459 lines
11 KiB
C++
459 lines
11 KiB
C++
#include <iostream>
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#include <fstream>
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#include <sstream>
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#include <string>
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#include <vector>
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#include <algorithm>
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using namespace std;
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int intype=0, outype=0;
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char *fn;
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char *otn;
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class Sample {
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public:
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unsigned ntax, nchar;
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string *taxas, *chars;
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Sample(unsigned ntax, unsigned nchar):
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ntax(ntax), nchar(nchar) {
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taxas = new string[ntax];
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chars = new string[ntax];
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};
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// ~Sample(){
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// delete[] taxas;
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// delete[] chars;
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// }
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};
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void show_help(int help_num);
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Sample read_input();
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Sample readFas();
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Sample readPhy();
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Sample readTnt();
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Sample readNex();
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void write_output(class Sample sam);
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void writeFas(class Sample sam);
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void writePhy(class Sample sam);
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void writeTnt(class Sample sam);
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void writeNex(class Sample sam);
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bool isNum(string strnum);
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string to_lower(string stri);
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string add_space(char x, string str_old);
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string checktype(string str);
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int countfre(string str, char c);
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Sample readPhy(){
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//read file
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ifstream seqfile;
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seqfile.open(fn);
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//read number of taxa and charcter
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string sntax, snseq, snall;
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cout << "Reading from the file" << endl;
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getline(seqfile,snall);
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istringstream istr(snall);
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istr >> sntax; istr >> snseq;
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int ntax, nchar;
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ntax = stoi (sntax); nchar = stoi (snseq); // string to int
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cout << "ntax=" << ntax << " nseq=" << nchar << endl;
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Sample sam(ntax, nchar);
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//read sequence
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int lennum;
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for(lennum=0;lennum<sam.ntax;lennum++){
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getline(seqfile,snall);
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istringstream istr(snall);
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istr >> sam.taxas[lennum]; istr >> sam.chars[lennum];
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cout << "tax" << lennum << " is " << sam.taxas[lennum] << "; seq" << lennum << " is " << sam.chars[lennum] << endl;
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}
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seqfile.close();
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// return to class
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return sam;
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}
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Sample readFas(){
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int ntax, nchar, lnum;
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ifstream seqfile;
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seqfile.open(fn);
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// check line number and taxa number
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ntax = 0;
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string temln;
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for(lnum=0;getline(seqfile,temln);lnum++){
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if(temln[0]=='>'){
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ntax++;
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}
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}
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cout << "lnum= " << lnum << ", ntax= " << ntax << endl;
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seqfile.clear();
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seqfile.seekg(0);
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// check the nchar
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string *str_a = new string;
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string *str_b = new string;
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int r = lnum/ntax;
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for (int i=0; i<r;i++){
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getline(seqfile, *str_a);
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if(i>0){
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*str_b = *str_b + *str_a;
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}
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}
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nchar = (*str_b).length();
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delete str_a;
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str_a = nullptr;
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delete str_b;
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str_b = nullptr;
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cout << "ntax= " << ntax << ", nchar= " << nchar << endl;
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seqfile.clear();
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seqfile.seekg(0);
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// create class
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Sample sam(ntax, nchar);
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// get class
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string *str_c = new string;
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for (int a=1, b=0;a<=lnum;a++){
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if(a%r==1){
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getline(seqfile,sam.taxas[b]);
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sam.taxas[b].erase(0,1);
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}
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if(a%r>1){
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getline(seqfile,*str_c);
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sam.chars[b] = sam.chars[b] + *str_c;
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}
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if(a%r==0){
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getline(seqfile,*str_c);
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sam.chars[b] = sam.chars[b] + *str_c;
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b++;
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}
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}
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delete str_c;
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str_c = nullptr;
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seqfile.close();
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return sam;
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}
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Sample readTnt(){
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int ntax, nchar;
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ifstream seqfile;
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seqfile.open(fn);
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// get nchar and ntax
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string stri, sntax, snchar;
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for(int i=0;i<1;){
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getline(seqfile,stri);
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istringstream istr(stri);
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istr >> snchar; istr >> sntax;
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if(isNum(sntax) && isNum(snchar)){
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ntax=stoi(sntax);
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nchar=stoi(snchar);
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i++;
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}
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}
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// create class
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Sample sam(ntax,nchar);
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// get class
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int lennum;
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for(lennum=0;lennum<sam.ntax;lennum++){
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getline(seqfile,stri);
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istringstream istr(stri);
