try {
globaldata = GlobalData::getInstance();
validCalculator = new ValidCalculators();
- ends = globaldata->getEnds();
- seqDB = globaldata->gSequenceDB;
+ countends = globaldata->getCountEnds();
convert(globaldata->getProcessors(), processors);
convert(globaldata->getCutOff(), cutoff);
- distFile = getRootName(globaldata->getFastaFile()) + "dist";
+ phylip = globaldata->getPhylipFile();
+
+ //open file
+ string filename = globaldata->getFastaFile();
+ openInputFile(filename, in);
+
+
int i;
- if (ends != "T") {
+ if (isTrue(countends) == true) {
for (i=0; i<globaldata->Estimators.size(); i++) {
if (validCalculator->isValidCalculator("distance", globaldata->Estimators[i]) == true) {
if (globaldata->Estimators[i] == "nogaps") {
}else if (globaldata->Estimators[i] == "eachgap") {
distCalculator = new eachGapDist();
}else if (globaldata->Estimators[i] == "onegap") {
- distCalculator = new oneGapDist(); }
+ distCalculator = new oneGapDist(); }
}
}
}else {
}
}
}
-
-
+
//reset calc for next command
globaldata->setCalc("");
-
-
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the DistanceCommand class Function DistanceCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
int DistanceCommand::execute(){
try {
+
+ //reads fasta file and fills sequenceDB
+ if(globaldata->getFastaFile() != "") { seqDB = new SequenceDB(in); }
+ else { cout << "Error no fasta file." << endl; return 0; }
+
int numSeqs = seqDB->getNumSeqs();
+ cutoff += 0.005;
- system(("rm "+distFile).c_str() );
- if(processors == 1){
- driver(distCalculator, seqDB, 0, numSeqs, distFile, cutoff);
- }
- else if(processors == 2){
+ string phylipFile = "";
+ string distFile = getRootName(globaldata->getFastaFile()) + "dist";
+ remove(distFile.c_str());
- int pid = fork();
- if(pid > 0){
- driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", cutoff);
-// system(("cat " + distFile + "tempa" + " >> " + distFile).c_str());
-// system(("rm " + distFile + "tempa").c_str());
- }
- else{
- driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", cutoff);
-// system(("cat " + distFile + "tempb" + " >> " + distFile).c_str());
-// system(("rm " + distFile + "tempb").c_str());
- }
- wait(NULL);
-
+ //doses the user want the phylip formatted file as well
+ if (isTrue(phylip) == true) {
+ phylipFile = getRootName(globaldata->getFastaFile()) + "phylip.dist";
+ remove(phylipFile.c_str());
+
+ //output numSeqs to phylip formatted dist file
+ openOutputFile(phylipFile, phylipOut);
+ phylipOut << numSeqs << endl;
+ phylipOut.close();
}
- else if(processors == 3){
- int pid1 = fork();
- if(pid1 > 0){
- int pid2 = fork();
- if(pid2 > 0){
- driver(distCalculator, seqDB, 0, sqrt(3) * numSeqs / 3, distFile + "tempa", cutoff);
- #ifdef HAVE_CAT
- system(("cat " + distFile + "tempa" + " >> " + distFile).c_str());
- #else
- #ifdef HAVE_COPY
-//get system call from pat system(("copy " + distFile + "tempa").c_str());
- #else
- cout << "Sorry but I can't continue because this operating system doesn't appear to support the cat() or copy() system calls." << endl;
- #endif
- #endif
-
- #ifdef HAVE_RM
- system(("rm " + distFile + "tempa").c_str());
- #else
- #ifdef HAVE_ERASE
- system(("erase " + distFile + "tempa").c_str());
- #else
- cout << "Sorry but I can't remove the required files because this operating system doesn't appear to support the rm() or erase() system calls." << endl;
- #endif
- #endif
- }
- else{
- driver(distCalculator, seqDB, sqrt(3) * numSeqs / 3, sqrt(6) * numSeqs / 3, distFile + "tempb", cutoff);
- system(("cat " + distFile + "tempb" + " >> " + distFile).c_str());
