convert(globaldata->getProcessors(), processors);
convert(globaldata->getCutOff(), cutoff);
+ //open file
+ string filename = globaldata->getFastaFile();
+ openInputFile(filename, in);
+
+
int i;
if (isTrue(countends) == true) {
for (i=0; i<globaldata->Estimators.size(); i++) {
int DistanceCommand::execute(){
try {
- //read file
- string filename = globaldata->inputFileName;
-
- if(globaldata->getFastaFile() != "") {
- readSeqs = new ReadFasta(filename); }
- else if(globaldata->getNexusFile() != "") {
- readSeqs = new ReadNexus(filename); }
- else if(globaldata->getClustalFile() != "") {
- readSeqs = new ReadClustal(filename); }
- else if(globaldata->getPhylipFile() != "") {
- readSeqs = new ReadPhylip(filename); }
-
- readSeqs->read();
- seqDB = readSeqs->getDB();
-
+ //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;
string distFile = getRootName(globaldata->getFastaFile()) + "dist";
+ string phylipFile = getRootName(globaldata->getFastaFile()) + "phylip.dist";
+ remove(phylipFile.c_str());
remove(distFile.c_str());
+ //output numSeqs to phylip formatted dist file
+ openOutputFile(phylipFile, phylipOut);
+ phylipOut << numSeqs << endl;
+ phylipOut.close();
+
//# if defined (_WIN32)
//figure out how to implement the fork and wait commands in windows
- // driver(distCalculator, seqDB, 0, numSeqs, distFile, cutoff);
+ // driver(distCalculator, seqDB, 0, numSeqs, distFile, phylipFile, cutoff);
//# endif
#if defined (__APPLE__) || (__MACH__)
if(processors == 1){
- driver(distCalculator, seqDB, 0, numSeqs, distFile, cutoff);
+ driver(distCalculator, seqDB, 0, numSeqs, distFile, phylipFile + "tempPhylipA", cutoff);
+ appendFiles((phylipFile + "tempPhylipA"), phylipFile);
+ remove((phylipFile + "tempPhylipA").c_str());
}
else if(processors == 2){
int pid = fork();
if(pid > 0){
- driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", cutoff);
+ driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", phylipFile + "tempPhylipA", cutoff);
appendFiles((distFile+"tempa"), distFile);
- remove((distFile + "tempa").c_str());
+ remove((distFile + "tempa").c_str());
+ appendFiles((phylipFile + "tempPhylipA"), phylipFile);
+ remove((phylipFile + "tempPhylipA").c_str());
}
else{
- driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", cutoff);
+ driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", phylipFile + "tempPhylipB", cutoff);
appendFiles((distFile+"tempb"), distFile);
- remove((distFile + "tempb").c_str());
+ remove((distFile + "tempb").c_str());
+ appendFiles((phylipFile + "tempPhylipB"), phylipFile);
+ remove((phylipFile + "tempPhylipB").c_str());
}
wait(NULL);
if(pid1 > 0){
int pid2 = fork();
if(pid2 > 0){
- driver(distCalculator, seqDB, 0, sqrt(3) * numSeqs / 3, distFile + "tempa", cutoff);
+ driver(distCalculator, seqDB, 0, sqrt(3) * numSeqs / 3, distFile + "tempa", phylipFile + "tempPhylipA", cutoff);
appendFiles(distFile+"tempa", distFile);
- remove((distFile + "tempa").c_str());
+ appendFiles((phylipFile + "tempPhylipA"), phylipFile);
+ remove((distFile + "tempa").c_str());
+ remove((phylipFile + "tempPhylipA").c_str());
}
else{
- driver(distCalculator, seqDB, sqrt(3) * numSeqs / 3, sqrt(6) * numSeqs / 3, distFile + "tempb", cutoff);
+ driver(distCalculator, seqDB, sqrt(3) * numSeqs / 3, sqrt(6) * numSeqs / 3, distFile + "tempb", phylipFile + "tempPhylipB", cutoff);
appendFiles(distFile+"tempb", distFile);
- remove((distFile + "tempb").c_str());
+ appendFiles((phylipFile + "tempPhylipB"), phylipFile);
+ remove((distFile + "tempb").c_str());
+ remove((phylipFile + "tempPhylipB").c_str());
}
wait(NULL);
}
else{
- driver(distCalculator, seqDB, sqrt(6) * numSeqs / 3, numSeqs, distFile + "tempc", cutoff);
+ driver(distCalculator, seqDB, sqrt(6) * numSeqs / 3, numSeqs, distFile + "tempc", phylipFile + "tempPhylipC", cutoff);
appendFiles(distFile+"tempc", distFile);
