Updates related files to include blastLocation

#223
mothur · 2ee0071371a357d218e579b58b1fd5fe5adcac01 · mothur-westcott committed Aug 15, 2016 · Aug 15, 2016 · 2ee0071
1 parent 3c6e19e
commit 2ee0071371a357d218e579b58b1fd5fe5adcac01
diff --git a/source/commands/catchallcommand.cpp b/source/commands/catchallcommand.cpp
@@ -200,8 +200,8 @@ int CatchAllCommand::execute() {
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		//get location of catchall
-		path = m->argv;
-		path = path.substr(0, (path.find_last_of("othur")-5));
+		path = m->mothurProgramPath;
+		//path = path.substr(0, (path.find_last_of("othur")-5));
 		path = m->getFullPathName(path);
 		
         if (m->debug) { m->mothurOut("[DEBUG]: mothur's path = " + path + "\n"); }
diff --git a/source/commands/chimerauchimecommand.cpp b/source/commands/chimerauchimecommand.cpp
@@ -556,10 +556,10 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
 			if (hasGroup && (templatefile != "self")) { m->mothurOut("You have provided a group file and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
 			
 			//look for uchime exe
-			path = m->argv;
-			string tempPath = path;
-			for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
-			path = path.substr(0, (tempPath.find_last_of('m')));
+			path = m->mothurProgramPath;
+			//string tempPath = path;
+			//for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+			//path = path.substr(0, (tempPath.find_last_of('m')));
 			
 			string uchimeCommand;
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
diff --git a/source/commands/chimeravsearchcommand.cpp b/source/commands/chimeravsearchcommand.cpp
@@ -510,10 +510,10 @@ ChimeraVsearchCommand::ChimeraVsearchCommand(string option)  {
             if (hasGroup && (templatefile != "self")) { m->mothurOut("You have provided a group file and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
             
             //look for uchime exe
-            path = m->argv;
-            string tempPath = path;
-            for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
-            path = path.substr(0, (tempPath.find_last_of('m')));
+            path = m->mothurProgramPath;
+            //string tempPath = path;
+            //for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+            //path = path.substr(0, (tempPath.find_last_of('m')));
             
             string vsearchCommand;
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
diff --git a/source/commands/clustercommand.cpp b/source/commands/clustercommand.cpp
@@ -371,11 +371,11 @@ int ClusterCommand::execute(){
 
 int ClusterCommand::runVsearchCluster(){
     try {
-        //look for uchime exe
-        string path = m->argv;
-        string tempPath = path;
-        for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
-        path = path.substr(0, (tempPath.find_last_of('m')));
+        //look for vsearch exe
+        string path = m->mothurProgramPath;
+        //string tempPath = path;
+        //for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+        //path = path.substr(0, (tempPath.find_last_of('m')));
         
         string vsearchCommand;
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
diff --git a/source/commands/clustersplitcommand.cpp b/source/commands/clustersplitcommand.cpp
@@ -1686,10 +1686,10 @@ bool ClusterSplitCommand::findVsearch(){
         if (cutoffNotSet) {  m->mothurOut("\nYou did not set a cutoff, using 0.03.\n"); cutoff = 0.03; }
         
         //look for uchime exe
-        string path = m->argv;
-        string tempPath = path;
-        for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
-        path = path.substr(0, (tempPath.find_last_of('m')));
+        string path = m->mothurProgramPath;
+        //string tempPath = path;
+        //for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+        //path = path.substr(0, (tempPath.find_last_of('m')));
         
         string vsearchCommand;
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
diff --git a/source/commands/getcommandinfocommand.cpp b/source/commands/getcommandinfocommand.cpp
@@ -84,7 +84,7 @@ int GetCommandInfoCommand::execute(){
 		
 		int numNonHidden = 0;
 		
-		out << "mothurLocation=" << m->getFullPathName(m->argv) << endl;
+		out << "mothurLocation=" << m->getFullPathName(m->mothurProgramPath) << endl;
 		out << "mothurVersion=" << m->getVersion() << endl;
 		
 		map<string, string> commands = commandFactory->getListCommands();
diff --git a/source/commands/makecontigscommand.cpp b/source/commands/makecontigscommand.cpp
@@ -2981,10 +2981,10 @@ vector< vector<string> > MakeContigsCommand::readFileNames(string filename){
             }
             
             //look for mothur exe
-            string mpath = m->argv;
-            string tempPath = mpath;
-            for (int i = 0; i < mpath.length(); i++) { tempPath[i] = tolower(mpath[i]); }
-            mpath = mpath.substr(0, (tempPath.find_last_of('m')));
+            string mpath = m->mothurProgramPath;
+            //string tempPath = mpath;
+            //for (int i = 0; i < mpath.length(); i++) { tempPath[i] = tolower(mpath[i]); }
+            //mpath = mpath.substr(0, (tempPath.find_last_of('m')));
             