- system(("rm " + distFile + "tempb").c_str());
- }
- wait(NULL);
- }
- else{
- driver(distCalculator, seqDB, sqrt(6) * numSeqs / 3, numSeqs, distFile + "tempc", cutoff);
- system(("cat " + distFile + "tempc" + " >> " + distFile).c_str());
- system(("rm " + distFile + "tempc").c_str());
+
+
+ //# if defined (_WIN32)
+ //figure out how to implement the fork and wait commands in windows
+ // driver(distCalculator, seqDB, 0, numSeqs, distFile, phylipFile, cutoff);
+ //# endif
+
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ //if you don't need to fork anything
+ if(processors == 1){
+ driver(distCalculator, seqDB, 0, numSeqs, distFile, phylipFile + "tempPhylipA", cutoff);
+
+ if (isTrue(phylip) == true) {
+ appendFiles((phylipFile + "tempPhylipA"), phylipFile);
+ remove((phylipFile + "tempPhylipA").c_str());
}
- wait(NULL);
- }
- else if(processors == 4){
- int pid1 = fork();
- if(pid1 > 0){
- int pid2 = fork();
- if(pid2 > 0){
- driver(distCalculator, seqDB, 0, numSeqs / 2, distFile + "tempa", cutoff);
- system(("cat " + distFile + "tempa" + " >> " + distFile).c_str());
- system(("rm " + distFile + "tempa").c_str());
- }
- else{
- driver(distCalculator, seqDB, numSeqs / 2, (numSeqs/sqrt(2)), distFile + "tempb", cutoff);
- system(("cat " + distFile + "tempb" + " >> " + distFile).c_str());
- system(("rm " + distFile + "tempb").c_str());
- }
- wait(NULL);
+ }else{ //you have multiple processors
+
+ //create line pairs
+ int numPerGroup = numSeqs / processors;
+ int remainder = numSeqs % processors;
+
+ for (int i = 0; i < processors; i++) {
+ lines.push_back(new linePair());
+ lines[i]->start = i*numPerGroup;
+ lines[i]->end = (i+1)*numPerGroup;
}
- else{
- int pid3 = fork();
- if(pid3 > 0){
- driver(distCalculator, seqDB, (numSeqs/sqrt(2)), (sqrt(3) * numSeqs / 2), distFile + "tempc", cutoff);
- system(("cat " + distFile + "tempc" + " >> " + distFile).c_str());
- system(("rm " + distFile + "tempc").c_str());
- }
- else{
- driver(distCalculator, seqDB, (sqrt(3) * numSeqs / 2), numSeqs, distFile + "tempd", cutoff);
- system(("cat " + distFile + "tempd" + " >> " + distFile).c_str());
- system(("rm " + distFile + "tempd").c_str());
+ //give the last one any extra line
+ lines[lines.size()-1]->end += remainder;
+
+ createProcesses(distFile, phylipFile);
+
+ //append and remove temp files
+ for (it = processIDS.begin(); it != processIDS.end(); it++) {
+ appendFiles((distFile + toString(it->second) + ".temp"), distFile);
+ remove((distFile + toString(it->second) + ".temp").c_str());
+
+ if (isTrue(phylip) == true) {
+ appendFiles((phylipFile + toString(it->second) + ".temp"), phylipFile);
+ remove((phylipFile + toString(it->second) + ".temp").c_str());
}
- wait(NULL);
}
- wait(NULL);
}
- wait(NULL);
-
+#else
+ driver(distCalculator, seqDB, 0, numSeqs, distFile, phylipFile + "tempPhylipA", cutoff);
+
+ if (isTrue(phylip) = true) {
+ appendFiles((phylipFile + "tempPhylipA"), phylipFile);
+ remove((phylipFile + "tempPhylipA").c_str());
+ }
+#endif
+
delete distCalculator;
-
+
return 0;
-
+
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the DistanceCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
}
+/**************************************************************************************************/
+void DistanceCommand::createProcesses(string column, string phylip) {
+ try {
+ int process = 0;
+ processIDS.clear();
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+
+ if (pid > 0) {
+ processIDS[lines[process]->end] = pid; //create map from line number to pid so you can append files in correct order later
