added code to check path for uchime and catchall executables

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index 61b39514e43b79bc146eb3e37ed4dc8d41017a62..6ecb86f94e5533165551ed5ae571f0c51f3c9ff9 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -117,6 +117,81 @@ void MothurOut::clearCurrentFiles()  {
                exit(1);
        }
 }
+/***********************************************************************/
+string MothurOut::findProgramPath(string programName){
+       try { 
+               
+               string envPath = getenv("PATH");
+               string pPath = "";
+               
+               //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;
+               splitAtChar(envPath, dirs, delim);
+               
+        if (debug) { mothurOut("[DEBUG]: dir's in path: \n"); }
+        
+               //get path related to mothur
+               for (int i = 0; i < dirs.size(); i++) {
+            
+            if (debug) { mothurOut("[DEBUG]: " + dirs[i] + "\n"); }
+            
+                       //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(programName) != -1) {  pPath = dirs[i]; break;  }
+               }
+        
+               if (debug) { mothurOut("[DEBUG]: programPath = " + pPath + "\n"); }
+        
+               if (pPath != "") {
+                       //add programName so it looks like what argv would look like
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+            pPath += "/" + programName;
+#else
+            pPath += "\\" + programName;
+#endif
+               }else {
+                       //okay programName is not in the path, so the folder programName is in must be in the path
+                       //lets find out which one
+                       
+                       //get path related to the program
+                       for (int i = 0; i < dirs.size(); i++) {
+                
+                if (debug) { mothurOut("[DEBUG]: looking in " + dirs[i] + " for " + programName + " \n"); }
+                
+                               //is this the programs path?
+                               ifstream in;
+                               string tempIn = dirs[i];
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+                tempIn += "/" + programName;
+#else
+                tempIn += "\\" + programName;
+#endif
+                               openInputFile(tempIn, in, "");
+                               
+                               //if this file exists
+                               if (in) { in.close(); pPath = tempIn; if (debug) { mothurOut("[DEBUG]: found it, programPath = " + pPath + "\n"); } break;   }
+                       }
+               }
+               
+               return pPath;
+               
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "findProgramPath");
+               exit(1);
+       }
+}
 /*********************************************************************************************/
 void MothurOut::setFileName(string filename)  {
        try {