTAGGAAGGATACTTGCA"
					+"TCCATGGAAGATAAAGAAGTATGTGAAGTTAATGGAGAAAGTAATGAAATGAATAAAAAT"
					+"TTGGACAGCCATTTCAAGGCCAAACATGCCTCTAATTTTTTGCCTACATCAAGAAGAATT"
					+"GTTCAGTTT";

		String EL372564 = "AAGAAACGTATCCGTGTGTACATGGATGGATGTTTTGATCTCATGCATTATGGTCACGCAAATGCTTTAAGACAAGCTAAAGCTTTAGGAGACGAATTAGTGGTTGGAATTGTAAGTGATGAAGAAATCATCAAGAACAAAGGTCCTCCTGTTTTATCAATGGAGGAAAGATTGGCACTTGTTAGTGGATTGAAGTGGGTTGATGAAGTTATTGCTAATGCACCTTATGCTATTACTGAAGACTTCATGAACAGTCTATTTAAAGAACATAAGATTGATTATATCATTCATGGAGATGATCCTTGTTTGCTTCCTGATGGAAGTGATGCATATGCTTTAGCAAAAAAA";
		String EL371249 = "AAGAAACGTATCCGTGTGTACATGGATGGATGTTTTGATCTCATGCATTATGGTCACGCAAATGCTTTAAGACAAGCTAAAGCTTTAGGAGACGAATTAGTGGTTGGAATTGTAAGTGATGAAGAAATCGTCAAGAACAAAGGTCCTCCTGTTTTATCAATGGAGGAAAGATTGGCACTTGTTAGTGGATTGAAGTGGGTTGATGAAGTTATTGCTAATGCACCTTATGCTATTACTGAAGACTTCATGAACAGTCTATTTAAAGAACATAAGATTGATTATATCATTCATGGAGATGATCCTTGTTTGCTTCCTGATGGAAGTGATGCATATGCTTTAGCAAAAAAA";
		String EL347301 = "AAGAAACGTATCCGTGTGTACATGGATGGATGTTTTGATCTCATGCATTATGGTCACGCAAATGCTTTAAGACAAGCTAAAGCTTTAGGAGACGAATTAGTGGTTGGAATTGTAAGTGATGAAGAAATCATCAAGAACAAAGGTCCTCCTGTTTTATCAATGGAGGAAAGATTGGCACTTGTTAGTGGATTGAAGTGGGTTGATGAAGTTATTGCTAATGCACCTTATGCTATTACTGAAGACTTCATGAACAGTCTATTTAAAGAACATAAGATTGATTATATCATTCATGGAGATGATCCTTGTTTGCTTCCTGATGGAAGTGATGCATATGCTTTAGCAAAAAAAGTTGGTCGTTACAAACAAATTAAACGTACAGAAGGCGTATCAAGCACCGACATTGTAGGAAGGATACTTGCATCCATGGAAGAT";
		String EH685069 = "AAGAAACGTATCCGTGTTTACATGGATGGATGTTTCGATCTCATGCATTATGGACACGCAAATGCTTTAAGACAAGCTAAAGCTTTAGGAGATGAACTAGTAGTTGGAATTGTAAGTGATGAAGAAATCATCAAGAACAAAGGTCCTCCTGTTTTATCAATGGAGGAAACATTGGCACTTGTTAGTGGATTGAAGTGGGTTGATGAAGTTATTGCTAATGCACCATATGCTATTACCGAAGACTTCATGAACAGTCTATTTAAAGAACATAAGATTGATTATATCATTCATGGAGATGATCCTTGTCTGCTTCCTGATGGAAGTGATGCATATGCTTTAGCAAAAAAAGTCGGTCGTTACAAGCAAATTAAACGTACAGAAAGCGTATCAAGCACCGACATTGTAGGAAGGGTACTTGCATCCATGGAAGATAAAGAACTATGTGAA";
		
		//		String str3 = "AAGAAACGTATCCGTGT--TTACATGGATGGATGTTTCGATCTCATGCATTATGGACACGCAAATGC";
		System.out.println("--------contig1 and EL372564---------");
		CompareTest(contig1, EL372564);
		System.out.println("\n--------EL371249 and EL372564---------");
		CompareTest(EL371249, EL372564);
		
		System.out.println("\n--------EL372564 and EL347301---------");
		CompareTest(EL372564, EL347301);

		System.out.println("\n--------contig1 and EH685069---------");
		CompareTest(contig1, EH685069);
		
