forced rarefaction.single to output ending line for all groups. added subsample...

[mothur.git] / engine.cpp

diff --git a/engine.cpp b/engine.cpp
index ea1c0e14dc9f89fe0157d24828a2e9552297389c..98d730c31c2d03e3222057f8cef3da571aca0877 100644 (file)
--- 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;