From b0e35fa3d188181b73572717626927f5b56ccabf Mon Sep 17 00:00:00 2001
From: Kuoi <starsareintherose@outlook.com>
Date: Sun, 19 Mar 2023 02:17:39 +0800
Subject: [PATCH] add more function

---
 main.cpp | 216 +++++++++++++++++++++++++++++++++++++++++++++++--------
 1 file changed, 185 insertions(+), 31 deletions(-)

diff --git a/main.cpp b/main.cpp
index 3afbb22..6778275 100644
--- a/main.cpp
+++ b/main.cpp
@@ -1,21 +1,46 @@
 #include <iostream>
 #include <fstream>
-#include<sstream> 
+#include <sstream> 
 #include <string>
 #include <vector>
 #include <algorithm>
 
 using namespace std;
 
-int intype=0, outype=0, ntax, nseq;
-char * fn;
+int intype=0, outype=0;
+char *fn;
+char *otn;
+
+class Sample {
+public:
+	unsigned ntax, nchar;
+	string *taxas, *chars;
+	Sample(unsigned ntax, unsigned nchar):
+       		ntax(ntax), nchar(nchar) {
+			taxas = new string[ntax];
+			chars = new string[ntax];
+		};
+//	~Sample(){
+//		delete[] taxas;
+//		delete[] chars;	
+//	}
+};
 
 void show_help(int help_num);
-void read_input(void);
+Sample read_input();
+Sample readFas();
+Sample readPhy();
+void write_output(class Sample sam);
+void writeFas(class Sample sam);
+void writePhy(class Sample sam);
+void writeTnt(class Sample sam);
+void writeNexus(class Sample sam);
 
-void readPhy(){
+Sample readPhy(){
+//  unsigned ntax, nchar;
+//  string *taxas, *chars;
+//  Sample sam(ntax, nchar); 
   int num=0;
-  cout << "readphy is working, filename is " << fn << endl;
   //read file
   ifstream seqfile;
   seqfile.open(fn);
@@ -25,31 +50,154 @@ void readPhy(){
   getline(seqfile,snall);
   istringstream istr(snall); 
   istr >> sntax; istr >> snseq;
-  ntax = stoi (sntax); nseq = stoi (snseq); // string to int
-  cout << "ntax=" << ntax << " nseq=" << nseq << endl;    
+  int ntax, nchar;
+  ntax = stoi (sntax); nchar = stoi (snseq); // string to int
+  cout << "ntax=" << ntax << " nseq=" << nchar << endl;
+  Sample sam(ntax, nchar);   
   //read sequence
-  string taxa[ntax], sequ[ntax];
-  //taxa[ntax] = new string*[];
   int lennum;
-  for(lennum=0;lennum<ntax;lennum++){
+  for(lennum=0;lennum<sam.ntax;lennum++){
     getline(seqfile,snall);
     istringstream istr(snall);
-    istr >> taxa[lennum]; istr >> sequ[lennum];
-    cout << "tax" << lennum << " is " << taxa << "; seq" << lennum << " is " << sequ << endl;   
+    istr >> sam.taxas[lennum]; istr >> sam.chars[lennum];
+   cout << "tax" << lennum << " is " << sam.taxas[lennum] << "; seq" << lennum << " is " << sam.chars[lennum] << endl;   
   }
   seqfile.close();
-//  return taxa;
-//  return sequ;
+  // return to class
+  return sam;
 }
 
-void writeFas(){
-  
+Sample readFas(){
+  int ntax, nchar, lnum;
+  ifstream seqfile;
+  seqfile.open(fn);
+  ntax = 0;
+  string temln;
+  for(lnum=0;getline(seqfile,temln);lnum++){
+    if(temln[0]=='>'){
+      ntax++;
+    }
+  }
+  cout << "lnum= " << lnum << ", ntax= " << ntax << endl;
+  seqfile.clear();
+  seqfile.seekg(0);
+
+  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);
+    if(i>0){
+       *str_b = *str_b + *str_a; 
+    } 
+  }
+  nchar = (*str_b).length();
+  delete str_a;
+  str_a = nullptr;
+  delete str_b;
+  str_b = nullptr;
+
+  cout << "ntax= " << ntax << ", nchar= " << nchar << endl; 
+  seqfile.clear();
+  seqfile.seekg(0);
+
+  Sample sam(ntax, nchar);
+  string *str_c = new string;
+  for (int a=1, b=0;a<=lnum;a++){
+    if(a%r==1){
+      getline(seqfile,sam.taxas[b]);
+      sam.taxas[b].erase(0,1);  
+    }
+    if(a%r>1){
+      getline(seqfile,*str_c);
+      sam.chars[b] = sam.chars[b] + *str_c;
+    }
+    if(a%r==0){
+      getline(seqfile,*str_c);
+      sam.chars[b] = sam.chars[b] + *str_c;
+      b++;
+    }   
+  }
+  delete str_c;
+  str_c = nullptr; 
+  seqfile.close();
+  int lennum;
+  for(lennum=0;lennum<sam.ntax;lennum++){
+   cout << "tax" << lennum << " is " << sam.taxas[lennum] << "; seq" << lennum << " is " << sam.chars[lennum] << endl;
+  }
+  return sam;
 }
 
