add: function checkaligned, format the arg, clean code
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2 changed files with 329 additions and 271 deletions
47
README.md
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47
README.md
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# MiMi
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```
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／l、 . . . .
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（ﾟ､ ｡ ７ |\/|*|\/|*
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l ~ヽ | ||| ||
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じしf_,)ノ | ||| ||
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Morphology into Molecules into
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GPL Guoyi Zhang, 2023
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```
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## Functions
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Convert any formats listed in `Accepted formats` to each other.
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## Arguments
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- -h --help;
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- -i --input ${filename};
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- -o --output ${filename};
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## Accepted formats
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- fas fasta
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- nex nexus
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- phy phylip
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- tnt ss
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## Compile
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```
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g++ main.cpp -o mimi
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```
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## License
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You should note that the license is (GPL)[https://www.gnu.org/licenses/gpl-3.0.html].
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## Acknowledgements
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Thanks to my beloved daughter MiMi (Ragdoll cat) for accompanying me in my life, mom loves you forever.
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73
main.cpp
73
main.cpp
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@ -1,8 +1,8 @@
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#include <iostream>
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#include <algorithm>
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#include <fstream>
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#include <iostream>
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#include <sstream>
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#include <string>
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#include <algorithm>
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using namespace std;
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@ -10,18 +10,15 @@ class Basic_arg{
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public:
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int intype = 0, outype = 0;
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char *itn, *otn;
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Basic_arg(int intype, int outype, char* itn, char *otn):
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intype(intype), outype(outype),
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itn(itn), otn(otn)
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{};
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Basic_arg(int intype, int outype, char* itn, char* otn)
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: intype(intype), outype(outype), itn(itn), otn(otn){};
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};
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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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Sample(unsigned ntax, unsigned nchar) : 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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@ -55,16 +52,19 @@ Sample readPhy(char* itn){
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string sntax, snseq, snall;
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getline(matrixfile, snall);
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istringstream istr(snall);
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istr >> sntax; istr >> snseq;
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istr >> sntax;
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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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ntax = stoi(sntax);
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nchar = stoi(snseq); // string to int
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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(matrixfile, snall);
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istringstream istr(snall);
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istr >> sam.taxas[lennum]; istr >> sam.chars[lennum];
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istr >> sam.taxas[lennum];
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istr >> sam.chars[lennum];
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}
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matrixfile.close();
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// return to class
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@ -136,7 +136,8 @@ Sample readTnt(char* itn){
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for (int i = 0; i < 1;) {
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getline(matrixfile, stri);
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istringstream istr(stri);
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istr >> snchar; istr >> sntax;
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istr >> snchar;
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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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@ -150,7 +151,8 @@ Sample readTnt(char* itn){
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for (lennum = 0; lennum < sam.ntax; lennum++) {
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getline(matrixfile, stri);
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istringstream istr(stri);
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istr >> sam.taxas[lennum]; istr >> sam.chars[lennum];
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istr >> sam.taxas[lennum];
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istr >> sam.chars[lennum];
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}
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matrixfile.close();
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return sam;
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@ -169,7 +171,8 @@ Sample readNex(char* itn){
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matrixfile.open(itn);
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// some tem
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string snall, stri, str_a, str_b;
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bool found = false, found_ntax = false, found_nchar = false, found_equal = false;
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bool found = false, found_ntax = false, found_nchar = false,
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found_equal = false;
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char x = '=';
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int lnum, eulnum;
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// getline line by line
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@ -214,7 +217,8 @@ Sample readNex(char* itn){
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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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int z = 0;
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int l = 0;
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// read line by line
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while (getline(matrixfile, snall)) {
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// convert to word
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@ -270,7 +274,11 @@ void writeNex(class Sample sam, char* otn){
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string datatype;
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datatype = checktype(sam.chars[0]);
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matrixfile << "#NEXUS" << endl;
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matrixfile << "Begin data;" << endl << "\tDimensions nchar=" << sam.nchar << " ntax=" << sam.ntax << ";" << endl << "\tFormat datatype=" << datatype << " missing=? gap=-;" << endl << "\tMatrix" << endl;
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matrixfile << "Begin data;" << endl
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<< "\tDimensions nchar=" << sam.nchar << " ntax=" << sam.ntax
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<< ";" << endl
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<< "\tFormat datatype=" << datatype << " missing=? gap=-;" << endl
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<< "\tMatrix" << endl;
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for (int i2 = 0; i2 < sam.ntax; i2++) {
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matrixfile << "\t\t" << sam.taxas[i2] << "\t" << sam.chars[i2] << endl;
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}
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@ -281,7 +289,8 @@ void writeNex(class Sample sam, char* otn){
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string checktype(string str) {
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// some var
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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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char ca = 'a', cc = 'c', ct = 't', cg = 'g', czero = '0', cone = '1',
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ctwo = '2';
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string datatype;
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// count fre
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a = countfre(str, ca);
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@ -323,7 +332,6 @@ void writeTnt(class Sample sam, char* otn){
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matrixfile.close();
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}
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Basic_arg procargs(int nargs, char** arg, char* itn, char* otn) {
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int i, sta = 0, intype = 0, outype = 0;
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string para, inputfile, outputfile;
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@ -340,15 +348,13 @@ Basic_arg procargs (int nargs, char ** arg, char* itn, char* otn){
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if (para == "-h" | para == "--help") {
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show_help(1);
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sta = 2;
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}
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else if ( para =="-i"| para=="--input"){
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} else if (para == "-i" | para == "--input") {
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i++;
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itn = arg[i];
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string inputfile(arg[i]);
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intype = checkextension(inputfile);
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sta++;
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}
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else if ( para =="-o"| para=="--output"){
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} else if (para == "-o" | para == "--output") {
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i++;
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otn = arg[i];
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string outputfile(arg[i]);
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@ -394,16 +400,22 @@ int checkextension(string str){
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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 << "MiMi, GPL, Guoyi Zhang, 2023.\nPlease use -h to see more help" << endl;
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cout << "MiMi, GPL, Guoyi Zhang, 2023.\nPlease use -h to see more help"
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<< endl;
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} else {
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cout << "\n ／l、 \t. . . .\n（ﾟ､ ｡ ７ \t|\\/|*|\\/|*\n l ~ヽ \t| ||| ||\n じしf_,)ノ\t| ||| ||\n" << endl;
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cout << "Morphology into Molecules into\n" << "GPL\tGuoyi\tZhang,\t2023\n" << endl;
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cout << "-h\t--help;\n-i\t--input\t\t${filename};\n-o\t--output\t${filename};\n" << endl;
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cout << "Accepted format:\nfas\tfasta;\nnex\tnexus\nphy\tphylip\ntnt\tss" << endl;
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cout << "\n ／l、 \t. . . .\n（ﾟ､ ｡ ７ \t|\\/|*|\\/|*\n l ~ヽ "
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" \t| ||| ||\n じしf_,)ノ\t| ||| ||\n"
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<< endl;
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cout << "Morphology into Molecules into\n"
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<< "GPL;\tGuoyi Zhang;\t2023\n"
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<< endl;
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cout << "-h\t--help;\n-i\t--input\t\t${filename};\n-o\t--output\t${"
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"filename};\n"
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<< endl;
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cout
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<< "Accepted formats:\nfas\tfasta;\nnex\tnexus;\nphy\tphylip;\ntnt\tss;"
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<< endl;
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}
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}
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@ -453,7 +465,6 @@ bool checkalign(class Sample sam){
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return aligned;
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}
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int main(int argc, char** argv) {
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char *itn, *otn;
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Basic_arg arguvar = procargs(argc, argv, itn, otn);
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