             //check to make sure both are able to be opened
             ifstream in2;
diff --git a/source/commands/sffmultiplecommand.cpp b/source/commands/sffmultiplecommand.cpp
@@ -293,10 +293,10 @@ SffMultipleCommand::SffMultipleCommand(string option)  {
             
             temp = validParameter.validFile(parameters, "lookup", true);
 			if (temp == "not found")	{
-                string path = m->argv;
-                string tempPath = path;
-                for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
-                path = path.substr(0, (tempPath.find_last_of('m')));
+                string path = m->mothurProgramPath;
+                //string tempPath = path;
+                //for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+                //path = path.substr(0, (tempPath.find_last_of('m')));
                 
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                 path += "lookupFiles/";
@@ -311,10 +311,10 @@ SffMultipleCommand::SffMultipleCommand(string option)  {
 				lookupFileName = validParameter.validFile(parameters, "lookup", false);
 				
 				//if you can't open it its not inputDir, try mothur excutable location
-				string exepath = m->argv;
-				string tempPath = exepath;
-				for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
-				exepath = exepath.substr(0, (tempPath.find_last_of('m')));
+				string exepath = m->mothurProgramPath;
+				//string tempPath = exepath;
+				//for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
+				//exepath = exepath.substr(0, (tempPath.find_last_of('m')));
                 
 				string tryPath = m->getFullPathName(exepath) + m->getSimpleName(lookupFileName);
 				m->mothurOut("Unable to open " + lookupFileName + ". Trying mothur's executable location " + tryPath); m->mothurOutEndLine();
diff --git a/source/commands/shhhercommand.cpp b/source/commands/shhhercommand.cpp
@@ -231,10 +231,10 @@ ShhherCommand::ShhherCommand(string option) {
                     
                     //if you can't open it its not in current working directory or inputDir, try mothur excutable location
                     if (ableToOpen == 1) {
-                        string exepath = m->argv;
-                        string tempPath = exepath;
-                        for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
-                        exepath = exepath.substr(0, (tempPath.find_last_of('m')));
+                        string exepath = m->mothurProgramPath;
+                        //string tempPath = exepath;
+                        //for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
+                        //exepath = exepath.substr(0, (tempPath.find_last_of('m')));
                         
                         string tryPath = m->getFullPathName(exepath) + m->getSimpleName(fName);
                         m->mothurOut("Unable to open " + fName + ". Trying mothur's executable location " + tryPath); m->mothurOutEndLine();
@@ -261,10 +261,10 @@ ShhherCommand::ShhherCommand(string option) {
 			string temp;
 			temp = validParameter.validFile(parameters, "lookup", true);
 			if (temp == "not found")	{	
-				string path = m->argv;
-                string tempPath = path;
-                for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
-                path = path.substr(0, (tempPath.find_last_of('m')));
+				string path = m->mothurProgramPath;
+                //string tempPath = path;
+                //for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+                //path = path.substr(0, (tempPath.find_last_of('m')));
                 
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                 path += "lookupFiles/";
@@ -304,10 +304,10 @@ ShhherCommand::ShhherCommand(string option) {
 				
 				//if you can't open it its not in current working directory or inputDir, try mothur excutable location
 				if (ableToOpen == 1) {
-					string exepath = m->argv;
-					string tempPath = exepath;
-					for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
-					exepath = exepath.substr(0, (tempPath.find_last_of('m')));
+					string exepath = m->mothurProgramPath;
+					//string tempPath = exepath;
+					//for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
+					//exepath = exepath.substr(0, (tempPath.find_last_of('m')));
 					
 					string tryPath = m->getFullPathName(exepath) + m->getSimpleName(lookupFileName);
 					m->mothurOut("Unable to open " + lookupFileName + ". Trying mothur's executable location " + tryPath); m->mothurOutEndLine();
@@ -324,10 +324,10 @@ ShhherCommand::ShhherCommand(string option) {
 				lookupFileName = validParameter.validFile(parameters, "lookup", false);
 				
 				//if you can't open it its not inputDir, try mothur excutable location
-				string exepath = m->argv;
-				string tempPath = exepath;
-				for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
-				exepath = exepath.substr(0, (tempPath.find_last_of('m')));
+				string exepath = m->mothurProgramPath;
+				//string tempPath = exepath;
+				//for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
+				//exepath = exepath.substr(0, (tempPath.find_last_of('m')));
 					
 				string tryPath = m->getFullPathName(exepath) + m->getSimpleName(lookupFileName);
 				m->mothurOut("Unable to open " + lookupFileName + ". Trying mothur's executable location " + tryPath); m->mothurOutEndLine();
diff --git a/source/datastructures/blastalign.cpp b/source/datastructures/blastalign.cpp
@@ -22,8 +22,7 @@ BlastAlignment::BlastAlignment(float go, float ge, float ma, float mm) :
 			match(ma),				//	This is the score to award for two nucleotides matching (match >= 0)
 			mismatch(mm)			//	This is the penalty to assess for a mismatch (mismatch <= 0)
 {
-	path = m->argv;
-	path = path.substr(0, (path.find_last_of('m')));
+	path = m->getBlastPath();
 	
 	gapOpen = abs(go);				//	This is the penalty to assess for opening a gap (gapOpen >= 0)
 	gapExtend = abs(ge);				//	This is the penalty to assess for extending a gap (gapExtend >= 0)
diff --git a/source/datastructures/blastdb.cpp b/source/datastructures/blastdb.cpp
@@ -33,10 +33,10 @@ gapOpen(gO), gapExtend(gE), match(mm), misMatch(mM) {
 		