- remove((distFile + "tempc").c_str());
+ appendFiles((phylipFile + "tempPhylipC"), phylipFile);
+ remove((distFile + "tempc").c_str());
+ remove((phylipFile + "tempPhylipC").c_str());
}
wait(NULL);
}
if(pid1 > 0){
int pid2 = fork();
if(pid2 > 0){
- driver(distCalculator, seqDB, 0, numSeqs / 2, distFile + "tempa", cutoff);
+ driver(distCalculator, seqDB, 0, numSeqs / 2, distFile + "tempa", phylipFile + "tempPhylipA", cutoff);
appendFiles(distFile+"tempa", distFile);
- remove((distFile + "tempa").c_str());
+ appendFiles((phylipFile + "tempPhylipA"), phylipFile);
+ remove((distFile + "tempa").c_str());
+ remove((phylipFile + "tempPhylipA").c_str());
}
else{
- driver(distCalculator, seqDB, numSeqs / 2, (numSeqs/sqrt(2)), distFile + "tempb", cutoff);
+ driver(distCalculator, seqDB, numSeqs / 2, (numSeqs/sqrt(2)), distFile + "tempb", phylipFile + "tempPhylipB", cutoff);
appendFiles(distFile+"tempb", distFile);
- remove((distFile + "tempb").c_str());
+ appendFiles((phylipFile + "tempPhylipB"), phylipFile);
+ remove((distFile + "tempb").c_str());
+ remove((phylipFile + "tempPhylipB").c_str());
}
wait(NULL);
}
else{
int pid3 = fork();
if(pid3 > 0){
- driver(distCalculator, seqDB, (numSeqs/sqrt(2)), (sqrt(3) * numSeqs / 2), distFile + "tempc", cutoff);
+ driver(distCalculator, seqDB, (numSeqs/sqrt(2)), (sqrt(3) * numSeqs / 2), distFile + "tempc", phylipFile + "tempPhylipC", cutoff);
appendFiles(distFile+"tempc", distFile);
- remove((distFile + "tempc").c_str());
+ appendFiles((phylipFile + "tempPhylipC"), phylipFile);
+ remove((distFile + "tempc").c_str());
+ remove((phylipFile + "tempPhylipC").c_str());
+
}
else{
- driver(distCalculator, seqDB, (sqrt(3) * numSeqs / 2), numSeqs, distFile + "tempd", cutoff);
+ driver(distCalculator, seqDB, (sqrt(3) * numSeqs / 2), numSeqs, distFile + "tempd", phylipFile + "tempPhylipD", cutoff);
appendFiles(distFile+"tempd", distFile);
- remove((distFile + "tempd").c_str());
+ appendFiles((phylipFile + "tempPhylipD"), phylipFile);
+ remove((distFile + "tempd").c_str());
+ remove((phylipFile + "tempPhylipD").c_str());
}
wait(NULL);
}
wait(NULL);
#elif (linux) || (__linux)
if(processors == 1){
- driver(distCalculator, seqDB, 0, numSeqs, distFile, cutoff);
+ driver(distCalculator, seqDB, 0, numSeqs, distFile, phylipFile + "tempPhylipA", cutoff);
+ appendFiles((phylipFile + "tempPhylipA"), phylipFile);
+ remove((phylipFile + "tempPhylipA").c_str());
}
else if(processors == 2){
int pid = fork();
if(pid > 0){
- driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", cutoff);
+ driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", phylipFile + "tempPhylipA", cutoff);
appendFiles((distFile+"tempa"), distFile);
+ appendFiles((phylipFile + "tempPhylipA"), phylipFile);
remove((distFile + "tempa").c_str());
+ remove((phylipFile + "tempPhylipA").c_str());
+
}
else{
- driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", cutoff);
+ driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", phylipFile + "tempPhylipB", cutoff);
appendFiles((distFile+"tempb"), distFile);
- remove((distFile + "tempb").c_str());
+ appendFiles((phylipFile + "tempPhylipB"), phylipFile);
+ remove((distFile + "tempb").c_str());
+ remove((phylipFile + "tempPhylipB").c_str());
}
wait();
if(pid1 > 0){
int pid2 = fork();
if(pid2 > 0){
- driver(distCalculator, seqDB, 0, sqrt(3) * numSeqs / 3, distFile + "tempa", cutoff);
- appendFiles(distFile+"tempa", distFile);
+ driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", phylipFile + "tempPhylipA", cutoff);
+ appendFiles((distFile+"tempa"), distFile);
+ appendFiles((phylipFile + "tempPhylipA"), phylipFile);
remove((distFile + "tempa").c_str());
+ remove((phylipFile + "tempPhylipA").c_str());
+
}
else{
- driver(distCalculator, seqDB, sqrt(3) * numSeqs / 3, sqrt(6) * numSeqs / 3, distFile + "tempb", cutoff);
