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7 commits
Author | SHA1 | Date | |
---|---|---|---|
247224a3e4 | |||
bbbf71374c | |||
1051374b13 | |||
d81bfbd8d9 | |||
c32f318f85 | |||
0cbec45015 | |||
26e358ffef |
3 changed files with 240 additions and 110 deletions
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242
main.cpp
242
main.cpp
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@ -3,6 +3,7 @@
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#include <iostream>
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#include <sstream>
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#include <string>
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#include <vector>
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using namespace std;
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@ -24,7 +25,7 @@ class Sample {
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};
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};
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Basic_arg procargs(int nargs, char** arg, char* itn, char* otn);
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Basic_arg procargs(int nargs, char** arg);
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Sample read_input(char* itn, int intype);
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void show_help(int help_num);
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Sample readFas(char* itn);
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@ -40,6 +41,8 @@ bool isNum(string strnum);
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bool checkalign(class Sample sam);
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string to_lower(string stri);
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string add_space(char x, string str_old);
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string rep_space(string str_old);
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string del_space(string str_old);
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string checktype(string str);
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int countfre(string str, char c);
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int checkextension(string str);
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@ -59,7 +62,7 @@ Sample readPhy(char* itn) {
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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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unsigned 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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@ -75,55 +78,53 @@ Sample readFas(char* itn) {
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int ntax, nchar, lnum;
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ifstream matrixfile;
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matrixfile.open(itn);
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// use vector to read once use serveral times
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vector<string> file_content;
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// check line number and taxa number
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ntax = 0;
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string temln;
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for (lnum = 0; getline(matrixfile, temln); lnum++) {
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file_content.push_back(temln);
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if (temln[0] == '>') {
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ntax++;
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}
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}
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matrixfile.clear();
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matrixfile.seekg(0);
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matrixfile.close();
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// check the nchar
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string* str_a = new string;
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string* str_b = new string;
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int r = lnum / ntax;
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string str_i;
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int r;
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if (file_content.size() != 0) {
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r = file_content.size() / ntax;
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} else {
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cout << "MiMi:\tInput file contains 0 line" << endl;
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exit(0);
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}
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for (int i = 0; i < r; i++) {
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getline(matrixfile, *str_a);
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if (i > 0) {
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*str_b = *str_b + *str_a;
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file_content[i] = del_space(file_content[i]);
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str_i = str_i + file_content[i];
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}
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}
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nchar = (*str_b).length();
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delete str_a;
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str_a = nullptr;
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delete str_b;
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str_b = nullptr;
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matrixfile.clear();
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matrixfile.seekg(0);
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nchar = str_i.length();
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// create class
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Sample sam(ntax, nchar);
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// get class
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string* str_c = new string;
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for (int a = 1, b = 0; a <= lnum; a++) {
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if (a % r == 1) {
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getline(matrixfile, sam.taxas[b]);
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for (int a = 0, b = 0; a < (int)file_content.size(); a++) {
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if ((a + 1) % r == 1) {
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sam.taxas[b] = file_content[a];
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sam.taxas[b].erase(0, 1);
