X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=98d730c31c2d03e3222057f8cef3da571aca0877;hb=2009a1a1f47e7467094d844e7c07ab8ddf7bb447;hp=3108f3733d59078c9c5273b0a2a2f1c145cd33d0;hpb=ef2b09798e381dbb9b9836e09c72f8af57825830;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
index 3108f37..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"); }  }
 			}
 		}
 		
@@ -180,15 +187,18 @@ bool InteractEngine::getInput(){
 					#endif
 					//executes valid command
 					mout->runParse = true;
-					mout->Groups.clear();
-					mout->namesOfGroups.clear();
+					mout->clearGroups();
+					mout->clearAllGroups();
 					mout->Treenames.clear();
-					mout->names.clear();
 					mout->saveNextLabel = "";
 					mout->printedHeaders = false;
+					mout->commandInputsConvertError = false;
+					mout->currentBinLabels.clear();
+					mout->binLabelsInFile.clear();
 							
 					Command* command = cFactory->getCommand(commandName, options);
-					quitCommandCalled = command->execute();
+					if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
+					else { quitCommandCalled = command->execute(); }
 							
 					//if we aborted command
 					if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
@@ -215,7 +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 > ");
@@ -362,15 +372,19 @@ bool BatchEngine::getInput(){
 					#endif
 					//executes valid command
 					mout->runParse = true;
-					mout->Groups.clear();
-					mout->namesOfGroups.clear();
+					mout->clearGroups();
+					mout->clearAllGroups();
 					mout->Treenames.clear();
-					mout->names.clear();
 					mout->saveNextLabel = "";
 					mout->printedHeaders = false;
+					mout->commandInputsConvertError = false;
+					mout->currentBinLabels.clear();
+					mout->binLabelsInFile.clear();
+
 							
 					Command* command = cFactory->getCommand(commandName, options);
-					quitCommandCalled = command->execute();
+					if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
+					else { quitCommandCalled = command->execute(); }
 							
 					//if we aborted command
 					if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
@@ -401,7 +415,7 @@ bool BatchEngine::getInput(){
 /***********************************************************************/
 string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
 	try {
-		
+			
 		string nextcommand = "";
 		
 		if (inputBatchFile.eof()) { nextcommand = "quit()"; }
@@ -526,15 +540,18 @@ bool ScriptEngine::getInput(){
 					#endif
 					//executes valid command
 					mout->runParse = true;
-					mout->Groups.clear();
-					mout->namesOfGroups.clear();
+					mout->clearGroups();
+					mout->clearAllGroups();
 					mout->Treenames.clear();
-					mout->names.clear();
 					mout->saveNextLabel = "";
 					mout->printedHeaders = false;
-							
+					mout->commandInputsConvertError = false;
+					mout->currentBinLabels.clear();
+					mout->binLabelsInFile.clear();
+
 					Command* command = cFactory->getCommand(commandName, options);
-					quitCommandCalled = command->execute();
+					if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
+					else { quitCommandCalled = command->execute(); }
 					
 					//if we aborted command
 					if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }