From 5a337fd47a72e1cacf00e381126f87e4f81338a4 Mon Sep 17 00:00:00 2001
From: Kuoi <starsareintherose@outlook.com>
Date: Mon, 20 Mar 2023 14:30:42 +0800
Subject: [PATCH] add: function checkaligned and format the arg

---
 main.cpp | 425 ++++++++++++++++++++++++++++---------------------------
 1 file changed, 219 insertions(+), 206 deletions(-)

diff --git a/main.cpp b/main.cpp
index c966931..81ce952 100644
--- a/main.cpp
+++ b/main.cpp
@@ -2,14 +2,19 @@
 #include <fstream>
 #include <sstream> 
 #include <string>
-#include <vector>
 #include <algorithm>
 
 using namespace std;
 
-int intype=0, outype=0;
-char *fn;
-char *otn;
+class Basic_arg{
+public:
+	int intype=0, outype=0;
+	char *itn, *otn;
+	Basic_arg(int intype, int outype, char* itn, char *otn):
+		intype(intype), outype(outype),
+		itn(itn), otn(otn)
+	{}; 
+};
 
 class Sample {
 public:
@@ -20,77 +25,72 @@ public:
 			taxas = new string[ntax];
 			chars = new string[ntax];
 		};
-//	~Sample(){
-//		delete[] taxas;
-//		delete[] chars;	
-//	}
 };
 
+Basic_arg procargs (int nargs, char ** arg, char* itn, char* otn);
+Sample read_input(char* itn, int intype);
 void show_help(int help_num);
-Sample read_input();
-Sample readFas();
-Sample readPhy();
-Sample readTnt();
-Sample readNex();
-void write_output(class Sample sam);
-void writeFas(class Sample sam);
-void writePhy(class Sample sam);
-void writeTnt(class Sample sam);
-void writeNex(class Sample sam);
+Sample readFas(char* itn);
+Sample readPhy(char* itn);
+Sample readTnt(char* itn);
+Sample readNex(char* itn);
+void write_output(class Sample sam, char* otn, int outype);
+void writeFas(class Sample sam, char* otn);
+void writePhy(class Sample sam, char* otn);
+void writeTnt(class Sample sam, char* otn);
+void writeNex(class Sample sam, char* otn);
 bool isNum(string strnum);
+bool checkalign(class Sample sam);
 string to_lower(string stri);
 string add_space(char x, string str_old);
 string checktype(string str);
 int countfre(string str, char c);
-
-Sample readPhy(){
+int checkextension(string str);
+	
+Sample readPhy(char* itn){
   //read file
-  ifstream seqfile;
-  seqfile.open(fn);
+  ifstream matrixfile;
+  matrixfile.open(itn);
   //read number of taxa and charcter
   string sntax, snseq, snall;
-  cout << "Reading from the file" << endl; 
-  getline(seqfile,snall);
+  getline(matrixfile,snall);
   istringstream istr(snall); 
   istr >> sntax; istr >> snseq;
   int ntax, nchar;
   ntax = stoi (sntax); nchar = stoi (snseq); // string to int
-  cout << "ntax=" << ntax << " nseq=" << nchar << endl;
   Sample sam(ntax, nchar);   
   //read sequence
   int lennum;
   for(lennum=0;lennum<sam.ntax;lennum++){
-    getline(seqfile,snall);
+    getline(matrixfile,snall);
     istringstream istr(snall);
     istr >> sam.taxas[lennum]; istr >> sam.chars[lennum];
-   cout << "tax" << lennum << " is " << sam.taxas[lennum] << "; seq" << lennum << " is " << sam.chars[lennum] << endl;   
   }
-  seqfile.close();
+  matrixfile.close();
   // return to class
   return sam;
 }
 