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sam.taxas[b] = rep_space(sam.taxas[b]);
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}
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if (a % r > 1) {
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getline(matrixfile, *str_c);
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sam.chars[b] = sam.chars[b] + *str_c;
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if ((a + 1) % r > 1) {
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file_content[a] = del_space(file_content[a]);
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sam.chars[b] = sam.chars[b] + file_content[a];
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}
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if (a % r == 0) {
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getline(matrixfile, *str_c);
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sam.chars[b] = sam.chars[b] + *str_c;
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if ((a + 1) % r == 0) {
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file_content[a] = del_space(file_content[a]);
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sam.chars[b] = sam.chars[b] + file_content[a];
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b++;
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}
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}
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delete str_c;
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str_c = nullptr;
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matrixfile.close();
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return sam;
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}
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@ -147,7 +148,7 @@ Sample readTnt(char* itn) {
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// create class
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Sample sam(ntax, nchar);
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// get class
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int lennum;
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unsigned int lennum;
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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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@ -169,22 +170,26 @@ Sample readNex(char* itn) {
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// open file
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ifstream matrixfile;
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matrixfile.open(itn);
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// some tem
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// some var
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string snall, stri, str_a, str_b;
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bool found = false, found_ntax = false, found_nchar = false,
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found_equal = false;
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bool found_ntax = false, found_nchar = false, found_equal = false;
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char x = '=';
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int lnum, eulnum;
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// get line number and read line to vector
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int lnum;
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unsigned int eulnum;
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vector<string> file_content;
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while (getline(matrixfile, snall)) {
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file_content.push_back(snall);
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}
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matrixfile.close();
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// getline line by line
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for (lnum = 0; getline(matrixfile, snall); lnum++) {
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str_a = to_lower(snall);
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for (lnum = 0; lnum < (int)file_content.size(); lnum++) {
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str_a = to_lower(file_content[lnum]);
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str_b = add_space(x, str_a);
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istringstream istr(str_b);
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// convert to words
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while (istr >> stri) {
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if (stri == "dimensions") {
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found = true;
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} else if (stri == "ntax") {
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if (stri == "ntax") {
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found_ntax = true;
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} else if (stri == "nchar") {
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found_nchar = true;
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@ -193,7 +198,6 @@ Sample readNex(char* itn) {
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} else if (found_ntax && found_equal) {
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if (stri.back() == ';') {
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stri.pop_back();
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found = false;
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}
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ntax = stoi(stri);
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found_equal = false;
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@ -201,7 +205,6 @@ Sample readNex(char* itn) {
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} else if (found_nchar && found_equal) {
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if (stri.back() == ';') {
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stri.pop_back();
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found = false;
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}
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nchar = stoi(stri);
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found_equal = false;
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@ -211,32 +214,24 @@ Sample readNex(char* itn) {
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}
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}
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}
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// go back
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matrixfile.clear();
