X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=98d730c31c2d03e3222057f8cef3da571aca0877;hb=8e3e7b1e124f45cb1f2ca9d764ff67fa9b2e532b;hp=ea1c0e14dc9f89fe0157d24828a2e9552297389c;hpb=0ca63a8165baa0afa459e644ebe140ba496d5ba0;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
index ea1c0e1..98d730c 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -34,7 +34,7 @@ string Engine::findMothursPath(){
 		
 		//delimiting path char
 		char delim;
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			delim = ':';
 		#else
 			delim = ';';
@@ -44,8 +44,13 @@ string Engine::findMothursPath(){
 		vector<string> dirs;
 		mout->splitAtChar(envPath, dirs, delim);
 		
+        if (mout->debug) { mout->mothurOut("[DEBUG]: dir's in path: \n"); }
+        
 		//get path related to mothur
 		for (int i = 0; i < dirs.size(); i++) {
+            
+            if (mout->debug) { mout->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]);  }
@@ -53,10 +58,12 @@ string Engine::findMothursPath(){
 			//is this mothurs path?
 			if (tempLower.find("mothur") != -1) {  mothurPath = dirs[i]; break;  }
 		}
-		
+        
+		if (mout->debug) { mout->mothurOut("[DEBUG]: mothurPath = " + mothurPath + "\n"); }
+        
 		if (mothurPath != "") {
 			//add mothur so it looks like what argv would look like
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 				mothurPath += "/mothur";
 			#else
 				mothurPath += "\\mothur";
@@ -71,7 +78,7 @@ string Engine::findMothursPath(){
 				//is this mothurs path?
 				ifstream in;
 				string tempIn = dirs[i];
-				#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+				#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 					tempIn += "/mothur";
 				#else
 					tempIn += "\\mothur";
@@ -79,7 +86,7 @@ string Engine::findMothursPath(){
 				mout->openInputFile(tempIn, in, "");
 				
 				//if this file exists
-				if (in) { in.close(); mothurPath = tempIn;  break;  }
+				if (in) { in.close(); mothurPath = tempIn;  break; if (mout->debug) { mout->mothurOut("[DEBUG]: found it, mothurPath = " + mothurPath + "\n"); }  }
 			}
 		}
 		
@@ -183,7 +190,6 @@ bool InteractEngine::getInput(){
 					mout->clearGroups();
 					mout->clearAllGroups();
 					mout->Treenames.clear();
-					mout->names.clear();
 					mout->saveNextLabel = "";
 					mout->printedHeaders = false;
 					mout->commandInputsConvertError = false;
@@ -219,7 +225,7 @@ bool InteractEngine::getInput(){
 string Engine::getCommand()  {
 	try {
 	
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			#ifdef USE_READLINE
 				char* nextCommand = NULL;
 				nextCommand = readline("mothur > ");
@@ -369,7 +375,6 @@ bool BatchEngine::getInput(){
 					mout->clearGroups();
 					mout->clearAllGroups();
 					mout->Treenames.clear();
-					mout->names.clear();
 					mout->saveNextLabel = "";
 					mout->printedHeaders = false;
 					mout->commandInputsConvertError = false;
@@ -538,7 +543,6 @@ bool ScriptEngine::getInput(){
 					mout->clearGroups();
 					mout->clearAllGroups();
 					mout->Treenames.clear();
-					mout->names.clear();
 					mout->saveNextLabel = "";
 					mout->printedHeaders = false;
 					mout->commandInputsConvertError = false;