convert(temp, countends);
temp = validParameter.validFile(parameters, "cutoff", false); if(temp == "not found"){ temp = "1.0"; }
- convert(temp, cutoff);
+ m->mothurConvert(temp, cutoff);
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
temp = validParameter.validFile(parameters, "compress", false); if(temp == "not found"){ temp = "F"; }
convert(temp, compress);
driverMPI(start, end, outMPI, cutoff);
- if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); delete distCalculator; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); return 0; }
//wait on chidren
for(int i = 1; i < processors; i++) {
- if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); delete distCalculator; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); return 0; }
char buf[5];
MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
//do your part
driverMPI(start, end, outMPI, cutoff);
- if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); delete distCalculator; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); return 0; }
char buf[5];
strcpy(buf, "done");
if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
else { driverMPI(start, end, outputFile, mySize, output); }
- if (m->control_pressed) { outputTypes.clear(); delete distCalculator; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); return 0; }
int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
MPI_File outMPI;
for(int b = 1; b < processors; b++) {
unsigned long long fileSize;
- if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); delete distCalculator; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); return 0; }
MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status);
if (output != "square"){ driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size); }
else { driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size, output); }
- if (m->control_pressed) { delete distCalculator; return 0; }
+ if (m->control_pressed) { return 0; }
//tell parent you are done.
MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
exit(1);
}
}
-/**************************************************************************************************
+**************************************************************************************************
int DistanceCommand::convertToLowerTriangle(string outputFile) {
try{
exit(1);
}
}
-/**************************************************************************************************/
+**************************************************************************************************/
//its okay if the column file does not contain all the names in the fasta file, since some distance may have been above a cutoff,
//but no sequences can be in the column file that are not in oldfasta. also, if a distance is above the cutoff given then remove it.
//also check to make sure the 2 files have the same alignment length.