+ //force parent to wait until all the processes are done
+ for (int i=0;i<processors;i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ return exitCommand;
+#endif
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FilterSeqsCommand", "createProcessesRunFilter");
+ exit(1);
+ }
+}
+/**************************************************************************************/
+string FilterSeqsCommand::createFilter() {
+ try {
+ string filterString = "";
+ Filters F;
+
+ if (soft != 0) { F.setSoft(soft); }
+ if (trump != '*') { F.setTrump(trump); }
+
+ F.setLength(alignmentLength);
+
+ if(soft != 0 || isTrue(vertical)){
+ F.initialize();
+ }
+
+ if(hard.compare("") != 0) { F.doHard(hard); }
+ else { F.setFilter(string(alignmentLength, '1')); }
+
+ numSeqs = 0;
+ if(trump != '*' || isTrue(vertical) || soft != 0){
+ for (int s = 0; s < fastafileNames.size(); s++) {
+
+ for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
+
+#ifdef USE_MPI
+ int pid;
+ int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5;
+ int tag = 2001;
+
+ MPI_Status status;
+ MPI_File inMPI;
+ MPI_Comm_size(MPI_COMM_WORLD, &processors);
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
+ char* tempFileName = new char(fastafileNames[s].length());
+ tempFileName = &(fastafileNames[s][0]);
+
+ MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
+
+ if (pid == 0) { //you are the root process
+ setLines(fastafileNames[s]);
+
+ for (int j = 0; j < lines.size(); j++) { //each process
+ if (j != 0) { //don't send to yourself
+ MPI_Send(&lines[j]->start, 1, MPI_INT, j, tag, MPI_COMM_WORLD); //start position in file
+ MPI_Send(&numSeqs, 1, MPI_INT, j, tag, MPI_COMM_WORLD);
+ MPI_Send(&bufferSizes[j], 1, MPI_INT, j, tag, MPI_COMM_WORLD); //how bytes for the read
+ }
+ }
+
+ char buf[bufferSizes[0]];
+ MPI_File_read_at(inMPI, 0, buf, bufferSizes[0], MPI_CHAR, &status);
+
+ string tempBuf = buf;
+ if (tempBuf.length() > bufferSizes[0]) { tempBuf = tempBuf.substr(0, bufferSizes[0]); }
+
+ MPICreateFilter(F, tempBuf);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); return filterString; }
+
+ vector<int> temp; temp.resize(alignmentLength+1);
+
+ //get the frequencies from the child processes
+ for(int i = 0; i < ((processors-1)*5); i++) {
+ MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, MPI_ANY_SOURCE, tag, MPI_COMM_WORLD, &status);
+ int receiveTag = temp[temp.size()-1]; //child process added a int to the end to indicate what letter count this is for
+
+ if (receiveTag == Atag) { //you are recieveing the A frequencies
+ for (int k = 0; k < alignmentLength; k++) { F.a[k] += temp[k]; }
+ }else if (receiveTag == Ttag) { //you are recieveing the T frequencies
+ for (int k = 0; k < alignmentLength; k++) { F.t[k] += temp[k]; }
+ }else if (receiveTag == Ctag) { //you are recieveing the C frequencies
+ for (int k = 0; k < alignmentLength; k++) { F.c[k] += temp[k]; }
+ }else if (receiveTag == Gtag) { //you are recieveing the G frequencies
+ for (int k = 0; k < alignmentLength; k++) { F.g[k] += temp[k]; }
+ }else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies
+ for (int k = 0; k < alignmentLength; k++) { F.gap[k] += temp[k]; }
+ }
+ }
+
+
+ }else { //i am the child process
+
+ int startPos, bufferSize;
+ MPI_Recv(&startPos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+ MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+ MPI_Recv(&bufferSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+
+ //send freqs
+ char buf2[bufferSize];
+ MPI_File_read_at(inMPI, startPos, buf2, bufferSize, MPI_CHAR, &status);
+
+ string tempBuf = buf2;
+ if (tempBuf.length() > bufferSize) { tempBuf = tempBuf.substr(0, bufferSize); }
+
+ MPICreateFilter(F, tempBuf);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); return filterString; }
+
+ //send my fequency counts
+ F.a.push_back(Atag);
+ int ierr = MPI_Send(&(F.a[0]), (alignmentLength+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
+ F.t.push_back(Ttag);
+ ierr = MPI_Send (&(F.t[0]), (alignmentLength+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
+ F.c.push_back(Ctag);
+ ierr = MPI_Send(&(F.c[0]), (alignmentLength+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
+ F.g.push_back(Gtag);
+ ierr = MPI_Send(&(F.g[0]), (alignmentLength+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
+ F.gap.push_back(Gaptag);
+ ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
+ }
+
+ MPI_Barrier(MPI_COMM_WORLD);
+ MPI_File_close(&inMPI);
+
+#else
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if(processors == 1){
+ ifstream inFASTA;
+ openInputFile(fastafileNames[s], inFASTA);
+ int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+ inFASTA.close();
+
+ numSeqs += numFastaSeqs;
+
+ lines.push_back(new linePair(0, numFastaSeqs));
+
+ driverCreateFilter(F, fastafileNames[s], lines[0]);
+ }else{
+ setLines(fastafileNames[s]);
+ createProcessesCreateFilter(F, fastafileNames[s]);
+ }
+
+ if (m->control_pressed) { return filterString; }
+ #else
+ ifstream inFASTA;
+ openInputFile(fastafileNames[s], inFASTA);
+ int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+ inFASTA.close();
+
+ numSeqs += numFastaSeqs;
+
+ lines.push_back(new linePair(0, numFastaSeqs));
+
+ driverCreateFilter(F, fastafileNames[s], lines[0]);
+ if (m->control_pressed) { return filterString; }
+ #endif
+#endif
+
+ }
+ }
+
+ F.setNumSeqs(numSeqs);
+
+ if(isTrue(vertical) == 1) { F.doVertical(); }
+ if(soft != 0) { F.doSoft(); }
+
+ filterString = F.getFilter();
+
+ return filterString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FilterSeqsCommand", "createFilter");
+ exit(1);
+ }
+}
+/**************************************************************************************/
+int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* line) {
+ try {
+
+ ifstream in;
+ openInputFile(filename, in);
+
+ in.seekg(line->start);
+
+ for(int i=0;i<line->num;i++){
+
+ if (m->control_pressed) { in.close(); return 1; }
+
+ Sequence seq(in);
+ if (seq.getName() != "") {
+ if (seq.getAligned().length() != alignmentLength) { m->mothurOut("Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ if(trump != '*'){ F.doTrump(seq); }
+ if(isTrue(vertical) || soft != 0){ F.getFreqs(seq); }
+ cout.flush();
+ }
+
+ //report progress
+ if((i+1) % 100 == 0){ m->mothurOut(toString(i+1)); m->mothurOutEndLine(); }
+ }
+
+ //report progress
+ if((line->num) % 100 != 0){ m->mothurOut(toString(line->num)); m->mothurOutEndLine(); }
+
+ in.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
+ exit(1);
+ }
+}
+/**************************************************************************************/
+int FilterSeqsCommand::MPICreateFilter(Filters& F, string input) {
+ try {
+
+ vector<string> seqStrings;
+ parseBuffer(input, seqStrings);
+
+ for(int i=0;i<seqStrings.size();i++){
+
+ if (seqStrings[i].length() != alignmentLength) { cout << i << '\t' << seqStrings[i].length() << "Sequences are not all the same length, please correct." << endl; m->control_pressed = true; }