-Sample readFas(){
+Sample readFas(char* itn){
   int ntax, nchar, lnum;
-  ifstream seqfile;
-  seqfile.open(fn);
+  ifstream matrixfile;
+  matrixfile.open(itn);
   // check line number and taxa number
   ntax = 0;
   string temln;
-  for(lnum=0;getline(seqfile,temln);lnum++){
+  for(lnum=0;getline(matrixfile,temln);lnum++){
     if(temln[0]=='>'){
       ntax++;
     }
   }
-  cout << "lnum= " << lnum << ", ntax= " << ntax << endl;
-  seqfile.clear();
-  seqfile.seekg(0);
+  matrixfile.clear();
+  matrixfile.seekg(0);
   // check the nchar
   string *str_a = new string;
   string *str_b = new string;
   int r = lnum/ntax;
   for (int i=0; i<r;i++){
-    getline(seqfile, *str_a);
+    getline(matrixfile, *str_a);
     if(i>0){
        *str_b = *str_b + *str_a; 
     } 
@@ -100,42 +100,41 @@ Sample readFas(){
   str_a = nullptr;
   delete str_b;
   str_b = nullptr;
-  cout << "ntax= " << ntax << ", nchar= " << nchar << endl; 
-  seqfile.clear();
-  seqfile.seekg(0);
+  matrixfile.clear();
+  matrixfile.seekg(0);
   // create class
   Sample sam(ntax, nchar);
   // get class
   string *str_c = new string;
   for (int a=1, b=0;a<=lnum;a++){
     if(a%r==1){
-      getline(seqfile,sam.taxas[b]);
+      getline(matrixfile,sam.taxas[b]);
       sam.taxas[b].erase(0,1);  
     }
     if(a%r>1){
-      getline(seqfile,*str_c);
+      getline(matrixfile,*str_c);
       sam.chars[b] = sam.chars[b] + *str_c;
     }
     if(a%r==0){
-      getline(seqfile,*str_c);
+      getline(matrixfile,*str_c);
       sam.chars[b] = sam.chars[b] + *str_c;
       b++;
     }   
   }
   delete str_c;
   str_c = nullptr; 
-  seqfile.close();
+  matrixfile.close();
   return sam;
 }
 
-Sample readTnt(){
+Sample readTnt(char* itn){
   int ntax, nchar;
-  ifstream seqfile;
-  seqfile.open(fn);
+  ifstream matrixfile;
+  matrixfile.open(itn);
   // get nchar and ntax
   string stri, sntax, snchar;
   for(int i=0;i<1;){
-      getline(seqfile,stri);
+      getline(matrixfile,stri);
       istringstream istr(stri); 
       istr >> snchar; istr >> sntax;
       if(isNum(sntax) && isNum(snchar)){
@@ -149,12 +148,11 @@ Sample readTnt(){
   // get class
   int lennum;
   for(lennum=0;lennum<sam.ntax;lennum++){
-    getline(seqfile,stri);
+    getline(matrixfile,stri);
     istringstream istr(stri);
     istr >> sam.taxas[lennum]; istr >> sam.chars[lennum];
-   cout << "tax" << lennum << " is " << sam.taxas[lennum] << "; seq" << lennum << " is " << sam.chars[lennum] << endl;   
   }
-  seqfile.close();
+  matrixfile.close();
   return sam;
 }
 
@@ -164,90 +162,67 @@ bool isNum(string strnum) {
 	return *p == 0;
 }
 
-Sample readNex(){
+Sample readNex(char* itn){
   int ntax, nchar;
   // open file 
-  ifstream seqfile;
-  seqfile.open(fn);
+  ifstream matrixfile;
+  matrixfile.open(itn);
   // some tem 
   string snall, stri, str_a, str_b;
-  bool found = false;
-  bool found_ntax = false;
-  bool found_nchar = false;
-  bool found_equal = false;
+  bool found = false, found_ntax = false, found_nchar = false, found_equal = false;
   char x = '=';
-  int lnum, e, eulnum;
-  e = 0;
+  int lnum, eulnum;
   // getline line by line
-  for(lnum=0;getline(seqfile,snall);lnum++){
+  for(lnum=0;getline(matrixfile,snall);lnum++){
   str_a = to_lower(snall);
   str_b = add_space(x,str_a);
   istringstream istr(str_b);
         // convert to words
-	// e will enter the ntax/nchar function just after statisfy the `=`
 	while(istr>> stri){
 	if(stri=="dimensions"){
 		found = true;
+	} else if(stri=="ntax"){
+		found_ntax = true;
+	} else if(stri=="nchar"){
+		found_nchar = true;
+	} else if(stri=="="){
+		found_equal = true;
+	} else if (found_ntax&&found_equal){
+		if(stri.back()==';'){
+			stri.pop_back();
+			found = false;
+		}
+		ntax = stoi(stri);
+		found_equal = false;
+		found_ntax = false;	
+	} else if (found_nchar&&found_equal){
+		if(stri.back()==';'){
+			stri.pop_back();
+			found = false;
+		} 
+		nchar = stoi(stri);
+		found_equal = false;
+		found_nchar = false;
+	} else if (stri=="matrix"){
+		eulnum = lnum+1;
 	} 
-	
-		if(stri=="ntax"){
-			found_ntax = true;
-		}
-		if(stri=="nchar"){
-			found_nchar = true;
-		}
-		if(stri=="="){
-			found_equal = true;
-		}
-		if (found_ntax&&found_equal){
-			e++;
-		       if(e>1){	
-			if(stri.back()==';'){
-				stri.pop_back();
-				found = false;
-			}
-			ntax = stoi(stri);
-			found_equal = false;
-			found_ntax = false;	
-			e=0;
-		       }
-		}
-		
-		if (found_nchar&&found_equal){
-			e++;
-			if(e>1){
-			if(stri.back()==';'){
-				stri.pop_back();
-				found = false;
-			} 
-			nchar = stoi(stri);
-			found_equal = false;
-			found_nchar = false;
-			e=0;
-			}
-		}
-		if(stri=="matrix"){
-			// get the position of matrix
-			eulnum = lnum+1;
-		}
     }
   }
   // go back
-  seqfile.clear();
-  seqfile.seekg(0);
+  matrixfile.clear();
+  matrixfile.seekg(0);
   // create class
   Sample sam(ntax,nchar);
   // some temp, z is line number, l is the string arrary number
   int z=0; int l=0;
   // read line by line
-  while(getline(seqfile,snall)){
+  while(getline(matrixfile,snall)){
   // convert to word
   istringstream istr(snall);
   // limit the read line number
   if(z>(eulnum-1)&&z<(eulnum+sam.ntax)){
     istr >> sam.taxas[l];
     istr >> sam.chars[l];
-    cout << "tax" << l << " is " << sam.taxas[l] << "; seq" << l << " is " << sam.chars[l] << "; l=" << l << endl; 
     l++;
   }
   z++;
@@ -272,58 +247,43 @@ string to_lower(string stri){
   return stri;
 }
 
