+//this code is a mess and should be rethought...-slw
+void Tree::parseTreeFile() {
+
+ //only takes names from the first tree and assumes that all trees use the same names.
+ try {
+ string filename = globaldata->getTreeFile();
+ ifstream filehandle;
+ openInputFile(filename, filehandle);
+ int c, comment;
+ comment = 0;
+ int done = 1;
+
+ //ifyou are not a nexus file
+ if((c = filehandle.peek()) != '#') {
+ while((c = filehandle.peek()) != ';') {
+ while ((c = filehandle.peek()) != ';') {
+ // get past comments
+ if(c == '[') {
+ comment = 1;
+ }
+ if(c == ']'){
+ comment = 0;
+ }
+ if((c == '(') && (comment != 1)){ break; }
+ filehandle.get();
+ }
+
+ done = readTreeString(filehandle);
+ if (done == 0) { break; }
+ }
+ //ifyou are a nexus file
+ }else if((c = filehandle.peek()) == '#') {
+ string holder = "";
+
+ // get past comments
+ while(holder != "translate" && holder != "Translate"){
+ if(holder == "[" || holder == "[!"){
+ comment = 1;
+ }
+ if(holder == "]"){
+ comment = 0;
+ }
+ filehandle >> holder;
+
+ //if there is no translate then you must read tree string otherwise use translate to get names
+ if((holder == "tree") && (comment != 1)){
+ //pass over the "tree rep.6878900 = "
+ while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF)) {;}
+
+ if(c == EOF) { break; }
+ filehandle.putback(c); //put back first ( of tree.
+ done = readTreeString(filehandle);
+
+ break;
+ }
+
+ if (done == 0) { break; }
+ }
+
+ //use nexus translation rather than parsing tree to save time
+ if((holder == "translate") || (holder == "Translate")) {
+
+ string number, name, h;
+ h = ""; // so it enters the loop the first time
+ while((h != ";") && (number != ";")) {
+ filehandle >> number;
+ filehandle >> name;
+
+ //c = , until done with translation then c = ;
+ h = name.substr(name.length()-1, name.length());
+ name.erase(name.end()-1); //erase the comma
+ globaldata->Treenames.push_back(number);
+ }
+ if(number == ";") { globaldata->Treenames.pop_back(); } //in case ';' from translation is on next line instead of next to last name
+ }
+ }
+ filehandle.close();
+
+ //for (int i = 0; i < globaldata->Treenames.size(); i++) {
+//cout << globaldata->Treenames[i] << endl; }
+//cout << globaldata->Treenames.size() << endl;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "parseTreeFile");
+ exit(1);
+ }
+}
+/*******************************************************/
+
+/*******************************************************/
+int Tree::readTreeString(ifstream& filehandle) {
+ try {
+ int c;
+ string name; //, k
+
+ while((c = filehandle.peek()) != ';') {
+//k = c;
+//cout << " at beginning of while " << k << endl;
+ if(c == ')') {
+ //to pass over labels in trees
+ c=filehandle.get();
+ while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ c=filehandle.get(); }
+ filehandle.putback(c);
+ }
+ if(c == ';') { return 0; }
+ if(c == -1) { return 0; }
+ //if you are a name
+ if((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != '\t') && (c != 32)) { //32 is space
+ name = "";
+ c = filehandle.get();
+ //k = c;
+//cout << k << endl;
+ while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {
+ name += c;
+ c = filehandle.get();
+ //k = c;
+//cout << " in name while " << k << endl;
+ }
+
+//cout << "name = " << name << endl;
+ globaldata->Treenames.push_back(name);
+ filehandle.putback(c);
+//k = c;
+//cout << " after putback" << k << endl;
+ }
+
+ if(c == ':') { //read until you reach the end of the branch length
+ while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) {
+ c = filehandle.get();
+ //k = c;
+ //cout << " in branch while " << k << endl;
+ }
+ filehandle.putback(c);
+ }
+
+ c = filehandle.get();
+//k = c;
+ //cout << " here after get " << k << endl;
+ if(c == ';') { return 0; }
+ if(c == ')') { filehandle.putback(c); }
+ //k = c;
+//cout << k << endl;
+
+ }
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "readTreeString");
+ exit(1);
+ }
+}
+
+/*******************************************************/