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istr >> sam.taxas[lennum]; istr >> sam.chars[lennum];
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cout << "tax" << lennum << " is " << sam.taxas[lennum] << "; seq" << lennum << " is " << sam.chars[lennum] << endl;
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}
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seqfile.close();
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return sam;
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}
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bool isNum(string strnum) {
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char* p;
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strtol(strnum.c_str(), &p, 10);
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return *p == 0;
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}
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Sample readNex(){
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int ntax, nchar;
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// open file
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ifstream seqfile;
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seqfile.open(fn);
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// some tem
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string snall, stri, str_a, str_b;
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bool found = false;
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bool found_ntax = false;
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bool found_nchar = false;
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bool found_equal = false;
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char x = '=';
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int lnum, e, eulnum;
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e = 0;
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// getline line by line
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for(lnum=0;getline(seqfile,snall);lnum++){
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str_a = to_lower(snall);
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str_b = add_space(x,str_a);
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istringstream istr(str_b);
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// convert to words
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// e will enter the ntax/nchar function just after statisfy the `=`
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while(istr>> stri){
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if(stri=="dimensions"){
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found = true;
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}
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if(stri=="ntax"){
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found_ntax = true;
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}
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if(stri=="nchar"){
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found_nchar = true;
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}
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if(stri=="="){
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found_equal = true;
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}
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if (found_ntax&&found_equal){
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e++;
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if(e>1){
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if(stri.back()==';'){
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stri.pop_back();
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found = false;
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}
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ntax = stoi(stri);
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found_equal = false;
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found_ntax = false;
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e=0;
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}
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}
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if (found_nchar&&found_equal){
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e++;
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if(e>1){
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if(stri.back()==';'){
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stri.pop_back();
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found = false;
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}
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nchar = stoi(stri);
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found_equal = false;
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found_nchar = false;
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e=0;
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}
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}
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if(stri=="matrix"){
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// get the position of matrix
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eulnum = lnum+1;
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}
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}
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}
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// go back
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seqfile.clear();
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seqfile.seekg(0);
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// create class
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Sample sam(ntax,nchar);
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// some temp, z is line number, l is the string arrary number
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int z=0; int l=0;
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// read line by line
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while(getline(seqfile,snall)){
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// convert to word
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istringstream istr(snall);
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// limit the read line number
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if(z>(eulnum-1)&&z<(eulnum+sam.ntax)){
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istr >> sam.taxas[l];
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istr >> sam.chars[l];
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cout << "tax" << l << " is " << sam.taxas[l] << "; seq" << l << " is " << sam.chars[l] << "; l=" << l << endl;
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l++;
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}
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z++;
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}
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return sam;
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}
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string add_space (char x, string str_old) {
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int i;
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string str_new;
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for (i=0; i<str_old.length(); i++) {
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if (str_old[i] != x) {
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str_new=str_new+str_old[i];
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} else {
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str_new=str_new+" "+str_old[i]+" ";
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}
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}
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return str_new;
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}
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string to_lower(string stri){
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transform(stri.begin(),stri.end(),stri.begin(),::tolower);
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return stri;
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}
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void writeFas(class Sample sam){
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ofstream outputFile(otn);
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if (outputFile.is_open()) {
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for(int i=0;i<sam.ntax;i++){
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outputFile << ">" << sam.taxas[i] << endl;
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outputFile << sam.chars[i] << endl;
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}
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} else {
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cout << "File can't be written" << endl;
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}
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outputFile.close();
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}
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void writePhy(class Sample sam){
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ofstream outputFile(otn);
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if (outputFile.is_open()) {
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outputFile << sam.ntax << " " << sam.nchar << endl;
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for(int i=0;i<sam.ntax;i++){
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outputFile << sam.taxas[i] << "\t" << sam.chars[i] << endl;
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}
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} else {
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cout << "File can't be written" << endl;
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}
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outputFile.close();
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}
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void writeNex(class Sample sam){
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ofstream outputFile(otn);
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string datatype;
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datatype = checktype(sam.chars[0]);
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if (outputFile.is_open()) {
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outputFile << "#NEXUS" << endl;
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// outputFile << "Begin TAXA;" << endl << "\tDimensions ntax=" << sam.ntax << ";" << endl << "\tTaxLabels";
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// for(int i1=0;i1<sam.ntax;i1++){