+ process++;
+ }else if (pid == 0){
+ driver(distCalculator, seqDB, lines[process]->start, lines[process]->end, column + toString(getpid()) + ".temp", phylip + toString(getpid()) + ".temp", cutoff);
+ exit(0);
+ }else { cout << "unable to spawn the necessary processes." << endl; exit(0); }
+ }
+
+ //force parent to wait until all the processes are done
+ for (it = processIDS.begin(); it != processIDS.end(); it++) {
+ int temp = it->second;
+ wait(&temp);
+ }
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the DistanceCommand class Function createProcesses. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the DistanceCommand class function createProcesses. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
/**************************************************************************************************/
/////// need to fix to work with calcs and sequencedb
-int DistanceCommand::driver(Dist* distCalculator, SequenceDB* align, int startLine, int endLine, string dFileName, float cutoff){
+int DistanceCommand::driver(Dist* distCalculator, SequenceDB* align, int startLine, int endLine, string dFileName, string pFilename, float cutoff){
try {
+
int startTime = time(NULL);
-
+
+ //column file
ofstream distFile(dFileName.c_str(), ios::trunc);
distFile.setf(ios::fixed, ios::showpoint);
distFile << setprecision(4);
-
- for(int i=startLine;i<endLine;i++){
- for(int j=0;j<i;j++){
+ ofstream philFile(pFilename.c_str(), ios::trunc);
+ philFile.setf(ios::fixed, ios::showpoint);
+ philFile << setprecision(4);
+
+ for(int i=startLine;i<endLine;i++){
- distCalculator->calcDist(align->get(i), align->get(j));
+ for(int j=0;j<i;j++){
+ distCalculator->calcDist(*(align->get(i)), *(align->get(j)));
double dist = distCalculator->getDist();
+
if(dist <= cutoff){
- distFile << align->get(i).getName() << ' ' << align->get(j).getName() << ' ' << dist << endl;
+ distFile << align->get(i)->getName() << ' ' << align->get(j)->getName() << ' ' << dist << endl;
}
-
+ if (isTrue(phylip) == true) { philFile << dist << '\t'; }
+
}
+
+ if (isTrue(phylip) == true) { philFile << endl; }
+
if(i % 100 == 0){
cout << i << '\t' << time(NULL) - startTime << endl;
}
-
+
}
cout << endLine-1 << '\t' << time(NULL) - startTime << endl;
-
+
+ if (isTrue(phylip) != true) { remove(pFilename.c_str()); }
+
+ //philFile.close();
+ //distFile.close();
+
return 1;
}
catch(exception& e) {
cout << "An unknown error has occurred in the DistanceCommand class function driver. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
-
+
}
/**************************************************************************************************/
-
+void DistanceCommand::appendFiles(string temp, string filename) {
+ try{
+ ofstream output;
+ ifstream input;
+
+ //open output file in append mode
+ openOutputFileAppend(filename, output);
+
+ //open temp file for reading
+ openInputFile(temp, input);
+
+ string line;
+ //read input file and write to output file
+ while(input.eof() != true) {
+ getline(input, line); //getline removes the newline char
+ if (line != "") {
+ output << line << endl; // Appending back newline char
+ }
+ }
+
+ input.close();
+ output.close();
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the DistanceCommand class Function appendFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the DistanceCommand class function appendFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/**************************************************************************************************/
\ No newline at end of file
projects / mothur.git / blobdiff