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 dbdcc36300f2fd5d3f5ea6135dbc8666f328bba0..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"); }  }
                        }
                }
                
@@ -179,8 +186,19 @@ bool InteractEngine::getInput(){
                                        //cout << pid << " is in execute " << commandName << endl;
                                        #endif
                                        //executes valid command
+                                       mout->runParse = true;
+                                       mout->clearGroups();
+                                       mout->clearAllGroups();
+                                       mout->Treenames.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(); }
@@ -207,14 +225,14 @@ 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);
                                }       
                                
@@ -353,8 +371,20 @@ bool BatchEngine::getInput(){
                                                if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
                                        #endif
                                        //executes valid command
+                                       mout->runParse = true;
+                                       mout->clearGroups();
+                                       mout->clearAllGroups();
+                                       mout->Treenames.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(); }
@@ -385,7 +415,7 @@ bool BatchEngine::getInput(){
 /***********************************************************************/
 string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
        try {
-               
+                       
                string nextcommand = "";
                
                if (inputBatchFile.eof()) { nextcommand = "quit()"; }
@@ -455,9 +485,13 @@ bool ScriptEngine::getInput(){
                        
                        if (input == "") { 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
                                //send commandName
@@ -505,8 +539,19 @@ bool ScriptEngine::getInput(){
                                                        //cout << pid << " is in execute" << endl;      
                                        #endif
                                        //executes valid command
+                                       mout->runParse = true;
+                                       mout->clearGroups();
+                                       mout->clearAllGroups();
+                                       mout->Treenames.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(); }