add: function checkaligned, format the arg, clean code

README.md

@@ -0,0 +1,47 @@
+# MiMi
+
+```
+  ／l、    	.  . .  .
+（ﾟ､ ｡ ７    	|\/|*|\/|*
+  l  ~ヽ    	|  |||  ||
+  じしf_,)ノ	|  |||  ||
+
+Morphology into Molecules into
+GPL	Guoyi	Zhang,	2023
+```
+
+## Functions
+
+Convert any formats listed in `Accepted formats` to each other.
+
+## Arguments
+
+- -h	--help;
+
+- -i	--input		${filename};
+
+- -o	--output	${filename};
+
+## Accepted formats
+
+- fas	fasta
+
+- nex	nexus
+
+- phy	phylip
+
+- tnt	ss
+
+## Compile
+
+```
+g++ main.cpp -o mimi
+```
+
+## License
+
+You should note that the license is (GPL)[https://www.gnu.org/licenses/gpl-3.0.html].
+
+## Acknowledgements
+
+Thanks to my beloved daughter MiMi (Ragdoll cat) for accompanying me in my life, mom loves you forever.

main.cpp

@@ -1,8 +1,8 @@
-#include <iostream>
+#include <algorithm>
 #include <fstream>
+#include <iostream>
 #include <sstream>
 #include <string>
-#include <algorithm>
 
 using namespace std;
 
@@ -10,18 +10,15 @@ class Basic_arg{
  public:
   int intype = 0, outype = 0;
   char *itn, *otn;
-	Basic_arg(int intype, int outype, char* itn, char *otn):
+  Basic_arg(int intype, int outype, char* itn, char* otn)
-		intype(intype), outype(outype),
+      : intype(intype), outype(outype), itn(itn), otn(otn){};
-		itn(itn), otn(otn)
-	{}; 
 };
 
 class Sample {
  public:
   unsigned ntax, nchar;
   string *taxas, *chars;
-	Sample(unsigned ntax, unsigned nchar):
+  Sample(unsigned ntax, unsigned nchar) : ntax(ntax), nchar(nchar) {
-       		ntax(ntax), nchar(nchar) {
     taxas = new string[ntax];
     chars = new string[ntax];
   };
@@ -55,16 +52,19 @@ Sample readPhy(char* itn){
   string sntax, snseq, snall;
   getline(matrixfile, snall);
   istringstream istr(snall);
-  istr >> sntax; istr >> snseq;
+  istr >> sntax;
+  istr >> snseq;
   int ntax, nchar;
-  ntax = stoi (sntax); nchar = stoi (snseq); // string to int
+  ntax = stoi(sntax);
+  nchar = stoi(snseq);  // string to int
   Sample sam(ntax, nchar);
   // read sequence
   int lennum;
   for (lennum = 0; lennum < sam.ntax; lennum++) {
     getline(matrixfile, snall);
     istringstream istr(snall);
-    istr >> sam.taxas[lennum]; istr >> sam.chars[lennum];
+    istr >> sam.taxas[lennum];
+    istr >> sam.chars[lennum];
   }
   matrixfile.close();
   // return to class
@@ -136,7 +136,8 @@ Sample readTnt(char* itn){
   for (int i = 0; i < 1;) {
     getline(matrixfile, stri);
     istringstream istr(stri);
-      istr >> snchar; istr >> sntax;
+    istr >> snchar;
+    istr >> sntax;
     if (isNum(sntax) && isNum(snchar)) {
       ntax = stoi(sntax);
       nchar = stoi(snchar);
@@ -150,7 +151,8 @@ Sample readTnt(char* itn){
   for (lennum = 0; lennum < sam.ntax; lennum++) {
     getline(matrixfile, stri);
     istringstream istr(stri);
-    istr >> sam.taxas[lennum]; istr >> sam.chars[lennum];
+    istr >> sam.taxas[lennum];
+    istr >> sam.chars[lennum];
   }
   matrixfile.close();
   return sam;
@@ -169,7 +171,8 @@ Sample readNex(char* itn){
   matrixfile.open(itn);
   // some tem
   string snall, stri, str_a, str_b;
-  bool found = false, found_ntax = false, found_nchar = false, found_equal = false;
+  bool found = false, found_ntax = false, found_nchar = false,
+       found_equal = false;
   char x = '=';
   int lnum, eulnum;
   // getline line by line
@@ -214,7 +217,8 @@ Sample readNex(char* itn){
   // create class
   Sample sam(ntax, nchar);
   // some temp, z is line number, l is the string arrary number
-  int z=0; int l=0;
+  int z = 0;
+  int l = 0;
   // read line by line
   while (getline(matrixfile, snall)) {
     // convert to word
@@ -270,7 +274,11 @@ void writeNex(class Sample sam, char* otn){
   string datatype;
   datatype = checktype(sam.chars[0]);
   matrixfile << "#NEXUS" << endl;
-      matrixfile << "Begin data;" << endl << "\tDimensions nchar=" << sam.nchar << " ntax=" << sam.ntax << ";" << endl << "\tFormat datatype=" << datatype << " missing=? gap=-;" << endl << "\tMatrix" << endl;
+  matrixfile << "Begin data;" << endl
+             << "\tDimensions nchar=" << sam.nchar << " ntax=" << sam.ntax
+             << ";" << endl
+             << "\tFormat datatype=" << datatype << " missing=? gap=-;" << endl
+             << "\tMatrix" << endl;
   for (int i2 = 0; i2 < sam.ntax; i2++) {
     matrixfile << "\t\t" << sam.taxas[i2] << "\t" << sam.chars[i2] << endl;
   }
@@ -281,7 +289,8 @@ void writeNex(class Sample sam, char* otn){
 string checktype(string str) {
   // some var
   float a, c, t, g, zero, one, two, dna, standard;
-  char ca='a', cc='c', ct='t', cg='g', czero='0', cone='1', ctwo='2';
+  char ca = 'a', cc = 'c', ct = 't', cg = 'g', czero = '0', cone = '1',
+       ctwo = '2';
   string datatype;
   // count fre
   a = countfre(str, ca);
@@ -323,7 +332,6 @@ void writeTnt(class Sample sam, char* otn){
   matrixfile.close();
 }
 
