CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
CommandParameter pcutoff("cutoff", "Number", "", "-1.00", "", "", "",false,false); parameters.push_back(pcutoff);
CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
- CommandParameter phard("hard", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phard);
+ CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete list; return 0; }
+ if(m->control_pressed){
+ for (int i = 0; i < outputNames.size(); i++){ m->mothurRemove(outputNames[i]); } delete list; return 0;
+ }
if(allLines == 1 || labels.count(list->getLabel()) == 1){
exit(1);
}
}
+
//***************************************************************************************************************
+
int SensSpecCommand::fillSeqMap(map<string, int>& seqMap, ListVector*& list){
try {
//for each otu
return numSeqs;
}
catch(exception& e) {
- m->errorOut(e, "SensSpecCommand", "fillSeqMap");
+ m->errorOut(e, "SensSpecCommand", "fillSeqPairSet");
exit(1);
}
}
ifstream phylipFile;
m->openInputFile(distFile, phylipFile);
phylipFile >> pNumSeqs;
- if(pNumSeqs != lNumSeqs){ m->mothurOut("numSeq mismatch!\n"); m->control_pressed = true; }
+ if(pNumSeqs != lNumSeqs){ m->mothurOut("numSeq mismatch!\n"); /*m->control_pressed = true;*/ }
string seqName;
double distance;
m->mothurOut(label); m->mothurOutEndLine();
- for(int i=0;i<lNumSeqs;i++){
+ for(int i=0;i<pNumSeqs;i++){
if (m->control_pressed) { return 0; }