X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=engine.cpp;h=e4e107168c5723c82b90a7f103ccb8d9ee83cb60;hp=f128c4684040346110d519c56f45c9506e953866;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=65f2be9d8f9b4cf72b4aafd800fdd11ad26435fd

diff --git a/engine.cpp b/engine.cpp
index f128c46..e4e1071 100644
--- 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)
-			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)
-				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;
-		
-	}
-	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();	
@@ -179,15 +117,20 @@ bool InteractEngine::getInput(){
 					//cout << pid << " is in execute " << commandName << endl;
 					#endif
 					//executes valid command
+                    mout->changedSeqNames = false;
 					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(); }
@@ -214,14 +157,14 @@ 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 > ");
 				
 				if(nextCommand != NULL) {  add_history(nextCommand);  }	
 				else{ //^D causes null string and we want it to quit mothur
-					strcpy(nextCommand, "quit"); 
+					nextCommand = strdup("quit");
 					mout->mothurOut(nextCommand);
 				}	
 				
@@ -262,7 +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;
 				
@@ -336,7 +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();
@@ -360,15 +303,21 @@ bool BatchEngine::getInput(){
 						if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
 					#endif
 					//executes valid command
+                    mout->changedSeqNames = false;
 					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(); }
@@ -399,7 +348,7 @@ bool BatchEngine::getInput(){
 /***********************************************************************/
 string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
 	try {
-		
+			
 		string nextcommand = "";
 		
 		if (inputBatchFile.eof()) { nextcommand = "quit()"; }
@@ -425,7 +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;
 				
@@ -468,11 +417,15 @@ 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) || (input != "quit()")) {
-				mout->mothurOutEndLine();
-				mout->mothurOut("mothur > " + input);
-				mout->mothurOutEndLine();
+			if (mout->gui) {
+				if ((input.find("quit") != string::npos) || (input.find("set.logfile") != string::npos)) {}
+				else if ((input.find("get.current") != string::npos) && (!mout->hasCurrentFiles())) {}
+				else { mout->mothurOutEndLine(); mout->mothurOut("mothur > " + input); mout->mothurOutEndLine(); }
+			}else{
+				mout->mothurOutEndLine(); mout->mothurOut("mothur > " + input); mout->mothurOutEndLine();
 			}
 			
 			#ifdef USE_MPI
@@ -521,15 +474,20 @@ bool ScriptEngine::getInput(){
 							//cout << pid << " is in execute" << endl;	
 					#endif
 					//executes valid command
+                    mout->changedSeqNames = false;
 					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(); }