exit(1);
}
}
+/***********************************************************************/
/***********************************************************************/
InteractEngine::InteractEngine(string path){
- globaldata = GlobalData::getInstance();
- 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 == "") {
-
- 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;
- }
+ if (temppath == "") { path = mout->findProgramPath("mothur"); }
- globaldata->argv = path;
+ mout->argv = path;
}
/***********************************************************************/
if (pid == 0) {
#endif
-
+
+ if (mout->changedSeqNames) { mout->mothurOut("[WARNING]: your sequence names contained ':'. I changed them to '_' to avoid problems in your downstream analysis.\n"); }
+
mout->mothurOutEndLine();
input = getCommand();
//cout << pid << " is in execute " << commandName << endl;
#endif
//executes valid command
+ mout->changedSeqNames = false;
+ 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;
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);
}
//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 = mout->findProgramPath("mothur"); }
- 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) {
//CommandFactory cFactory;
int quitCommandCalled = 0;
int count = 0;
- while(quitCommandCalled == 0){
+ while(quitCommandCalled != 1){
#ifdef USE_MPI
int pid, processors;
if (input[0] != '#') {
-
+ if (mout->changedSeqNames) { mout->mothurOut("[WARNING]: your sequence names contained ':'. I changed them to '_' to avoid problems in your downstream analysis.\n"); }
mout->mothurOutEndLine();
mout->mothurOut("mothur > " + input);
mout->mothurOutEndLine();
if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
#endif
//executes valid command
+ mout->changedSeqNames = false;
+ 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;
/***********************************************************************/
string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
try {
-
+
string nextcommand = "";
if (inputBatchFile.eof()) { nextcommand = "quit()"; }
//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 = mout->findProgramPath("mothur"); }
- 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) {
//CommandFactory cFactory;
int quitCommandCalled = 0;
- while(quitCommandCalled == 0){
+ while(quitCommandCalled != 1){
#ifdef USE_MPI
int pid, processors;
input = getNextCommand(listOfCommands);
if (input == "") { input = "quit()"; }
-
- mout->mothurOutEndLine();
- mout->mothurOut("mothur > " + input);
- mout->mothurOutEndLine();
+
+ if (mout->changedSeqNames) { mout->mothurOut("[WARNING]: your sequence names contained ':'. I changed them to '_' to avoid problems in your downstream analysis.\n"); }
+
+ 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
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);
//cout << pid << " is in execute" << endl;
#endif
//executes valid command
+ mout->changedSeqNames = false;
+ 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;
projects / mothur.git / blobdiff