		//System.out.println("AAGAAACGTATCCGTGTTTACATGGATGGATGTTTCGATCTCATGCATTATGGACACGCA".length());
		String contig =  "TNNNNNNNNNNNNNNNNNNNNNACTTATGCACAGACCAACCTGAATGTTGACGTGCTCCA"
						+"CATTTCCTACCTATCTTACACTTACCATAATGGGTGGAATATGTTCTTTCTAAAGTATTT"
						+"TCATTAGGTTTTAAAGCCCACATGCATCTTAAAGAAAATGTAAACCACATGTTTGACATT"
						+"CATTTACACTTAACTACTTTTTTTCCTATAAAAAAGAAAAATGTAAATGTGATGTTCAAA"
						+"TTGCCAATTTGAGAGCCATATTGTGTACATTAAAATTAGTGGCATTTCAAGTCATTTTTC"
						+"TTTCCATGGAATTATTACAAAGGAAAATGCCTTTGAACAATAGAAAGTCATGGATCTATC"
						+"CCAACTCTAAATAAGTGGTATTTTAGTGGGTTTTAAACATGGTTAAAGTTCTTATCCCAG"
						+"AGCTCTAAACCACAAAGCCCAGTTATATTGGTTCTCTTCATCTGTCAGAGGTAAAAACAG"
						+"AGGGTATTGATCTTTTATTTATCTTTGAAGCTTTAAAGTATAATTAGTTAA"+       "AGAAAAAGT"
						+"TTCTGTACTTAGAACATCTCGGTTCTAGCCTTGACTTATGCTAGAAACAAGGATTATATC"
						+"TGTATTAGTCTGGTCATACACTGTTATAAAGAACTACCTGAGACTGGATAATTTATAAAG"
						+"AAAAGAGGTTTAATTAGCTTATGGTTCCACAGGCTGTACAGGAAGCATGCCTGGGGAGGC"
						+"CTTAAGAAACTTACAATCATGGCAGAATGTGAAGAGGAAGAAAGCATGTTTTCTCATGGC"
						+"CAGAGCAAGAGGAAGAGAGAGAAGGGGGAGGTGCTACTCCACTTTTAANGCAACCCAGAT"
						+"CTCATGAGAACTCCACTCCATTGTGCACAAAAATGGCCAAGGGCGGAAATTTCCACCCTC"
						+"GTGATCNNCAATCACCTCCCACCAGGCCCCTCCTCTATTATTGGGGATTACAATTTGGCA"
						+"TGAGATCTGGGTGAGGACACAAATCCAAACCATATCAACATCCCTACTCTACTTACTTTA"
						+"TAAACTTGGTGGGAGAATCAAGTGGCATGGGGATGAAAGTCAATGGATACCGGAAAGAGG"
						+"ACTAATCCATGGCTGAAAGGGGGGTATCCAATTACACCAAGGCTTTACAGGGGAAATATA"
						+"CAGAGGTTAAAACAAAGGTTTGGTCTTTCCAAAA";
		String ENV1180 = "TNNNNNNNNNNNNNNNNNNNNNACTTATGCACAGACCAACCTGAATGTTGACGTGCTCCA"
						+"CATTTCCTACCTATCTTACACTTACCATAATGGGTGGAATATGTTCTTTCTAAAGTATTT"
						+"TCATTAGGTTTTAAAGCCCACATGCATCTTAAAGAAAATGTAAACCACATGTTTGACATT"
						+"CATTTACACTTAACTACTTTTTTTCCTATAAAAAAGAAAAATGTAAATGTGATGTTCAAA"
						+"TTGCCAATTTGAGAGCCATATTGTGTACATTAAAATTAGTGGCATTTCAAGTCATTTTTC"
						+"TTTCCATGGAATTATTACAAAGGAAAATGCCTTTGAACAATAGAAAGTCATGGATCTATC"
						+"CCAACTCTAAATAAGTGGTATTTTAGTGGGTTTTAAACATGGTTAAAGTTCTTATCCCAG"
						+"AGCTCTAAACCACAAAGCCCAGTTATATTGGTTCTCTTCATCTGTCAGAGGTAAAAACAG"
						+"AGGGTATTGATCTTTTATTTATCTTTGAAGCTTTAAAGTATAATTAGTTAA"   +    "GGAAAAGTT"
						+"CTGTACTTAGAACATCTCGGTTCTAGCCTTGACTTATGCTAGAAACAAGGATTATATCTG"
						+"TATTAGTCTGGTCTACACTGTTATAAAGAACTACCTG";
		String ENV446 =  "CCXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTATCCAACTCTAAATAAGTGGTATTT"
						+"AGTGGGTTTTAAACATGGTTAAAGTTCTTATCCCAGAGCTCTAAACCACAAAGCCCAGTT"
						+"ATATTTGTTCTCTTCATCTGTCAGAGGTAAAAACAGAGGGTATTGATCTTTTATTTATCT"
						+"TTGAAGCTTTAAAGTATAATTTGTTCAAGGAAAAGTTTCTGTACTTAGAACATCTCGGTT"
						+"CTAGCCTTGACTTATGCTAGAAACAAGGATTATATCTGTATTAGTCTGTTCATACACTGT"
						+"TATAAAGAACTACCTGAGACTGGATAATTTATAAAGAAAAGAGGTTTAATTAGCTTATGG"
						+"TTCCACAGGCTGTACAGGAAGCATGCCTGGGGAGGCCTTAAGAAACTTACAATCATGGCA"
						+"GAATGTGAAGAGGAAGAAAGCATGTTTTCTCATGGCCAGAGCAAGAGGAAGAGAGAGAAG"
						+"GGGGAGGTGCTACTCCACTTTTAANGCAACCCAGATCTCATGAGAACTCCACTCCATTGT"
						+"GCACAAAAATGGCCAAGGGCGGAAATTTCCACCCTCGTGATCNNCAATCACCTCCCACCA"
						+"GGCCCCTCCTCTATTATTGGGGATTACAATTTGGCATGAGATCTGGGTGAGGACACAAAT"
						+"CCAAACCATATCAACATCCCTACTCTACTTACTTTATAAACTTGGTGGGAGAATCAAGTG"
						+"GCATGGGGATGAAAGTCAATGGATACCGGAAAGAGGACTAATCCATGGCTGAAAGGGGGG"
						+"TATCCAATTACACCAAGGCTTTACAGGGGAAATATACAGAGGTTAAAACAAAGGTTTGGT"
						+"CTTTCCAAAA";
		System.out.println("\n--------contig and ENV1180---------");
		CompareTest(ENV1180, contig);
		
