if (hasName && (templatefile != "self")) { m->mothurOut("You have provided a namefile and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
if (hasGroup && (templatefile != "self")) { m->mothurOut("You have provided a group file and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
+ //until we resolve the issue 10-18-11
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#else
+ processors=1;
+#endif
}
}
catch(exception& e) {
map<string, map<string, int> > fileToPriority;
map<string, map<string, int> >::iterator itFile;
map<string, string> fileGroup;
- map<string, int> priority;
fileToPriority[fastaFileNames[s]] = priority; //default
fileGroup[fastaFileNames[s]] = "noGroup";
SequenceParser* parser = NULL;
priority = sortFastaFile(fastaFileNames[s], nameFile);
m->mothurOut("Done."); m->mothurOutEndLine();
+ fileToPriority.clear();
+ fileGroup.clear();
fileToPriority[fastaFileNames[s]] = priority;
+ fileGroup[fastaFileNames[s]] = "noGroup";
if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
}else if ((templatefile == "self") && (groupFile != "")) {
fileGroup.clear();
fileToPriority.clear();
+ if (processors != 1) { m->mothurOut("When using template=self, mothur can only use 1 processor, continuing."); m->mothurOutEndLine(); processors = 1; }
string nameFile = "";
if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one
nameFile = nameFileNames[s];
if (print) {
out << name << '\t';
- cout << name<< endl;
+
namesInFile.insert(name);
//output parent1's name
pDataArray.push_back(tempslayer);
processIDS.push_back(i);
- //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
+ //MySlayerThreadFunction is in header. It must be global or static to work with the threads.
//default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
hThreadArray[i] = CreateThread(NULL, 0, MySlayerThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
}