changing command name classify.shared to classifyrf.shared

[mothur.git] / sffmultiplecommand.cpp

diff --git a/sffmultiplecommand.cpp b/sffmultiplecommand.cpp
index 00f23ed24cc83e8eddf66f328a1fe3ce765e122d..d8a4b96ec155d155c0ca6dae946b821cb1a238e5 100644 (file)
--- a/sffmultiplecommand.cpp
+++ b/sffmultiplecommand.cpp
@@ -291,8 +291,18 @@ SffMultipleCommand::SffMultipleCommand(string option)  {
                        keepforward = m->isTrue(temp);
             
             temp = validParameter.validFile(parameters, "lookup", true);
-                       if (temp == "not found")        {       
-                               lookupFileName = "LookUp_Titanium.pat"; 
+                       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')));
+                
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+                path += "lookupFiles/";
+#else
+                path += "lookupFiles\\";
+#endif
+                               lookupFileName = m->getFullPathName(path) + "LookUp_Titanium.pat";
                                
                                int ableToOpen;
                                ifstream in;
@@ -302,7 +312,7 @@ SffMultipleCommand::SffMultipleCommand(string option)  {
                                //if you can't open it, try input location
                                if (ableToOpen == 1) {
                                        if (inputDir != "") { //default path is set
-                                               string tryPath = inputDir + lookupFileName;
+                                               string tryPath = inputDir + m->getSimpleName(lookupFileName);
                                                m->mothurOut("Unable to open " + lookupFileName + ". Trying input directory " + tryPath); m->mothurOutEndLine();
                                                ifstream in2;
                                                ableToOpen = m->openInputFile(tryPath, in2, "noerror");
@@ -350,7 +360,7 @@ SffMultipleCommand::SffMultipleCommand(string option)  {
                                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) + lookupFileName;
+                               string tryPath = m->getFullPathName(exepath) + m->getSimpleName(lookupFileName);
                                m->mothurOut("Unable to open " + lookupFileName + ". Trying mothur's executable location " + tryPath); m->mothurOutEndLine();
                                ifstream in2;
                                int ableToOpen = m->openInputFile(tryPath, in2, "noerror");