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// outputFile << " " << sam.taxas[i1];
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// }
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// outputFile << ";" << endl << "End;" << endl << endl;
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outputFile << "Begin data;" << endl << "\tDimensions nchar=" << sam.nchar << " ntax=" << sam.ntax << ";" << endl << "\tFormat datatype=" << datatype << " missing=? gap=-;" << endl << "\tMatrix" << endl;
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for(int i2=0;i2<sam.ntax;i2++){
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outputFile << "\t\t" << sam.taxas[i2] << "\t" << sam.chars[i2] << endl;
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}
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outputFile << "\t;" << endl << "End;" << endl;
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} else {
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cout << "File can't be written" << endl;
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}
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outputFile.close();
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}
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string checktype(string str){
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float a, c, t, g, zero, one, two, dna, standard;
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char ca='a', cc='c', ct='t', cg='g', czero='0', cone='1', ctwo='2';
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string datatype;
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a = countfre(str, ca);
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c = countfre(str, cc);
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t = countfre(str, ct);
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g = countfre(str, cg);
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zero = countfre(str, czero);
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one = countfre(str, cone);
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two = countfre(str, ctwo);
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dna = a+c+t+g;
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standard = zero+one+two;
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if((dna/str.length())>0.7){
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datatype = "dna";
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} else if ((standard/str.length())>0.7){
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datatype = "standard";
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} else {
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datatype = "protein";
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}
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return datatype;
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}
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int countfre(string str, char c){
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int num;
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str = to_lower(str);
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num = count(str.begin(),str.end(),c);
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return num;
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}
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void writeTnt(class Sample sam){
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ofstream outputFile(otn);
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if (outputFile.is_open()) {
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outputFile << "xread" << endl << "\' \'" << endl;
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outputFile << sam.nchar << " " << sam.ntax << endl;
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for(int i=0;i<sam.ntax;i++){
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outputFile << sam.taxas[i] << "\t" << sam.chars[i] << endl;
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}
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outputFile << "proc / ;" << endl;
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} else {
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cout << "File can't be written" << endl;
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}
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outputFile.close();
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}
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void procargs (int nargs, char ** arg){ //*arg 视为整体，是字符串指针
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int i;
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char * cp;//cp 字符指针 *p 第一个char
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//string ext1, ext2;
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//no arg, show help
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if (nargs==1){
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show_help(0);
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exit(0);
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}
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//recognize arg
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for (i=1;i<nargs;i++){
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cp = *(arg+i);
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//error arg
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if (*cp != '-'){
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cout << "Unknown arguments, please use -h to check" << endl;
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exit(0);
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}
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//check arg
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switch (*++cp){//先++
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case 'f':
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cp++;
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if (*cp=='f') {intype=1; cout << "intype is fasta, " << intype << endl;}
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if (*cp=='n') intype=2;
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if (*cp=='p') {intype=3; cout << "intype is phylip, " << intype << endl;}
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if (*cp=='t') {intype=4;}
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break;
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case 'h': show_help(1); break;
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case 'i': cp++; fn = cp; break;
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case 'o': cp++; otn = cp; break;
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case 't':
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cp++;
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if (*cp=='f') outype=1;
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if (*cp=='n') outype=2;
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if (*cp=='p') {outype=3; cout << "outype is phylip, " << intype << endl;}
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if (*cp=='t') outype=4;
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break;
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default: cout << "Unrecognized agruments " << *(arg+i) << endl; exit(0);
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}
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}
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}
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void show_help (int help_num){
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if (help_num == 0){
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cout << "SeqConvert GPL, please use -h to see more help" << endl;
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} else {
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cout << "-f from: -ff fasta; -fn nexus; -fp phylip;\n-h help;\n-i input: -i${filename};" << endl;
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}
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}
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Sample read_input (void){
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int ntax, nchar;
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Sample sam(ntax,nchar);
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if (intype==1) sam = readFas();
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if (intype==2) sam = readNex();
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if (intype==3) sam = readPhy();
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if (intype==4) sam = readTnt();
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return sam;
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}
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void write_output (class Sample sam){
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if (outype==1) writeFas(sam);
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if (outype==2) writeNex(sam);
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if (outype==3) writePhy(sam);
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if (outype==4) writeTnt(sam);
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}
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bool checkalign(class Sample sam){
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int a=0, b=0;
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a = sam.chars[0].length();
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bool aligned = true;
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for(int i=1;i<(sam.ntax-1)&&aligned;i++){
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b = sam.chars[i].length();
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aligned = (a==b);
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}
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return aligned;
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}
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int main(int argc, char **argv){
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procargs (argc, argv);
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if(intype!=0&&outype!=0){
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Sample sam = read_input();
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write_output(sam);
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}
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int i;
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for (i = 0; i < argc; i++) cout << "argument "<< i << " is " << *(argv+i) << endl;
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return 1;
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}
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