init

main.cpp

@@ -0,0 +1,87 @@
+#include <iostream>
+#include <fstream>
+#include<sstream> 
+#include <string>
+#include <vector>
+#include <algorithm>
+
+using namespace std;
+
+int datatype=0, ntax, nseq;
+char * fn;
+
+void show_help(int help_num);
+void read_input(void);
+
+int readPhy(){
+  int num=0;
+  cout << "readphy is working, filename is " << fn << endl;
+  //read file
+  ifstream seqfile;
+  seqfile.open(fn);
+  //read number of taxa and charcter
+  string sntax, snseq, snall;
+  cout << "Reading from the file" << endl; 
+  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;    
+  //read sequence
+
+  seqfile.close();
+  return num;
+}
+
+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
+
+  //no arg, show help
+  if (nargs==1){
+    show_help(0);
+    exit(0);
+  }
+  //recognize arg
+  for (i=1;i<nargs;i++){
+    cp = *(arg+i);
+    //error arg
+    if (*cp != '-'){
+      cout << "Unknown arguments, please use -h to check" << endl;
+      exit(0);
+    }
+    //check arg
+    switch (*++cp){//先++
+      case 'f':
+        cp++;
+	if (*cp=='f') datatype=1; 
+	if (*cp=='n') datatype=2;
+	if (*cp=='p') {datatype=3; cout << "datatype is phylip, " << datatype << endl;}
+	break;
+      case 'h': show_help(1); break;
+      case 'i': cp++; fn = cp; 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;
+  } else {
+    cout << "-f from: -ff fasta; -fn nexus; -fp phylip;\n-h help;\n-i input: -i${filename};" << endl;
+  }
+}
+
+void read_input (void){
+  if (datatype==3) readPhy();
+}
+
+int main(int argc, char **argv){
+  procargs (argc, argv);
+  read_input();
+  int  i;
+  for (i = 0; i < argc; i++) cout << "argument "<< i << " is " << *(argv+i) << endl;
+  return 1;
+}