exit(1);
}
}
+/***********************************************************************/
/***********************************************************************/
InteractEngine::InteractEngine(string path){
- globaldata = GlobalData::getInstance();
- globaldata->argv = 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 = mout->findProgramPath("mothur"); }
+
+ 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 = openInputFile(batchFileName, inputBatchFile);
- globaldata->argv = path;
+ openedBatch = mout->openInputFile(batchFileName, inputBatchFile);
+
+ 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 = mout->findProgramPath("mothur"); }
+
+ 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;
}
}
- gobble(inputBatchFile);
+ mout->gobble(inputBatchFile);
}
inputBatchFile.close();
/***********************************************************************/
string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
try {
-
+
string nextcommand = "";
if (inputBatchFile.eof()) { nextcommand = "quit()"; }
- else { nextcommand = getline(inputBatchFile); }
+ else { nextcommand = mout->getline(inputBatchFile); }
return nextcommand;
}
//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("othur")-5));
- globaldata->argv = path;
+ //this will happen if you set the path variable to contain mothur's exe location
+ if (temppath == "") { path = mout->findProgramPath("mothur"); }
+
+ 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()"; }
+
+ 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 (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;
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++;
projects / mothur.git / blobdiff