		String str = "";
//		Compare2Str("abcdbce","cbce",2);
		Compare2Str(ENV446,ENV1180,20);
//		System.out.println(ENV446.indexOf());
	}

	public static void CompareTest(String str1, String str2){
		
		int len1 = str1.length();
		int len2= str2.length();
		StringBuffer strb = new StringBuffer();
		int k = (len1>len2 ? len2 : len1);
		//System.out.println("k = "+k);
//		int num = 0;
		for (int i = 0; i<k; i++){
			if(str1.charAt(i) == str2.charAt(i)){
				strb.append(str1.charAt(i));
			}
			else {
//				num = i;
				break;
			}
		}
		System.out.println("the num of the same char :  "+strb.length());
		System.out.println("the same String is : " +strb.toString());
//		System.out.println("the arrays1 is : " +strb.toString());
//		if(strb.toString().equals(str1.substring(0,num))){
//			System.out.println("Very Good!!!");
//		}
		
	}
	
	public static void Compare2Str(String str1, String str2, int min){
  //找出两个字符串中，连续相同的字符个数最少为min的字符串
  int len1 = str1.length();
  int len2= str2.length();
  StringBuffer strb = new StringBuffer();
  String maxStr, minStr;
  int minLen = 0;
  int maxLen = 0;
  if(len1 > len2){
   maxLen = len1;
   minLen = len2;
   maxStr = str1;
   minStr = str2;
  }
  else{
   maxLen = len2;
   minLen = len1;
   maxStr = str2;
   minStr = str1;
  }
  List strList = new ArrayList();
  char c1, c2;
  
  for (int i=0; i<maxLen; i++){
   StringBuffer tempStr = new StringBuffer("");
   c1 = maxStr.charAt(i);
   for(int j=0; j<minLen; j++){
     c2 = minStr.charAt(j);
     while(c1 == c2){
     tempStr.append(c1);
     if(++i<maxLen && ++j<minLen){
      c1 = maxStr.charAt(i);
      c2 = minStr.charAt(j);
     }
     else{
      break;
     }
    }
    if(tempStr.length()>=min){
     strList.add(tempStr);
    }
   }
  }
  Iterator iter = strList.iterator();
  while(iter.hasNext()){
   StringBuffer s = (StringBuffer)iter.next();
   System.out.println("-------" + s.toString());
  }
 }	
	public static void isHaveSubString(String str1, String str2){
		
		if(str1.startsWith(str2)){
			System.out.println("---OK--");
		}
	}
}