string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found"){ temp = "0.50"; }
temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found"){ temp = "0.50"; }
temp = validParameter.validFile(parameters, "alpha", false); if (temp == "not found"){ temp = "-5.54"; }
temp = validParameter.validFile(parameters, "alpha", false); if (temp == "not found"){ temp = "-5.54"; }
temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found"){ temp = "0.33"; }
temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found"){ temp = "0.33"; }
string inputString = "fasta=" + inputFile;
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
string inputString = "fasta=" + inputFile;
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
Command* uniqueCommand = new DeconvoluteCommand(inputString);
uniqueCommand->execute();
map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
delete uniqueCommand;
Command* uniqueCommand = new DeconvoluteCommand(inputString);
uniqueCommand->execute();
map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
delete uniqueCommand;
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
nameFile = filenames["name"][0];
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
nameFile = filenames["name"][0];
else {
int num = m->getNumNames(it->second);
sequences.push_back(seqData(thisGroupsSeqs[i].getName(), thisGroupsSeqs[i].getUnaligned(), num));
else {
int num = m->getNumNames(it->second);
sequences.push_back(seqData(thisGroupsSeqs[i].getName(), thisGroupsSeqs[i].getUnaligned(), num));
if (it == nameMap.end()) { error = true; m->mothurOut("[ERROR]: " + temp.getName() + " is in your fasta file and not in your namefile, please correct."); m->mothurOutEndLine(); }
else {
sequences.push_back(seqData(temp.getName(), temp.getUnaligned(), it->second));
if (it == nameMap.end()) { error = true; m->mothurOut("[ERROR]: " + temp.getName() + " is in your fasta file and not in your namefile, please correct."); m->mothurOutEndLine(); }
else {
sequences.push_back(seqData(temp.getName(), temp.getUnaligned(), it->second));
for(int i=0;i<numSeqs;i++){
if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
for(int i=0;i<numSeqs;i++){
if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
minMismatchToChimera = myPerseus.getChimera(sequences, leftDiffs, rightDiffs, leftParentBi, rightParentBi, breakPointBi, singleLeft, bestLeft, singleRight, bestRight, restricted);
if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
minMismatchToChimera = myPerseus.getChimera(sequences, leftDiffs, rightDiffs, leftParentBi, rightParentBi, breakPointBi, singleLeft, bestLeft, singleRight, bestRight, restricted);
if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }