c_cpp/etc/KaKs_Calculator/src/ConcatenatePairs.cpp

   1 /************************************************************
   2 * Copyright (C) 2005, BGI of Chinese Academy of Sciences
   3 * All rights reserved.
   4
   5 * Filename: ConcatenatePairs.cpp
   6 * Abstract: Concatenate all pairs of sequences with AXT format
   7                         to a pair of sequences (maybe very long).
   8
   9 * Version: 1.0
  10 * Author: Zhang Zhang (zhanghzhang@genomics.org.cn)
  11 * Date: Feb.2, 2005
  12
  13 * Modified Version:
  14 * Modified Author:
  15 * Modified Date:
  16 *************************************************************/
  17 #include<string>
  18 #include<iostream>
  19 #include<fstream>
  20
  21 using namespace std;
  22
  23 string result;  //Result for outputing into a file
  24
  25 bool readFile(const char *filename) {
  26
  27         bool flag = true;
  28         string seq1, seq2;
  29         seq1 = seq2 ="";
  30
  31         try     {
  32                 ifstream is(filename);
  33                 if (!is) {
  34                         cout<<"\nError in opening file..."<<endl;
  35                         throw 1;
  36                 }
  37
  38                 cout<<"\nPlease wait while reading sequences and concatenating..."<<endl;
  39
  40                 string temp="", name="", str="";
  41
  42                 while (getline(is, temp, '\n')) {
  43
  44                         name = temp;
  45
  46                         getline(is, temp, '\n');
  47                         while (temp!="") {
  48                                 str += temp;
  49                                 getline(is, temp, '\n');
  50                         }
  51
  52                         seq1 += str.substr(0, str.length()/2);
  53                         seq2 += str.substr(str.length()/2, str.length()/2);
  54                         name = str = "";
  55                 }
  56
  57                 is.close();
  58                 is.clear();
  59
  60                 result += "Concatenate-";       result += filename;     result += '\n';
  61                 result += seq1;         result += '\n';
  62                 result += seq2;         result += '\n';
  63                 result += '\n';
  64
  65         }
  66         catch (...) {
  67
  68                 flag = false;
  69         }
  70
  71         return flag;
  72 }
  73
  74 bool writeFile(const char *filename, const char *content) {
  75
  76         bool flag=true;
  77
  78         try {
  79                 ofstream os(filename);
  80                 os<<content;
  81                 os.close();
  82         }
  83         catch (...) {
  84                 cout<<"Error in writing file..."<<endl;
  85                 flag = false;
  86         }
  87
  88         return flag;
  89 }
  90
  91
  92 int main(int argc, char* argv[]) {
  93
  94         if (argc!=3) {
  95                 cout<<"Description: Concatenate all pairs of sequences with AXT format to a pair of sequences."<<endl;
  96                 cout<<"Usage: ConPairs [AXT Filename] [Output Filename]"<<endl;
  97                 return 0;
  98         }
  99
 100         try {
 101                 if (!readFile(argv[1])) throw 1;
 102                 if (!writeFile(argv[2], result.c_str())) throw 1;
 103                 cout<<"Mission accomplished."<<endl;
 104
 105         }
 106         catch (...) {
 107                 cout<<"Mission failed."<<endl;
 108         }
 109
 110         return 1;
 111 }