-void writeFas(class Sample sam){
-  ofstream outputFile(otn);
-  if (outputFile.is_open()) {
+void writeFas(class Sample sam, char* otn){
+  ofstream matrixfile(otn);
       for(int i=0;i<sam.ntax;i++){
-        outputFile << ">" << sam.taxas[i] << endl;
-        outputFile << sam.chars[i] << endl;
+        matrixfile << ">" << sam.taxas[i] << endl;
+        matrixfile << sam.chars[i] << endl;
       }
-    } else {
-      cout << "File can't be written" << endl;
-    }
-  outputFile.close();
+  matrixfile.close();
 }
 
-void writePhy(class Sample sam){
-  ofstream outputFile(otn);
-  if (outputFile.is_open()) {
-      outputFile << sam.ntax << " " << sam.nchar << endl;
+void writePhy(class Sample sam, char* otn){
+  ofstream matrixfile(otn);
+      matrixfile << sam.ntax << " " << sam.nchar << endl;
       for(int i=0;i<sam.ntax;i++){
-        outputFile << sam.taxas[i] << "\t" << sam.chars[i]  << endl;
+        matrixfile << sam.taxas[i] << "\t" << sam.chars[i]  << endl;
       }
-    } else {
-      cout << "File can't be written" << endl;
-    }
-  outputFile.close();
+  matrixfile.close();
 }
 
-void writeNex(class Sample sam){
-  ofstream outputFile(otn);
+void writeNex(class Sample sam, char* otn){
+  ofstream matrixfile(otn);
   string datatype;
   datatype = checktype(sam.chars[0]);
-  if (outputFile.is_open()) {
-      outputFile << "#NEXUS" << endl; 
-//      outputFile << "Begin TAXA;" << endl << "\tDimensions ntax=" << sam.ntax << ";" << endl << "\tTaxLabels";
-//      for(int i1=0;i1<sam.ntax;i1++){
-//        outputFile << " " << sam.taxas[i1];
-//      }
-//      outputFile << ";" << endl << "End;" << endl << endl;
-      outputFile << "Begin data;" << endl << "\tDimensions nchar=" << sam.nchar << " ntax=" << sam.ntax << ";" << endl << "\tFormat datatype=" << datatype << " missing=? gap=-;" << endl << "\tMatrix" << endl;
+      matrixfile << "#NEXUS" << 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++){
-        outputFile << "\t\t" << sam.taxas[i2] << "\t" << sam.chars[i2] << endl;
+        matrixfile << "\t\t" << sam.taxas[i2] << "\t" << sam.chars[i2] << endl;
       }
-      outputFile << "\t;" << endl << "End;" << endl;
-    } else {
-      cout << "File can't be written" << endl;
-    }
-  outputFile.close();
+      matrixfile << "\t;" << endl << "End;" << endl;
+  matrixfile.close();
 }
 
