add apo related, c++ source code to convert winclada.tre

README.md

@@ -1,6 +1,6 @@
 # TNT Script used by Guoyi
 
-This script follows MIT and part of script is from setk.run belonging to Salvador Arias (Instituto Miguel Lillo, San Miguel de Tucumán, Argentina).
+The TNT script follows MIT and part of script is from setk.run belonging to Salvador Arias (Instituto Miguel Lillo, San Miguel de Tucumán, Argentina).
 
 ## Usage
 
@@ -20,19 +20,59 @@ This script follows MIT and part of script is from setk.run belonging to Salvado
 
 - Calculate Relative Bremer support, jackknifing, and bootstrap.
 
+- Map apomorphic characters on the consensus tree.
+
 - Calculate TL, CI, and RI. 
 
 ## Options
 
 - Results instructions are at the end of `tnt.log`.
 
-- `trees.tre`, `con.tre` are trees with taxaname.
+- `trees.tre`, `con.tre` are trees with taxname.
 
-- `trees_no.tre`, `con_no.tre` are trees without taxaname.
+- `trees_no.tre`, `con_no.tre` are trees without taxname.
-
-- `con_no.tre` can be put into Winclada with your tnt matrix file `filename`.
 
 - `nelsen` can be replaced by `majority`.
 
 - `xmult` and `mult` replications and hold trees number can be adjusted.
 
+- `winclada.tre` can be transferred to the acceptable format for WinClada by tnt2winclada and the output file can be put into Winclada with your tnt matrix file `filename` for mapping apomorphic characters and homoplasy.
+
+# TNT2WinClada
+
+```
+~|~|\ |~|~  ~)  |    |o._ |~| _  _| _ 
+ | | \| |   /_   \/\/ || ||_|(_|(_|(_|
+
+MIT, Guoyi Zhang, 2023
+```
+
+## Function
+
+Convert TNT output tree file without tags and taxname, e.g. `winclada.tre` produced by TNT script, to WinClada acceptable format tree.
+
+## Compile
+
+### Linux & Unix
+
+```
+g++ tnt2winclada.cpp -o tnt2winclada
+```
+
+or
+
+```
+clang++ -o tnt2winclada tnt2winclada.cpp
+```
+
+### Windows
+
+```
+cl /EHsc tnt2winclada.cpp
+```
+
+## Usage
+
+```
+tnt2winclada -i ${input_file} -o ${output_file}
+```

guoyi.run

@@ -1,5 +1,6 @@
 log tnt.log;
 macro=;
+taxname+1000;
 taxname=;
 mxram 10240;
 nstates 32;
@@ -22,7 +23,9 @@ quote -   |    Implied weighting will be estimated.        |;
 quote -   |    TBR Mult and Xmult will be performed.       |;
 quote -   |    Strict consensus will be used.              |;
 quote -   |    Relative bremer support, jackknifing and    |;
-quote -   |        bootstrap will be shown on the svg.     |;
+quote -   |        bootstrap will be shown on the con.svg. |;
+quote -   |    Apomorphic characters mapping will be shown |;
+quote -   |        on the apo.svg and saved to apo*.tre.   |;
 quote -   |    TL, CI and RI will be calculated finally.   |;
 quote -   \------------------------------------------------/;
 
@@ -40,11 +43,10 @@ var:
  maxIts
 ;
 if (ntax<0)
-  quote NO HAY DATOS!;
+  quote There is no data;
   proc/;
 end
-set gVal 1;
+/** find the value of g **/
-/** busca el valor de g **/
 loop 0 nchar
   if (!isinfo[#1]) continue; end
   if (!isact[#1]) continue; end
@@ -54,21 +56,21 @@ loop 0 nchar
     set gVal 'a'-'b';
   end
 stop
-quote valor de g = 'gVal';
+quote g value: 'gVal';
 set actK 10;
 set minK 0;
-set maxK 500; /** Asume 500 como el maximo posible valor de K **/
+set maxK 500; /** Assume 500 as the maximum possible value of K **/
 set maxIts 0;
-/** busca el mejor valor de K **/
+/** find the best value of K **/
 loop 0 1
-  quote actual valor de k = 'actK';
+  quote actual k value: 'actK';
   set a 1-('actK'/('actK'+1));
   quote 'a';
   set b ('actK'/('actK'+'gVal'-1))-('actK'/('actK'+'gVal'));
   quote 'b';
   set Nval 'a'/'b';
-  quote valor de N = 'Nval';
+  quote N value: 'Nval';
-  if (('Nval'>14.8)&&('Nval'<15.2)) endloop; end /** N esta en el rango **/
+  if (('Nval'>14.8)&&('Nval'<15.2)) endloop; end /** N is in range **/
   if ('Nval'>15.2)
     set minK 'actK';
   else
@@ -77,16 +79,16 @@ loop 0 1
   set a ('maxK'-'minK')/2;
   set actK 'minK' + 'a';
   set maxIts ++;
-  if ('maxIts'==100) endloop; end /** salida de emergencia **/
+  if ('maxIts'==100) endloop; end /** emergency exit **/
   setloop 0;
 stop
-/** Si salio de emergencia **/
+/** If out of emergency **/
 if ('maxIts'==100)
-  quote NO SE TERMINARON LAS ITERACIONES;
+  quote Iterations are not finished;
-  quote mejor K encontrado: 'actK';
+  quote Best K is 'actK';
   proc /;
 end
-quote Valor de K: 'actK' (N='Nval');
+quote K value: 'actK' (N='Nval');
 piwe='actK';
 
