fixed bug in read.tree updates help and validparameters strings, added ability for...

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index da81879f48fff6fbe87ac67ba950afd84c03a69e..67c49bd28c942d5c432538b6f965406c0b592ae6 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -30,6 +30,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        clear();
                        gGroupmap = NULL;
                        gTree.clear();
+                       Treenames.clear();
                        labels.clear(); lines.clear(); groups.clear();
                        allLines = 1;
                }
@@ -325,3 +326,144 @@ GlobalData::~GlobalData() {
        if(gorder != NULL)                      {       delete gorder;          }
 }
 /*******************************************************/
+
+/*******************************************************/
+void GlobalData::parseTreeFile() {
+       //only takes names from the first tree and assumes that all trees use the same names.
+       try {
+               string filename = treefile;
+               ifstream filehandle;
+               openInputFile(filename, filehandle);
+               int c, comment;
+               comment = 0;
+               
+               //if you 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();
+                               }
+
+                               readTreeString(filehandle); 
+                       }
+               //if you 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.
+                                       readTreeString(filehandle);     
+                                       break;
+                               }
+                       }
+                       
+                       //use nexus translation rather than parsing tree to save time
+                       if ((holder == "translate") || (holder == "Translate")) {
+cout << "there is a translate " << endl;
+                               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
+                                       Treenames.push_back(number);
+                               }
+                               if (number == ";") { Treenames.pop_back(); }  //in case ';' from translation is on next line instead of next to last name
+                       }
+               }
+               
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }               
+}
+/*******************************************************/
+
+/*******************************************************/
+void GlobalData::readTreeString(ifstream& filehandle)  {
+       try {
+               int c;
+               string name; //k
+               
+               while((c = filehandle.peek()) != ';') { 
+                               //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;
+                               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();
+                       if (c == ';') { break; }
+               //      k = c;
+//cout << k << endl;
+
+               }
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }               
+}      
+
+/*******************************************************/
+
+/*******************************************************/
+
+