 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';
   string datatype;
+  // count fre
   a = countfre(str, ca);
   c = countfre(str, cc);
   t = countfre(str, ct);
@@ -331,10 +291,10 @@ string checktype(string str){
   zero = countfre(str, czero);
   one = countfre(str, cone);
   two = countfre(str, ctwo);
-
+  // summary dna or morphology
   dna = a+c+t+g;
   standard = zero+one+two;
-
+  // use percentage to test
   if((dna/str.length())>0.7){
       datatype = "dna"; 
   } else if ((standard/str.length())>0.7){
@@ -352,107 +312,160 @@ int countfre(string str, char c){
   return num; 
 }
 
-void writeTnt(class Sample sam){
-  ofstream outputFile(otn);
-  if (outputFile.is_open()) { 
-      outputFile << "xread" << endl << "\' \'" << endl;
-      outputFile << sam.nchar << " " << sam.ntax << endl;
+void writeTnt(class Sample sam, char* otn){
+  ofstream matrixfile(otn);
+      matrixfile << "xread" << endl << "\' \'" << endl;
+      matrixfile << sam.nchar << " " << sam.ntax << endl;
       for(int i=0;i<sam.ntax;i++){
-        outputFile << sam.taxas[i] << "\t" << sam.chars[i]  << endl;
+        matrixfile << sam.taxas[i] << "\t" << sam.chars[i]  << endl;
       }
-      outputFile << "proc / ;" << endl;
-    } else {
-      cout << "File can't be written" << endl;
-    }
-  outputFile.close();
+      matrixfile << "proc / ;" << endl;
+  matrixfile.close();
 }
 
 
-void procargs (int nargs, char ** arg){ //*arg 视为整体，是字符串指针
-  int i;
-  char * cp;//cp 字符指针 *p 第一个char
-  //string ext1, ext2;
+Basic_arg procargs (int nargs, char ** arg, char* itn, char* otn){
+  int i, sta = 0, intype=0, outype=0;
+  string para, inputfile, outputfile;
   //no arg, show help
   if (nargs==1){
     show_help(0);
     exit(0);
+    sta=2;
   }
   //recognize arg
   for (i=1;i<nargs;i++){
-    cp = *(arg+i);
-    //error arg
-    if (*cp != '-'){
-      cout << "Unknown arguments, please use -h to check" << endl;
+    //to string
+    string para (arg[i]);
+    if ( para =="-h"| para=="--help" ) {
+	    show_help(1);
+	    sta=2;
+    }   
+    else if ( para =="-i"| para=="--input"){
+    	i++;
+	itn=arg[i];
+        string inputfile (arg[i]);
+        intype = checkextension(inputfile);
+	sta++;	
+    }
+    else if ( para =="-o"| para=="--output"){
+        i++;
+	otn=arg[i];
+        string outputfile (arg[i]);
+        outype = checkextension(outputfile);
+	sta++;	
+    } else {
+      cout << "MiMi\tUnknown arguments, please use -h to check" << endl;
       exit(0);
     }
-    //check arg
-    switch (*++cp){//先++
-      case 'f':
-        cp++;
-	if (*cp=='f') {intype=1;  cout << "intype is fasta, " << intype << endl;}
-	if (*cp=='n') intype=2;
-	if (*cp=='p') {intype=3; cout << "intype is phylip, " << intype << endl;}
-	if (*cp=='t') {intype=4;}
-	break;
-      case 'h': show_help(1); break;
-      case 'i': cp++; fn = cp; break;
-      case 'o': cp++; otn = cp; break;
-      case 't':
-	cp++;
-	if (*cp=='f') outype=1; 
-	if (*cp=='n') outype=2;
-	if (*cp=='p') {outype=3; cout << "outype is phylip, " << intype << endl;}
-	if (*cp=='t') outype=4;
-	break;
-      default: cout << "Unrecognized agruments " << *(arg+i) << endl; exit(0);
-    }
   }
+    if(sta!=2){ 
+	cout << "MiMi\tInput and Output can't be empty" << endl;
+	exit(0);
+  }
+   Basic_arg arguvar(intype,outype,itn,otn);
+   return arguvar;
+}
+
+int checkextension(string str){
+	int loc, type;
+	string extension;
+	loc = str.rfind('.');
+	if(loc){
+	  extension = str.substr(loc+1);
+	} else {
+	  cout << "MiMi\tPlease sepecifc the extension name" << endl;
+	  exit(0);
+	}
+	extension = to_lower(extension);
+	if(extension=="fas"|extension=="fasta"){
+		type = 1;
+	} else if (extension=="nex"|extension=="nexus"){
+		type = 2;
+	} else if (extension=="phy"|extension=="phylip"){
+		type = 3;
+	} else if (extension=="tnt"|extension=="ss"){
+		type = 4;
+	} else {
+		cout << "MiMi\tUnknown format" << endl;
+		exit(0);
+	}	
+	return type;
 }
 
