changes while testing

[mothur.git] / engine.cpp

diff --git a/engine.cpp b/engine.cpp
index ffbe324acd490ec6eb621ce0fe8d26b3b38d3ac0..e4e107168c5723c82b90a7f103ccb8d9ee83cb60 100644 (file)
--- a/engine.cpp
+++ b/engine.cpp
@@ -26,71 +26,7 @@ Engine::Engine(){
        }
 }
 /***********************************************************************/
-string Engine::findMothursPath(){
-       try { 
-               
-               string envPath = getenv("PATH");
-               string mothurPath = "";
-               
-               //delimiting path char
-               char delim;
-               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
-                       delim = ':';
-               #else
-                       delim = ';';
-               #endif
-               
-               //break apart path variable by ':'
-               vector<string> dirs;
-               mout->splitAtChar(envPath, dirs, delim);
-               
-               //get path related to mothur
-               for (int i = 0; i < dirs.size(); i++) {
-                       //to lower so we can find it
-                       string tempLower = "";
-                       for (int j = 0; j < dirs[i].length(); j++) {  tempLower += tolower(dirs[i][j]);  }
-                       
-                       //is this mothurs path?
-                       if (tempLower.find("mothur") != -1) {  mothurPath = dirs[i]; break;  }
-               }
-               
-               if (mothurPath != "") {
-                       //add mothur so it looks like what argv would look like
-                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
-                               mothurPath += "/mothur";
-                       #else
-                               mothurPath += "\\mothur";
-                       #endif
-               }else {
-                       //okay mothur is not in the path, so the folder mothur is in must be in the path
-                       //lets find out which one
-                       
-                       //get path related to mothur
-                       for (int i = 0; i < dirs.size(); i++) {
-                                                               
-                               //is this mothurs path?
-                               ifstream in;
-                               string tempIn = dirs[i];
-                               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
-                                       tempIn += "/mothur";
-                               #else
-                                       tempIn += "\\mothur";
-                               #endif
-                               mout->openInputFile(tempIn, in, "");
-                               
-                               //if this file exists
-                               if (in) { in.close(); mothurPath = tempIn;  break;  }
-                       }
-               }
-               
-               return mothurPath;
-               
-       }
-       catch(exception& e) {
-               mout->errorOut(e, "Engine", "findMothursPath");
-               exit(1);
-       }
-}
+
 /***********************************************************************/
 
 InteractEngine::InteractEngine(string path){
@@ -99,7 +35,7 @@ InteractEngine::InteractEngine(string path){
        string temppath = path.substr(0, (path.find_last_of("othur")-5));
        
        //this will happen if you set the path variable to contain mothur's exe location
-       if (temppath == "") { path = findMothursPath(); }
+       if (temppath == "") { path = mout->findProgramPath("mothur"); }
        
        mout->argv = path;
 }
@@ -129,7 +65,9 @@ bool InteractEngine::getInput(){
                                if (pid == 0) {
                                
                        #endif
-                       
+                    
+                       if (mout->changedSeqNames) { mout->mothurOut("[WARNING]: your sequence names contained ':'.  I changed them to '_' to avoid problems in your downstream analysis.\n"); }
+                    
                        mout->mothurOutEndLine();
                        
                        input = getCommand();   
@@ -179,11 +117,11 @@ bool InteractEngine::getInput(){
                                        //cout << pid << " is in execute " << commandName << endl;
                                        #endif
                                        //executes valid command
+                    mout->changedSeqNames = false;
                                        mout->runParse = true;
                                        mout->clearGroups();
                                        mout->clearAllGroups();
                                        mout->Treenames.clear();
-                                       mout->names.clear();
                                        mout->saveNextLabel = "";
                                        mout->printedHeaders = false;
                                        mout->commandInputsConvertError = false;
@@ -267,7 +205,7 @@ BatchEngine::BatchEngine(string path, string batchFileName){
                string temppath = path.substr(0, (path.find_last_of("othur")-5));
        
                //this will happen if you set the path variable to contain mothur's exe location
-               if (temppath == "") { path = findMothursPath(); }
+               if (temppath == "") { path = mout->findProgramPath("mothur"); }
                
                mout->argv = path;
                                
@@ -341,7 +279,7 @@ bool BatchEngine::getInput(){
                        
                        
                        if (input[0] != '#') {
-                               
+                               if (mout->changedSeqNames) { mout->mothurOut("[WARNING]: your sequence names contained ':'.  I changed them to '_' to avoid problems in your downstream analysis.\n"); }
                                mout->mothurOutEndLine();
                                mout->mothurOut("mothur > " + input);
                                mout->mothurOutEndLine();
@@ -365,11 +303,11 @@ bool BatchEngine::getInput(){
                                                if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
                                        #endif
                                        //executes valid command
+                    mout->changedSeqNames = false;
                                        mout->runParse = true;
                                        mout->clearGroups();
                                        mout->clearAllGroups();
                                        mout->Treenames.clear();
-                                       mout->names.clear();
                                        mout->saveNextLabel = "";
                                        mout->printedHeaders = false;
                                        mout->commandInputsConvertError = false;
@@ -436,7 +374,7 @@ ScriptEngine::ScriptEngine(string path, string commandString){
                string temppath = path.substr(0, (path.find_last_of("othur")-5));
 
                //this will happen if you set the path variable to contain mothur's exe location
-               if (temppath == "") { path = findMothursPath(); }
+               if (temppath == "") { path = mout->findProgramPath("mothur"); }
                
                mout->argv = path;
                                
@@ -479,6 +417,8 @@ bool ScriptEngine::getInput(){
                        input = getNextCommand(listOfCommands); 
                        
                        if (input == "") { input = "quit()"; }
+                    
+            if (mout->changedSeqNames) { mout->mothurOut("[WARNING]: your sequence names contained ':'.  I changed them to '_' to avoid problems in your downstream analysis.\n"); }
                        
                        if (mout->gui) {
                                if ((input.find("quit") != string::npos) || (input.find("set.logfile") != string::npos)) {}
@@ -534,11 +474,11 @@ bool ScriptEngine::getInput(){
                                                        //cout << pid << " is in execute" << endl;      
                                        #endif
                                        //executes valid command
+                    mout->changedSeqNames = false;
                                        mout->runParse = true;
                                        mout->clearGroups();
                                        mout->clearAllGroups();
                                        mout->Treenames.clear();
-                                       mout->names.clear();
                                        mout->saveNextLabel = "";
                                        mout->printedHeaders = false;
                                        mout->commandInputsConvertError = false;