fixed catchall PATH variable bug added trimera to chimera.slayer

[mothur.git] / engine.cpp

diff --git a/engine.cpp b/engine.cpp
index dd61de67d36974af09bf700879c8b59821ebd83f..54197174e1fa3da14861614734b1dc58314a466a 100644 (file)
--- a/engine.cpp
+++ b/engine.cpp
@@ -25,19 +25,12 @@ Engine::Engine(){
                exit(1);
        }
 }
-
 /***********************************************************************/
-
-InteractEngine::InteractEngine(string path){
-
-       globaldata = GlobalData::getInstance();
-       
-       string temppath = path.substr(0, (path.find_last_of('m')));
-       
-       //this will happen if you set the path variable to contain mothur's exe location
-       if (temppath == "") { 
-       
+string Engine::findMothursPath(){
+       try { 
+               
                string envPath = getenv("PATH");
+               string mothurPath = "";
                
                //delimiting path char
                char delim;
@@ -52,7 +45,6 @@ InteractEngine::InteractEngine(string path){
                mout->splitAtChar(envPath, dirs, delim);
                
                //get path related to mothur
-               string mothurPath = "";
                for (int i = 0; i < dirs.size(); i++) {
                        //to lower so we can find it
                        string tempLower = "";
@@ -62,15 +54,53 @@ InteractEngine::InteractEngine(string path){
                        if (tempLower.find("mothur") != -1) {  mothurPath = dirs[i]; break;  }
                }
                
-               //add mothur so it looks like what argv would look like
-               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-                       mothurPath += "/mothur";
-               #else
-                       mothurPath += "\\mothur";
-               #endif
+               if (mothurPath != "") {
+                       //add mothur so it looks like what argv would look like
+                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                               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)
+                                       tempIn += "/mothur";
+                               #else
+                                       tempIn += "\\mothur";
+                               #endif
+                               mout->openInputFile(tempIn, in, "");
+                               
+                               //if this file exists
+                               if (in) { in.close(); mothurPath = tempIn;  break;  }
+                       }
+               }
+               
+               return mothurPath;
                
-               path = mothurPath;
        }
+       catch(exception& e) {
+               mout->errorOut(e, "Engine", "findMothursPath");
+               exit(1);
+       }
+}
+/***********************************************************************/
+
+InteractEngine::InteractEngine(string path){
+
+       globaldata = GlobalData::getInstance();
+       
+       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(); }
        
        globaldata->argv = path;
 }
@@ -224,46 +254,11 @@ BatchEngine::BatchEngine(string path, string batchFileName){
        
                openedBatch = mout->openInputFile(batchFileName, inputBatchFile);
                
-               string temppath = path.substr(0, (path.find_last_of('m')));
+               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 == "") { 
+               if (temppath == "") { path = findMothursPath(); }
                
-                       string envPath = getenv("PATH");
-                       
-                       //delimiting path char
-                       char delim;
-                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-                               delim = ':';
-                       #else
-                               delim = ';';
-                       #endif
-                       
-                       //break apart path variable by ':'
-                       vector<string> dirs;
-                       mout->splitAtChar(envPath, dirs, delim);
-                       
-                       //get path related to mothur
-                       string mothurPath = "";
-                       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;  }
-                       }
-                       
-                       //add mothur so it looks like what argv would look like
-                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-                               mothurPath += "/mothur";
-                       #else
-                               mothurPath += "\\mothur";
-                       #endif
-                       
-                       path = mothurPath;
-               }
-
                globaldata->argv = path;
                                
        }
@@ -416,46 +411,11 @@ ScriptEngine::ScriptEngine(string path, string commandString){
                //remove quotes
                listOfCommands = commandString.substr(1, (commandString.length()-1));
                
-               string temppath = path.substr(0, (path.find_last_of('m')));
-       
+               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 == "") { 
+               if (temppath == "") { path = findMothursPath(); }
                
-                       string envPath = getenv("PATH");
-                       
-                       //delimiting path char
-                       char delim;
-                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-                               delim = ':';
-                       #else
-                               delim = ';';
-                       #endif
-                       
-                       //break apart path variable by ':'
-                       vector<string> dirs;
-                       mout->splitAtChar(envPath, dirs, delim);
-                       
-                       //get path related to mothur
-                       string mothurPath = "";
-                       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;  }
-                       }
-                       
-                       //add mothur so it looks like what argv would look like
-                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-                               mothurPath += "/mothur";
-                       #else
-                               mothurPath += "\\mothur";
-                       #endif
-                       
-                       path = mothurPath;
-               }
-
                globaldata->argv = path;
                                
        }