 void show_help (int help_num){
+
+
+
   if (help_num == 0){
-    cout  << "SeqConvert GPL, please use -h to see more help" << endl;
+    cout  << "MiMi, GPL, Guoyi Zhang, 2023.\nPlease use -h to see more help" << endl;
   } else {
-    cout << "-f from: -ff fasta; -fn nexus; -fp phylip;\n-h help;\n-i input: -i${filename};" << endl;
+    cout << "\n  ／l、    \t.  . .  .\n（ﾟ､ ｡ ７    \t|\\/|*|\\/|*\n  l  ~ヽ    \t|  |||  ||\n  じしf_,)ノ\t|  |||  ||\n" << endl;
+    cout << "Morphology into Molecules into\n" << "GPL\tGuoyi\tZhang,\t2023\n" << endl;
+    cout << "-h\t--help;\n-i\t--input\t\t${filename};\n-o\t--output\t${filename};\n" << endl;
+    cout << "Accepted format:\nfas\tfasta;\nnex\tnexus\nphy\tphylip\ntnt\tss" << endl;
   }
 }
 
-Sample read_input (void){
+Sample read_input (char* itn, int intype){
   int ntax, nchar;
   Sample sam(ntax,nchar);
-  if (intype==1) sam = readFas();
-  if (intype==2) sam = readNex();
-  if (intype==3) sam = readPhy();
-  if (intype==4) sam = readTnt();
+  ifstream matrixfile;
+  matrixfile.open(itn);
+  if (matrixfile.is_open()){
+  if (intype==1) sam = readFas(itn);
+  if (intype==2) sam = readNex(itn);
+  if (intype==3) sam = readPhy(itn);
+  if (intype==4) sam = readTnt(itn);
+  } else {
+    cout << "MiMi\tInput file can't be open" << endl;
+    exit(0);
+  }
   return sam;
 }
 
-void write_output (class Sample sam){
-  if (outype==1) writeFas(sam);
-  if (outype==2) writeNex(sam);
-  if (outype==3) writePhy(sam);
-  if (outype==4) writeTnt(sam);
+void write_output (class Sample sam, char* otn, int outype){
+  ofstream matrixfile(otn);
+  if (matrixfile.is_open()) {
+  if (outype==1) writeFas(sam,otn);
+  if (outype==2) writeNex(sam,otn);
+  if (outype==3) writePhy(sam,otn);
+  if (outype==4) writeTnt(sam,otn);
+  } else {
+    cout << "MiMi\tOutput file can't be open" << endl;
+    exit(0);
+  }
 }
 
 bool checkalign(class Sample sam){
-  int a=0, b=0;
-  a = sam.chars[0].length();
+  int a=0, b=0, x=0;
+  a = sam.nchar;
   bool aligned = true;
-  for(int i=1;i<(sam.ntax-1)&&aligned;i++){
-    b = sam.chars[i].length();
-    aligned = (a==b);
+  for(int i=0;i<sam.ntax;i++){
+  	b=sam.chars[i].length();
+	if(a==b){
+		x++;
+	}
+  }
+  if (x!=sam.ntax){
+      aligned = false;
   }
   return aligned;
 }
 
 
 int main(int argc, char **argv){
-  procargs (argc, argv);
-  if(intype!=0&&outype!=0){
-  Sample sam = read_input();
-  write_output(sam);
+  char *itn, *otn;
+  Basic_arg arguvar = procargs (argc, argv, itn, otn);
+  if(arguvar.intype!=0&&arguvar.outype!=0){
+  Sample sam = read_input(arguvar.itn,arguvar.intype);
+  cout << "MiMi:\tInput\tfinished" << endl;
+  if(!checkalign(sam)){
+    cout << "MiMi:\tInput file should be aligned" << endl;
+    exit(0);
   }
-  int  i;
-  for (i = 0; i < argc; i++) cout << "argument "<< i << " is " << *(argv+i) << endl;
-  return 1;
+  write_output(sam,arguvar.otn,arguvar.outype);
+  cout << "MiMi:\tOutput\tfinished" << endl;
+  }
+  return 0;
 }