-
 Basic_arg procargs(int nargs, char** arg, char* itn, char* otn) {
   int i, sta = 0, intype = 0, outype = 0;
   string para, inputfile, outputfile;
@@ -340,15 +348,13 @@ Basic_arg procargs (int nargs, char ** arg, char* itn, char* otn){
     if (para == "-h" | para == "--help") {
       show_help(1);
       sta = 2;
-    }   
+    } else if (para == "-i" | para == "--input") {
-    else if ( para =="-i"| para=="--input"){
       i++;
       itn = arg[i];
       string inputfile(arg[i]);
       intype = checkextension(inputfile);
       sta++;
-    }
+    } else if (para == "-o" | para == "--output") {
-    else if ( para =="-o"| para=="--output"){
       i++;
       otn = arg[i];
       string outputfile(arg[i]);
@@ -394,16 +400,22 @@ int checkextension(string str){
 }
 
 void show_help(int help_num) {
-
-
-
   if (help_num == 0) {
-    cout  << "MiMi, GPL, Guoyi Zhang, 2023.\nPlease use -h to see more help" << endl;
+    cout << "MiMi, GPL, Guoyi Zhang, 2023.\nPlease use -h to see more help"
+         << endl;
   } else {
-    cout << "\n  ／l、    \t.  . .  .\n（ﾟ､ ｡ ７    \t|\\/|*|\\/|*\n  l  ~ヽ    \t|  |||  ||\n  じしf_,)ノ\t|  |||  ||\n" << endl;
+    cout << "\n  ／l、    \t.  . .  .\n（ﾟ､ ｡ ７    \t|\\/|*|\\/|*\n  l  ~ヽ   "
-    cout << "Morphology into Molecules into\n" << "GPL\tGuoyi\tZhang,\t2023\n" << endl;
+            " \t|  |||  ||\n  じしf_,)ノ\t|  |||  ||\n"
-    cout << "-h\t--help;\n-i\t--input\t\t${filename};\n-o\t--output\t${filename};\n" << endl;
+         << endl;
-    cout << "Accepted format:\nfas\tfasta;\nnex\tnexus\nphy\tphylip\ntnt\tss" << endl;
+    cout << "Morphology into Molecules into\n"
+         << "GPL;\tGuoyi Zhang;\t2023\n"
+         << endl;
+    cout << "-h\t--help;\n-i\t--input\t\t${filename};\n-o\t--output\t${"
+            "filename};\n"
+         << endl;
+    cout
+        << "Accepted formats:\nfas\tfasta;\nnex\tnexus;\nphy\tphylip;\ntnt\tss;"
+        << endl;
   }
 }
 
@@ -453,7 +465,6 @@ bool checkalign(class Sample sam){
   return aligned;
 }
 
-
 int main(int argc, char** argv) {
   char *itn, *otn;
   Basic_arg arguvar = procargs(argc, argv, itn, otn);