string 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, "save", false); if (temp == "not found"){ temp = "f"; }
save = m->isTrue(temp);
temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found") { temp = "7"; }
- convert(temp, ksize);
+ m->mothurConvert(temp, ksize);
temp = validParameter.validFile(parameters, "svg", false); if (temp == "not found") { temp = "F"; }
svg = m->isTrue(temp);
if (nameFileNames.size() != 0) { svg = true; }
temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "10"; }
- convert(temp, increment);
+ m->mothurConvert(temp, increment);
}
}
catch(exception& e) {
//break up file
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
vector<unsigned long long> positions = m->divideFile(fastaFileNames[i], processors);
for (int s = 0; s < (positions.size()-1); s++) {
}
delete candidateSeq;
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
unsigned long long pos = inFASTA.tellg();
if ((pos == -1) || (pos >= filePos->end)) { break; }
#else
int ChimeraCheckCommand::createProcesses(string outputFileName, string filename) {
try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
int process = 0;
int num = 0;