 /*Reopen tnt*/
@@ -130,6 +132,18 @@ export < con.tre;
 taxname-;
 export - con_no.tre;
 
+/*Apomorphic characters*/
+export = winclada.tre;
+taxname =;
+ttags-;
+ttags=;
+apo >0;
+ttags & apo.svg thickness 7 italics fontsize 15;
+export < apo.tre;
+taxname-;
+export - apo_no.tre;
+ttags-;
+
 /*Caulculate TL/CI/RI score*/
 length *;
 report-;
@@ -164,12 +178,18 @@ quote -         |      The file `trees*.tre` contain           |;
 quote -         |          trees found by mult and xmult       |;
 quote -         |      The file `con*.tre` contain             |;
 quote -         |          strict consensus tree               |;
+quote -         |      The file `apo*.tre` contain             |;
+quote -         |          tree with apomorphic character      |;
 quote -         |      The file `*_no.tre` contain             |;
 quote -         |          tree with `taxaname-`               |;
 quote -         |      The file `con.svg` contain              |;
 quote -         |          strict consensus tree with          |;
 quote -         |          relative bremer, jak and boot       |;
 quote -         |          support on the tree                 |;
+quote -         |      The file `apo.svg` contain the          |;
+quote -         |          tree with apomorphy mapping         |;
+quote -         |      The file `winclada.tre` can be          |;
+quote -         |          converted by tnt2winclada           |;
 quote -         \----------------------------------------------/;
 
 /*Quit*/

tnt2winclada.cpp

@@ -0,0 +1,128 @@
+#include <iostream>
+#include <fstream>
+#include <sstream> 
+#include <string>
+
+using namespace std;
+
+string inputFileName, outputFileName, tnt_format, winclada_format;
+
+void argument(int argc, char** argv);
+int read_tnt();
+void showhelp(int help_num);
+void parse_line(int trelen);
+void add_space (string winclada, char x);
+bool isNum(string strnum);
+
+void show_help (int help_num){
+if (help_num == 0) {
+	cout << "~|~|\\ |~|~  ~)  |    |o._ |~| _  _| _ " << endl;
+	cout << " | | \\| |   /_   \\/\\/ || ||_|(_|(_|(_|" << endl;
+	cout  << "TNT2WinClada MIT\nplease use -h to see more help" << endl;
+	} else {
+		cout << "~|~|\\ |~|~  ~)  |    |o._ |~| _  _| _ " << endl;
+		cout << " | | \\| |   /_   \\/\\/ || ||_|(_|(_|(_|" << endl;
+		cout << "-h help;\n-i input: -i ${input_file};\n-o output: -o ${output_file}" << endl;
+	}
+}
+
+void argument(int argc, char **argv) {
+	// -i -h -o option
+	int x=0, y = 0, z=0;
+	for (int i = 0; i < argc; i++) {
+		if (argc == 2 && string(argv[1]) == "-h") {
+			show_help(1);
+			x++;
+			return;
+		}
+		if (argc != 5 || string(argv[1]) != "-i" || string(argv[3]) != "-o") {
+			show_help(0);
+			return;
+		}
+		if (string(argv[i]) == "-i") {
+			i++;
+			inputFileName = argv[i];
+			y++;
+		}
+		if (string(argv[i]) == "-o") {
+			i++;
+			outputFileName = argv[i];
+			z++;
+		}
+	}
+	if (x==0 && (y==0 || z==0)) {
+		cout << "input or output can't be empty." << endl;
+	}
+}
+
+int read_tnt() {
+	int trelen;
+	ifstream inputFile(inputFileName);
+	if (inputFile.is_open()) {
+		getline(inputFile, tnt_format);
+		inputFile.close();
+		trelen = tnt_format.length();
+	} else {
+		cout << "File can't be opened" << endl;
+	}
+	inputFile.close();
+	return trelen;
+}
+
+void add_space (char x) {
+	int i = 0;
+	string winclada;
+	for (i=0; i<tnt_format.length(); i++) {
+		if (tnt_format[i] != x) {
+			winclada=winclada+tnt_format[i];
+		} else {
+			winclada=winclada+" "+tnt_format[i]+" ";
+		} 
+	}
+	tnt_format=winclada;
+}
+
+bool isNum(string strnum) {
+	char* p;
+	strtol(strnum.c_str(), &p, 10);
+	return *p == 0;
+}
+
+void parse_line (int trelen) {
+	// add space
+	char x1 = '(', x2 = ')', x3= ',';
+	add_space(x1);
+	add_space(x2);
+	add_space(x3);
+	// use space as separator
+	istringstream istr(tnt_format);
+	string buffer;
+	int tem;
+	while (getline(istr, buffer, ' ')) {
+		istr >> buffer;
+		if(isNum(buffer)){
+			tem = stoi(buffer)-1;
+			buffer = to_string(tem);
+		}
+		winclada_format=winclada_format+buffer;
+	}
+}
+
+void write_winclada() {
+	ofstream outputFile(outputFileName);
+	if (outputFile.is_open()) {
+		outputFile << winclada_format;
+	} else {
+		cout << "File can't be written" << endl;
+	}
+	outputFile.close();
+}
+
+int main (int argc, char **argv){
+	argument(argc, argv);
+	int trelen;
+	trelen = read_tnt();
+	parse_line(trelen);
+	write_winclada();
+	return 0;
+}