+Sample readTnt(){
+  int ntax, nchar;
+  Sample sam(ntax,nchar);
+  return sam;
+}
+
+void writeFas(class Sample sam){
+  ofstream outputFile(otn);
+  if (outputFile.is_open()) {
+      for(int i=0;i<sam.ntax;i++){
+        outputFile << ">" << sam.taxas[i] << endl;
+        outputFile << sam.chars[i] << endl;
+      }
+    } else {
+      cout << "File can't be written" << endl;
+    }
+  outputFile.close();
+}
+
+void writePhy(class Sample sam){
+  ofstream outputFile(otn);
+  if (outputFile.is_open()) {
+      outputFile << sam.ntax << " " << sam.nchar << endl;
+      for(int i=0;i<sam.ntax;i++){
+        outputFile << sam.taxas[i] << "\t" << sam.chars[i]  << endl;
+      }
+    } else {
+      cout << "File can't be written" << endl;
+    }
+  outputFile.close();
+}
+
+void writeNexus(class Sample sam){
+  ofstream outputFile(otn);
+  if (outputFile.is_open()) {
+      outputFile << "#NEXUS" << endl << "Begin TAXA;" << endl << "\tDimensions ntax=" << sam.ntax << ";" << endl << "\tTaxLabels";
+      for(int i1=0;i1<sam.ntax;i1++){
+        outputFile << " " << sam.taxas[i1] << endl;
+      }
+      outputFile << ";" << endl << "End;" << endl << endl << "Begin data;" << endl << "\tDimensions nchar=" << sam.nchar << ";" << endl << "\tFormat datatype=dna missing=? gap=-;" << endl << "\tMatrix" << endl;
+      for(int i2=0;i2<sam.ntax;i2++){
+        outputFile << "\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();
+}
+
+void writeTnt(class Sample sam){
+  ofstream outputFile(otn);
+  if (outputFile.is_open()) {
+      outputFile << sam.nchar << " " << sam.ntax << endl;
+      outputFile << "\' \'" << endl;
+      for(int i=0;i<sam.ntax;i++){
+        outputFile << sam.taxas[i] << "\t" << sam.chars[i]  << endl;
+      }
+      outputFile << "proc / ;" << endl;
+    } else {
+      cout << "File can't be written" << endl;
+    }
+  outputFile.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;
   //no arg, show help
   if (nargs==1){
     show_help(0);
@@ -67,24 +215,25 @@ void procargs (int nargs, char ** arg){ //*arg 视为整体，是字符串指针
     switch (*++cp){//先++
       case 'f':
         cp++;
-	if (*cp=='f') intype=1; 
+	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;}
 	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 << "intype is phylip, " << intype << endl;}
+	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);
     }
   }
 }
 
-
 void show_help (int help_num){
   if (help_num == 0){
     cout  << "SeqConvert GPL, please use -h to see more help" << endl;
@@ -93,22 +242,27 @@ void show_help (int help_num){
   }
 }
 
-void read_input (void){
-  if (intype==3) readPhy();
+Sample read_input (void){
+  int ntax, nchar;
+  Sample sam(ntax,nchar);
+  if (intype==1) sam = readFas();
+  if (intype==3) sam = readPhy();
+  return sam;
 }
 
-void write_output (void){
-  switch(outype){
-    case '1': ; break;
-    case '2': ; break;
-    case '3': ; break;
-  }
+void write_output (class Sample sam){
+  if (outype==1) writeFas(sam);
+  if (outype==2) writeNexus(sam);
+  if (outype==3) writePhy(sam);
+  if (outype==4) writeTnt(sam);
 }
 
 int main(int argc, char **argv){
   procargs (argc, argv);
-  read_input();
-  write_output();
+  if(intype!=0&&outype!=0){
+  Sample sam = read_input();
+  write_output(sam);
+  }
   int  i;
   for (i = 0; i < argc; i++) cout << "argument "<< i << " is " << *(argv+i) << endl;
   return 1;