 		//make sure blast exists in the write place
 		if (path == "") {
-			path = m->argv;
-			string tempPath = path;
-			for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
-			path = path.substr(0, (tempPath.find_last_of('m')));
+			path = m->getBlastPath();
+			//string tempPath = path;
+			//for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+			//path = path.substr(0, (tempPath.find_last_of('m')));
 			
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			path += "blast/bin/";	
@@ -87,7 +87,7 @@ gapOpen(gO), gapExtend(gE), match(mm), misMatch(mM) {
 		megablastCommand = m->getFullPathName(megablastCommand);
 		ableToOpen = m->openInputFile(megablastCommand, in3, "no error"); in3.close();
 		if(ableToOpen == 1) {	m->mothurOut("[ERROR]: " +  megablastCommand + " file does not exist. mothur requires megablast.exe."); m->mothurOutEndLine(); m->control_pressed = true; }
-		
+        
 	}
 	catch(exception& e) {
 		m->errorOut(e, "BlastDB", "BlastDB");
@@ -105,10 +105,10 @@ BlastDB::BlastDB(string b, int tid) : Database() {
 		
 		//make sure blast exists in the write place
 		if (path == "") {
-			path = m->argv;
-			string tempPath = path;
-			for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
-			path = path.substr(0, (tempPath.find_last_of('m')));
+			path = m->getBlastPath();
+			//string tempPath = path;
+			//for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+			//path = path.substr(0, (tempPath.find_last_of('m')));
 			
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			path += "blast/bin/";	
diff --git a/source/engine.cpp b/source/engine.cpp
@@ -36,8 +36,10 @@ InteractEngine::InteractEngine(string path){
 	
 	//this will happen if you set the path variable to contain mothur's exe location
 	if (temppath == "") { path = mout->findProgramPath("mothur"); }
+    else { path = temppath; }
 	
-	mout->argv = path;
+	mout->mothurProgramPath = mout->getFullPathName(path);
+    mout->setBlastPath(mout->mothurProgramPath);
 
     //if you haven't set your own location
     #ifdef MOTHUR_FILES
@@ -173,8 +175,10 @@ BatchEngine::BatchEngine(string path, string batchFileName){
 	
 		//this will happen if you set the path variable to contain mothur's exe location
 		if (temppath == "") { path = mout->findProgramPath("mothur"); }
+        else { path = temppath; }
 		
-		mout->argv = path;
+		mout->mothurProgramPath = mout->getFullPathName(path);
+        mout->setBlastPath(mout->mothurProgramPath);
         
         //if you haven't set your own location
 #ifdef MOTHUR_FILES
@@ -308,8 +312,10 @@ ScriptEngine::ScriptEngine(string path, string commandString){
 
 		//this will happen if you set the path variable to contain mothur's exe location
 		if (temppath == "") { path = mout->findProgramPath("mothur"); }
+        else { path = temppath; }
 		
-		mout->argv = path;
+		mout->mothurProgramPath = mout->getFullPathName(path);
+        mout->setBlastPath(mout->mothurProgramPath);
     
         //if you haven't set your own location
 #ifdef MOTHUR_FILES
diff --git a/source/validparameter.cpp b/source/validparameter.cpp
@@ -247,11 +247,11 @@ string ValidParameters::validFile(map<string, string>& container, string paramet
 				
                 //if you can't open it, try mothur's location
                 if (ableToOpen == 1) {
-                    //look for uchime exe
-                    string mpath = m->argv;
-                    string tempPath = mpath;
-                    for (int i = 0; i < mpath.length(); i++) { tempPath[i] = tolower(mpath[i]); }
-                    mpath = mpath.substr(0, (tempPath.find_last_of('m')));
+                    //look for mothurs exe
+                    string mpath = m->mothurProgramPath;
+                    //string tempPath = mpath;
+                    //for (int i = 0; i < mpath.length(); i++) { tempPath[i] = tolower(mpath[i]); }
+                    //mpath = mpath.substr(0, (tempPath.find_last_of('m')));
                         
                     string tryPath = mpath + m->getSimpleName(it->second);
                     m->mothurOut("Unable to open " + it->second + ". Trying mothur's location " + tryPath); m->mothurOutEndLine();