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matrixfile.seekg(0);
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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;
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// read line by line, limit line number
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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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for (unsigned int z = eulnum; z < (eulnum + sam.ntax); z++) {
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// convert to word
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istringstream istr(snall);
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// limit the read line number
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if (z > (eulnum - 1) && z < (eulnum + sam.ntax)) {
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istr >> sam.taxas[l];
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istr >> sam.chars[l];
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l++;
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}
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z++;
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istringstream istr(file_content[z]);
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istr >> sam.taxas[l];
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istr >> sam.chars[l];
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l++;
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}
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return sam;
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}
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string add_space(char x, string str_old) {
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int i;
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string str_new;
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for (i = 0; i < str_old.length(); i++) {
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for (i = 0; i < (int)str_old.length(); i++) {
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if (str_old[i] != x) {
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str_new = str_new + str_old[i];
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} else {
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@ -246,6 +241,32 @@ string add_space(char x, string str_old) {
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return str_new;
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}
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string del_space(string str_old) {
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int i;
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string str_new;
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char x = ' ';
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for (i = 0; i < (int)str_old.length(); i++) {
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if (str_old[i] != x) {
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str_new = str_new + str_old[i];
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}
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}
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return str_new;
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}
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string rep_space(string str_old) {
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int i;
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string str_new;
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char x = ' ', c = '_';
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for (i = 0; i < (int)str_old.length(); i++) {
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if (str_old[i] != x) {
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str_new = str_new + str_old[i];
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} else {
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str_new = str_new + c;
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}
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}
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return str_new;
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}
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string to_lower(string stri) {
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transform(stri.begin(), stri.end(), stri.begin(), ::tolower);
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return stri;
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@ -253,7 +274,7 @@ string to_lower(string stri) {
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void writeFas(class Sample sam, char* otn) {
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ofstream matrixfile(otn);
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for (int i = 0; i < sam.ntax; i++) {
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for (unsigned int i = 0; i < sam.ntax; i++) {
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matrixfile << ">" << sam.taxas[i] << endl;
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matrixfile << sam.chars[i] << endl;
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}
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@ -263,7 +284,7 @@ void writeFas(class Sample sam, char* otn) {
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void writePhy(class Sample sam, char* otn) {
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ofstream matrixfile(otn);
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matrixfile << sam.ntax << " " << sam.nchar << endl;
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for (int i = 0; i < sam.ntax; i++) {
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for (unsigned int i = 0; i < sam.ntax; i++) {
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matrixfile << sam.taxas[i] << "\t" << sam.chars[i] << endl;
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}
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matrixfile.close();
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@ -273,16 +294,14 @@ void writeNex(class Sample sam, char* otn) {
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ofstream matrixfile(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
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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 << "#NEXUS\nBegin data;\n\tDimensions nchar=" << sam.nchar
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<< " ntax=" << sam.ntax << ";\n\tFormat datatype=" << datatype
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<< " missing=? gap=-;\n\tMatrix" << endl;
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for (unsigned 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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matrixfile << "\t;" << endl << "End;" << endl;
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matrixfile << "\t;\nEnd;" << endl;
