+}
+#endif
+/**************************************************************************************************/
+
+int AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
+ try {
+ int num = 0;
+ processIDS.resize(0);
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ int process = 1;
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+
+ if (pid > 0) {
+ processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
+ process++;
+ }else if (pid == 0){
+ num = driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
+
+ //pass numSeqs to parent
+ ofstream out;
+ string tempFile = alignFileName + toString(getpid()) + ".num.temp";
+ m->openOutputFile(tempFile, out);
+ out << num << endl;
+ out.close();
+
+ exit(0);
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
+ }
+
+ //do my part
+ num = driver(lines[0], alignFileName, reportFileName, accnosFName, filename);
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processIDS.size();i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ vector<string> nonBlankAccnosFiles;
+ if (!(m->isBlank(accnosFName))) { nonBlankAccnosFiles.push_back(accnosFName); }
+ else { m->mothurRemove(accnosFName); } //remove so other files can be renamed to it
+
+ for (int i = 0; i < processIDS.size(); i++) {
+ ifstream in;
+ string tempFile = alignFileName + toString(processIDS[i]) + ".num.temp";
+ m->openInputFile(tempFile, in);
+ if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
+ in.close(); m->mothurRemove(tempFile);
+
+ m->appendFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
+ m->mothurRemove((alignFileName + toString(processIDS[i]) + ".temp"));
+
+ appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
+ m->mothurRemove((reportFileName + toString(processIDS[i]) + ".temp"));
+
+ if (!(m->isBlank(accnosFName + toString(processIDS[i]) + ".temp"))) {
+ nonBlankAccnosFiles.push_back(accnosFName + toString(processIDS[i]) + ".temp");
+ }else { m->mothurRemove((accnosFName + toString(processIDS[i]) + ".temp")); }
+
+ }
+
+ //append accnos files
+ if (nonBlankAccnosFiles.size() != 0) {
+ rename(nonBlankAccnosFiles[0].c_str(), accnosFName.c_str());
+
+ for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
+ m->appendFiles(nonBlankAccnosFiles[h], accnosFName);
+ m->mothurRemove(nonBlankAccnosFiles[h]);
+ }
+ }else { //recreate the accnosfile if needed
+ ofstream out;
+ m->openOutputFile(accnosFName, out);
+ out.close();
+ }
+#else
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the alignData struct.
+ //Above fork() will clone, so memory is separate, but that's not the case with windows,
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+
+ vector<alignData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+
+ //Create processor worker threads.
+ for( int i=0; i<processors-1; i++ ){
+ //copy templateDb
+ //AlignmentDB* tempDB = new AlignmentDB(*templateDB);
+
+ // Allocate memory for thread data.
+ string extension = "";
+ if (i != 0) { extension = toString(i) + ".temp"; }
+
+ alignData* tempalign = new alignData(templateFileName, (alignFileName + extension), (reportFileName + extension), (accnosFName + extension), filename, align, search, kmerSize, m, lines[i]->start, lines[i]->end, flip, match, misMatch, gapOpen, gapExtend, threshold, i);
+ pDataArray.push_back(tempalign);
+ processIDS.push_back(i);
+
+ //MySeqSumThreadFunction 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, MyAlignThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
+ }
+
+ //need to check for line ending error
+ ifstream inFASTA;
+ m->openInputFile(filename, inFASTA);
+ inFASTA.seekg(lines[processors-1]->start-1);
+ char c = inFASTA.peek();
+
+ if (c != '>') { //we need to move back
+ lines[processors-1]->start--;
+ }
+
+ //using the main process as a worker saves time and memory
+ //do my part - do last piece because windows is looking for eof
+ num = driver(lines[processors-1], (alignFileName + toString(processors-1) + ".temp"), (reportFileName + toString(processors-1) + ".temp"), (accnosFName + toString(processors-1) + ".temp"), filename);
+
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ num += pDataArray[i]->count;
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+
+ vector<string> nonBlankAccnosFiles;
+ if (!(m->isBlank(accnosFName))) { nonBlankAccnosFiles.push_back(accnosFName); }
+ else { m->mothurRemove(accnosFName); } //remove so other files can be renamed to it
+
+ for (int i = 1; i < processors; i++) {
+ m->appendFiles((alignFileName + toString(i) + ".temp"), alignFileName);
+ m->mothurRemove((alignFileName + toString(i) + ".temp"));
+
+ appendReportFiles((reportFileName + toString(i) + ".temp"), reportFileName);
+ m->mothurRemove((reportFileName + toString(i) + ".temp"));
+
+ if (!(m->isBlank(accnosFName + toString(i) + ".temp"))) {
+ nonBlankAccnosFiles.push_back(accnosFName + toString(i) + ".temp");
+ }else { m->mothurRemove((accnosFName + toString(i) + ".temp")); }
+ }
+
+ //append accnos files
+ if (nonBlankAccnosFiles.size() != 0) {
+ rename(nonBlankAccnosFiles[0].c_str(), accnosFName.c_str());
+
+ for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
+ m->appendFiles(nonBlankAccnosFiles[h], accnosFName);
+ m->mothurRemove(nonBlankAccnosFiles[h]);
+ }
+ }else { //recreate the accnosfile if needed
+ ofstream out;
+ m->openOutputFile(accnosFName, out);
+ out.close();
+ }
+#endif
+
+ return num;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AlignCommand", "createProcesses");