- appendFiles(distFile+"tempb", distFile);
- remove((distFile + "tempb").c_str());
+ driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", phylipFile + "tempPhylipB", cutoff);
+ appendFiles((distFile+"tempb"), distFile);
+ appendFiles((phylipFile + "tempPhylipB"), phylipFile);
+ remove((distFile + "tempb").c_str());
+ remove((phylipFile + "tempPhylipB").c_str());
}
wait();
}
else{
- driver(distCalculator, seqDB, sqrt(6) * numSeqs / 3, numSeqs, distFile + "tempc", cutoff);
+ driver(distCalculator, seqDB, sqrt(6) * numSeqs / 3, numSeqs, distFile + "tempc", phylipFile + "tempPhylipC", cutoff);
appendFiles(distFile+"tempc", distFile);
- remove((distFile + "tempc").c_str());
+ appendFiles((phylipFile + "tempPhylipC"), phylipFile);
+ remove((distFile + "tempc").c_str());
+ remove((phylipFile + "tempPhylipC").c_str());
}
wait();
}
if(pid1 > 0){
int pid2 = fork();
if(pid2 > 0){
- driver(distCalculator, seqDB, 0, numSeqs / 2, distFile + "tempa", cutoff);
- appendFiles(distFile+"tempa", distFile);
- remove((distFile + "tempa").c_str());
+ driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", phylipFile + "tempPhylipA", cutoff);
+ appendFiles((distFile+"tempa"), distFile);
+ appendFiles((phylipFile + "tempPhylipA"), phylipFile);
+ remove((distFile + "tempa").c_str());
+ remove((phylipFile + "tempPhylipA").c_str());
}
else{
- driver(distCalculator, seqDB, numSeqs / 2, (numSeqs/sqrt(2)), distFile + "tempb", cutoff);
- appendFiles(distFile+"tempb", distFile);
- remove((distFile + "tempb").c_str());
+ driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", phylipFile + "tempPhylipB", cutoff);
+ appendFiles((distFile+"tempb"), distFile);
+ appendFiles((phylipFile + "tempPhylipB"), phylipFile);
+ remove((distFile + "tempb").c_str());
+ remove((phylipFile + "tempPhylipB").c_str());
}
wait();
}
else{
int pid3 = fork();
if(pid3 > 0){
- driver(distCalculator, seqDB, (numSeqs/sqrt(2)), (sqrt(3) * numSeqs / 2), distFile + "tempc", cutoff);
+ driver(distCalculator, seqDB, sqrt(6) * numSeqs / 3, numSeqs, distFile + "tempc", phylipFile + "tempPhylipC", cutoff);
appendFiles(distFile+"tempc", distFile);
- remove((distFile + "tempc").c_str());
+ appendFiles((phylipFile + "tempPhylipC"), phylipFile);
+ remove((distFile + "tempc").c_str());
+ remove((phylipFile + "tempPhylipC").c_str());
}
else{
- driver(distCalculator, seqDB, (sqrt(3) * numSeqs / 2), numSeqs, distFile + "tempd", cutoff);
+ driver(distCalculator, seqDB, (sqrt(3) * numSeqs / 2), numSeqs, distFile + "tempd", phylipFile + "tempPhylipD", cutoff);
appendFiles(distFile+"tempd", distFile);
- remove((distFile + "tempd").c_str());
+ appendFiles((phylipFile + "tempPhylipD"), phylipFile);
+ remove((distFile + "tempd").c_str());
+ remove((phylipFile + "tempPhylipD").c_str());
}
wait();
}
wait();
#else
- driver(distCalculator, seqDB, 0, numSeqs, distFile, cutoff);
+ driver(distCalculator, seqDB, 0, numSeqs, distFile, phylipFile + "tempPhylipA", cutoff);
+ appendFiles((phylipFile + "tempPhylipA"), phylipFile);
+ remove((phylipFile + "tempPhylipA").c_str());
#endif
delete distCalculator;
/**************************************************************************************************/
/////// 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);
+ //column file
+ ofstream philFile(pFilename.c_str(), ios::trunc);
+ philFile.setf(ios::fixed, ios::showpoint);
+ philFile << setprecision(4);
+
for(int i=startLine;i<endLine;i++){
for(int j=0;j<i;j++){
- distCalculator->calcDist(align->get(i), align->get(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;
}
-
+ philFile << dist << '\t';
}
+
+ philFile << endl;
+
if(i % 100 == 0){
cout << i << '\t' << time(NULL) - startTime << endl;
}
}
cout << endLine-1 << '\t' << time(NULL) - startTime << endl;
+ //philFile.close();
+ //distFile.close();
+
return 1;
}
catch(exception& e) {
projects / mothur.git / blobdiff