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matrixfile.close();
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}
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@ -323,18 +342,18 @@ int countfre(string str, char c) {
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void writeTnt(class Sample sam, char* otn) {
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ofstream matrixfile(otn);
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matrixfile << "xread" << endl << "\' \'" << endl;
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matrixfile << sam.nchar << " " << sam.ntax << endl;
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for (int i = 0; i < sam.ntax; i++) {
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matrixfile << "xread\n\' \'\n" << sam.nchar << " " << sam.ntax << endl;
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for (unsigned int i = 0; i < sam.ntax; i++) {
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matrixfile << sam.taxas[i] << "\t" << sam.chars[i] << endl;
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}
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matrixfile << "proc / ;" << endl;
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matrixfile << "\n;\nproc / ;" << endl;
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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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Basic_arg procargs(int nargs, char** arg) {
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int i, sta = 0, intype = 0, outype = 0;
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string para, inputfile, outputfile;
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char *itn, *otn;
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// no arg, show help
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if (nargs == 1) {
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show_help(0);
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|
@ -345,28 +364,36 @@ Basic_arg procargs(int nargs, char** arg, char* itn, char* otn) {
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for (i = 1; i < nargs; i++) {
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// to string
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string para(arg[i]);
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if (para == "-h" | para == "--help") {
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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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} 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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} 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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outype = checkextension(outputfile);
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sta++;
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} else if ((para == "-i") || (para == "--input")) {
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if ((i + 1) < nargs) {
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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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} else {
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cout << "MiMi:\tOInput file name must be defined" << endl;
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}
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} else if (((para == "-o") || (para == "--output"))) {
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if ((i + 1) < nargs) {
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i++;
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otn = arg[i];
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string outputfile(arg[i]);
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outype = checkextension(outputfile);
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sta++;
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} else {
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cout << "MiMi:\tOutput file name must be defined" << endl;
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}
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} else {
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cout << "MiMi\tUnknown arguments, please use -h to check" << endl;
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cout << "MiMi:\tUnknown arguments, please use -h to check" << endl;
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exit(0);
|
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}
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}
|
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if (sta != 2) {
|
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cout << "MiMi\tInput and Output can't be empty" << endl;
|
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cout << "MiMi:\tInput and Output can't be empty" << endl;
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exit(0);
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}
|
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Basic_arg arguvar(intype, outype, itn, otn);
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|
@ -380,20 +407,20 @@ int checkextension(string str) {
|
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if (loc) {
|
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extension = str.substr(loc + 1);
|
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} else {
|
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cout << "MiMi\tPlease sepecifc the extension name" << endl;
|
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cout << "MiMi:\tPlease sepecifc the extension name" << endl;
|
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exit(0);
|
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}
|
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extension = to_lower(extension);
|
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if (extension == "fas" | extension == "fasta") {
|
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if ((extension == "fas") || (extension == "fasta")) {
|
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type = 1;
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} else if (extension == "nex" | extension == "nexus") {
|
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} else if ((extension == "nex") || (extension == "nexus")) {
|
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type = 2;
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} else if (extension == "phy" | extension == "phylip") {
|
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} else if ((extension == "phy") || (extension == "phylip")) {
|
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type = 3;
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} else if (extension == "tnt" | extension == "ss") {
