}else { m->setFastaFile(fastafile); }
namefile = validParameter.validFile(parameters, "name", true);
- if (namefile == "not open") { abort = true; }
+ if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
else { m->setNameFile(namefile); }
}
string temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "100"; }
- convert(temp, cutoff);
+ m->mothurConvert(temp, cutoff);
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(fastafile); }
-
+
+ if (namefile == ""){
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
}
}
catch(exception& e) {
int seqLength = 0;
for (map<string, string>::iterator it = nameMap.begin(); it != nameMap.end(); it++) {
- if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
string seq = fastaMap[it->second];
seqs.push_back(seq);
//get counts
for (int j = 0; j < seqLength; j++) {
- if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
vector<int> counts; counts.resize(5, 0); //A,T,G,C,Gap
int numDots = 0;
//as long as you are not at the end of the file or done wih the lines you want
while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete list; delete input; return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete list; delete input; return 0; }
if(allLines == 1 || labels.count(list->getLabel()) == 1){
}
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } if (list != NULL) { delete list; } delete input; return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } if (list != NULL) { delete list; } delete input; return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;