]> git.donarmstrong.com Git - mothur.git/blobdiff - engine.cpp
removing chime source files from mother project.
[mothur.git] / engine.cpp
index 5e82d1344d9fa068078e0176b1e655a8290cd42b..24adcb53b59f39f049269d74b4da953a5f387262 100644 (file)
@@ -25,23 +25,16 @@ Engine::Engine(){
                exit(1);
        }
 }
-
 /***********************************************************************/
-
-InteractEngine::InteractEngine(string path){
-
-       globaldata = GlobalData::getInstance();
-       
-       string temppath = path.substr(0, (path.find_last_of('m')));
-       
-       //this will happen if you set the path variable to contain mothur's exe location
-       if (temppath == "") { 
-       
+string Engine::findMothursPath(){
+       try { 
+               
                string envPath = getenv("PATH");
+               string mothurPath = "";
                
                //delimiting path char
                char delim;
-               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                        delim = ':';
                #else
                        delim = ';';
@@ -52,7 +45,6 @@ InteractEngine::InteractEngine(string path){
                mout->splitAtChar(envPath, dirs, delim);
                
                //get path related to mothur
-               string mothurPath = "";
                for (int i = 0; i < dirs.size(); i++) {
                        //to lower so we can find it
                        string tempLower = "";
@@ -62,17 +54,54 @@ InteractEngine::InteractEngine(string path){
                        if (tempLower.find("mothur") != -1) {  mothurPath = dirs[i]; break;  }
                }
                
-               //add mothur so it looks like what argv would look like
-               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-                       mothurPath += "/mothur";
-               #else
-                       mothurPath += "\\mothur";
-               #endif
+               if (mothurPath != "") {
+                       //add mothur so it looks like what argv would look like
+                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+                               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) || (__linux__) || (__unix__) || (__unix)
+                                       tempIn += "/mothur";
+                               #else
+                                       tempIn += "\\mothur";
+                               #endif
+                               mout->openInputFile(tempIn, in, "");
+                               
+                               //if this file exists
+                               if (in) { in.close(); mothurPath = tempIn;  break;  }
+                       }
+               }
+               
+               return mothurPath;
                
-               path = mothurPath;
        }
+       catch(exception& e) {
+               mout->errorOut(e, "Engine", "findMothursPath");
+               exit(1);
+       }
+}
+/***********************************************************************/
+
+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(); }
        
-       globaldata->argv = path;
+       mout->argv = path;
 }
 
 /***********************************************************************/
@@ -150,8 +179,23 @@ 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(); }
+
                                        mout->control_pressed = 0;
                                        mout->executing = false;
                                                                                
@@ -174,14 +218,14 @@ 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
-                                       nextCommand = "quit"; 
+                                       nextCommand = strdup("quit");
                                        mout->mothurOut(nextCommand);
                                }       
                                
@@ -199,7 +243,7 @@ string Engine::getCommand()  {
                                string nextCommand = "";
                                
                                mout->mothurOut("mothur > ");
-                               m->getline(cin, nextCommand);
+                               getline(cin, nextCommand);
                                mout->mothurOutJustToLog(toString(nextCommand));
                                
                                return nextCommand;
@@ -216,51 +260,15 @@ string Engine::getCommand()  {
 //This function opens the batchfile to be used by BatchEngine::getInput.
 BatchEngine::BatchEngine(string path, string batchFileName){
        try {
-               globaldata = GlobalData::getInstance();
        
                openedBatch = mout->openInputFile(batchFileName, inputBatchFile);
                
-               string temppath = path.substr(0, (path.find_last_of('m')));
+               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 == "") { 
+               if (temppath == "") { path = findMothursPath(); }
                
-                       string envPath = getenv("PATH");
-                       
-                       //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
-                       string mothurPath = "";
-                       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;  }
-                       }
-                       
-                       //add mothur so it looks like what argv would look like
-                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-                               mothurPath += "/mothur";
-                       #else
-                               mothurPath += "\\mothur";
-                       #endif
-                       
-                       path = mothurPath;
-               }
-
-               globaldata->argv = path;
+               mout->argv = path;
                                
        }
        catch(exception& e) {
@@ -291,7 +299,7 @@ bool BatchEngine::getInput(){
                //CommandFactory cFactory;
                int quitCommandCalled = 0;
            int count = 0;
-               while(quitCommandCalled == 0){
+               while(quitCommandCalled != 1){
                        
                        #ifdef USE_MPI
                                int pid, processors;
@@ -356,8 +364,24 @@ 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(); }
+
                                        mout->control_pressed = 0;
                                        mout->executing = false;
                                                                                
@@ -384,7 +408,7 @@ bool BatchEngine::getInput(){
 /***********************************************************************/
 string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
        try {
-               
+                       
                string nextcommand = "";
                
                if (inputBatchFile.eof()) { nextcommand = "quit()"; }
@@ -403,52 +427,16 @@ string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
 //This function opens the batchfile to be used by BatchEngine::getInput.
 ScriptEngine::ScriptEngine(string path, string commandString){
        try {
-               globaldata = GlobalData::getInstance();
                
                //remove quotes
                listOfCommands = commandString.substr(1, (commandString.length()-1));
                
-               string temppath = path.substr(0, (path.find_last_of('m')));
-       
+               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 == "") { 
+               if (temppath == "") { path = findMothursPath(); }
                
-                       string envPath = getenv("PATH");
-                       
-                       //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
-                       string mothurPath = "";
-                       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;  }
-                       }
-                       
-                       //add mothur so it looks like what argv would look like
-                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-                               mothurPath += "/mothur";
-                       #else
-                               mothurPath += "\\mothur";
-                       #endif
-                       
-                       path = mothurPath;
-               }
-
-               globaldata->argv = path;
+               mout->argv = path;
                                
        }
        catch(exception& e) {
@@ -474,7 +462,7 @@ bool ScriptEngine::getInput(){
                //CommandFactory cFactory;
                int quitCommandCalled = 0;
        
-               while(quitCommandCalled == 0){
+               while(quitCommandCalled != 1){
                        
                        #ifdef USE_MPI
                                int pid, processors;
@@ -490,9 +478,13 @@ 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
@@ -531,7 +523,6 @@ bool ScriptEngine::getInput(){
                                        mout->executing = true;
                                        #ifdef USE_MPI
                                                int pid, numProcesses;
-                                               MPI_Status status; 
                                                
                                                MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
                                                MPI_Comm_size(MPI_COMM_WORLD, &numProcesses); 
@@ -541,8 +532,23 @@ 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(); }
+                                                       
                                        mout->control_pressed = 0;
                                        mout->executing = false;
                                                                        
@@ -571,11 +577,16 @@ string ScriptEngine::getNextCommand(string& commandString) {
                
                string nextcommand = "";
                int count = 0;
+               bool ignoreSemiColons = false;
                
                //go through string until you reach ; or end
                while (count < commandString.length()) { 
                        
-                       if (commandString[count] == ';') {  break;   }
+                        //you want to ignore any ; until you reach the next '
+                       if ((commandString[count] == '\'') && (!ignoreSemiColons)) {  ignoreSemiColons = true;  } 
+                       else if ((commandString[count] == '\'') && (ignoreSemiColons)) {  ignoreSemiColons = false;  } 
+                               
+                       if ((commandString[count] == ';') && (!ignoreSemiColons)) {  break;   }
                        else {          nextcommand += commandString[count];    }
                        
                        count++;