|
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} else if ((extension == "tnt") || (extension == "ss")) {
|
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type = 4;
|
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} else {
|
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cout << "MiMi\tUnknown format" << endl;
|
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cout << "MiMi:\tUnknown format" << endl;
|
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exit(0);
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}
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return type;
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|
@ -405,22 +432,17 @@ void show_help(int help_num) {
|
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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 "
|
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" \t| ||| ||\n じしf_,)ノ\t| ||| ||\n"
|
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" \t| ||| ||\n じしf_,)ノ\t| ||| ||\n\nMorphology into "
|
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"Molecules into\nGPL;\tGuoyi "
|
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"Zhang;\t2023\n\nArguments:\n-h\t--help;\n-i\t--input\t\t${"
|
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"filename};\n-o\t--output\t${filename};\n\nAccepted "
|
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"formats:\nfas\tfasta;\nnex\tnexus;\nphy\tphylip;\ntnt\tss;"
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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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Sample read_input(char* itn, int intype) {
|
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int ntax, nchar;
|
||||
int ntax = 0, nchar = 0;
|
||||
Sample sam(ntax, nchar);
|
||||
ifstream matrixfile;
|
||||
matrixfile.open(itn);
|
||||
|
@ -430,7 +452,7 @@ Sample read_input(char* itn, int intype) {
|
|||
if (intype == 3) sam = readPhy(itn);
|
||||
if (intype == 4) sam = readTnt(itn);
|
||||
} else {
|
||||
cout << "MiMi\tInput file can't be open" << endl;
|
||||
cout << "MiMi:\tInput file can't be open" << endl;
|
||||
exit(0);
|
||||
}
|
||||
return sam;
|
||||
|
@ -444,16 +466,17 @@ void write_output(class Sample sam, char* otn, int outype) {
|
|||
if (outype == 3) writePhy(sam, otn);
|
||||
if (outype == 4) writeTnt(sam, otn);
|
||||
} else {
|
||||
cout << "MiMi\tOutput file can't be open" << endl;
|
||||
cout << "MiMi:\tOutput file can't be open" << endl;
|
||||
exit(0);
|
||||
}
|
||||
}
|
||||
|
||||
bool checkalign(class Sample sam) {
|
||||
int a = 0, b = 0, x = 0;
|
||||
int a = 0, b = 0;
|
||||
unsigned int x = 0;
|
||||
a = sam.nchar;
|
||||
bool aligned = true;
|
||||
for (int i = 0; i < sam.ntax; i++) {
|
||||
for (unsigned int i = 0; i < sam.ntax; i++) {
|
||||
b = sam.chars[i].length();
|
||||
if (a == b) {
|
||||
x++;
|
||||
|
@ -466,8 +489,7 @@ bool checkalign(class Sample sam) {
|
|||
}
|
||||
|
||||
int main(int argc, char** argv) {
|
||||
char *itn, *otn;
|
||||
Basic_arg arguvar = procargs(argc, argv, itn, otn);
|
||||
Basic_arg arguvar = procargs(argc, argv);
|
||||
if (arguvar.intype != 0 && arguvar.outype != 0) {
|
||||
Sample sam = read_input(arguvar.itn, arguvar.intype);
|
||||
cout << "MiMi:\tInput\tfinished" << endl;
|
||||
|
|
108
mimi.tcl
Normal file
108
mimi.tcl
Normal file
|
@ -0,0 +1,108 @@
|
|||
package require Tk
|
||||
|
||||
proc ? L {lindex $L [expr {int (rand ()* [llength $L])}]}
|
||||
|
||||
proc validateFile name {
|
||||
set ext [file extension $name]
|
||||
if {$ext ni {.fas .fasta .nex .nexus .tnt .ss .phy .phylip}} {
|
||||
tk_messageBox -icon error -type ok -message "extension of file must be fas fasta nex nexus tnt ss phy phylip"
|
||||
return 0
|
||||
} else {
|
||||
return 1
|
||||
}
|
||||
}
|
||||
|
||||
proc runMimi {} {
|
||||
global input output mimi
|
||||
if {[validateFile $input] && [validateFile $output]} {
|
||||
if {[file exists $mimi]} {
|
||||
exec $mimi -i $input -o $output
|
||||
tk_messageBox -icon info -type ok -message "Success"
|
||||
} else {
|
||||
tk_messageBox -icon error -type ok -message "Can't find the path of MiMi"
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
proc clearAll {} {
|
||||
global input output mimi
|
||||
set input ""
|
||||
set output ""
|
||||
}
|
||||
|
||||
proc chooseMimi {} {
|
||||
global mimi
|
||||
set file [tk_getOpenFile]
|
||||
if {$file ne ""} {
|
||||
set mimi $file
|
||||
}
|
||||
}
|
||||
|
||||
proc chooseInput {} {
|
||||
global input
|
||||
set file [tk_getOpenFile]
|
||||
if {$file ne ""} {
|
||||
set input $file
|
||||
}
|
||||
}
|
||||
|
||||
proc chooseOutput {} {
|
||||
global output
|
||||
set file [tk_getSaveFile]
|
||||
if {$file ne ""} {
|
||||
set output $file
|
||||
}
|
||||
}
|
||||
|
||||
proc quitApp {} {
|
||||
exit
|
||||
}
|
||||
|
||||
proc helpApp {} {
|
||||
tk_messageBox -icon info -type ok -message "Thanks to my beloved daughter MiMi (Ragdoll cat) for accompanying me in my life, mom loves you forever.\n\nGuoyi"
|
||||
}
|
||||
|
||||
#bind . <Escape> {quitApp}
|
||||
wm protocol . WM_DELETE_WINDOW {quitApp}
|
||||
|
||||
wm iconphoto . [image create photo -file logo.gif]
|
||||
|
||||
set input ""
|
||||
set output ""
|
||||
set mimi ""
|
||||
|
||||
wm title . "Mimi GUI"
|
||||
|
||||
# 创建菜单栏
|
||||
menu .menubar
|
||||
.menubar add cascade -label "Settings" -menu .menubar.file
|
||||
menu .menubar.file
|
||||
.menubar.file add command -label "Select MiMi Path" -command chooseMimi
|
||||
.menubar.file add separator
|
||||
.menubar.file add command -label "Quit" -command quitApp
|
||||
|
||||
.menubar add cascade -label "Help" -menu .menubar.help
|
||||
menu .menubar.help
|
||||
.menubar.help add command -label "About" -command helpApp
|
||||
|
||||
# 配置菜单栏到顶层窗口
|
||||
. configure -menu .menubar
|
||||
|
||||
# 创建输入输出框和按钮
|
||||
grid [ttk::frame .c -padding "3 3 12 12"] -column 0 -row 0 -sticky nwes
|
||||
grid columnconfigure . 0 -weight 1; grid rowconfigure . 0 -weight 1
|
||||
|
||||
grid [ttk::label .c.ilbl -text "Input"] -column 1 -row 1 -sticky e
|
||||
grid [ttk::entry .c.input -width 20 -textvariable input] -column 2 -row 1 -sticky we
|
||||
grid [ttk::button .c.ibtn -text "Select" -command chooseInput] -column 3 -row 1
|
||||
|
||||
grid [ttk::label .c.olbl -text "Output"] -column 1 -row 2 -sticky e
|
||||
grid [ttk::entry .c.output -width 20 -textvariable output] -column 2 -row 2 -sticky we
|
||||
grid [ttk::button .c.obtn -text "Select" -command chooseOutput] -column 3 -row 2
|
||||
|
||||
grid [ttk::button .c.run -text "Run" -command runMimi] -column 2 -row 3
|
||||
grid [ttk::button .c.clear -text "Clean" -command clearAll] -column 3 -row 3
|
||||
|
||||
foreach w [winfo children .c] {grid configure $w -padx 5 -pady 5 }
|
||||
|
||||
vwait forever
|
Loading…
Add table
Reference in a new issue