}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;
int ConsensusSeqsCommand::readNames(){
try{
-
- ifstream in;
- m->openInputFile(namefile, in);
-
- string thisname, repnames;
- map<string, string>::iterator it;
-
- bool error = false;
-
- while(!in.eof()){
-
- if (m->control_pressed) { break; }
-
- in >> thisname; m->gobble(in); //read from first column
- in >> repnames; //read from second column
-
- it = nameMap.find(thisname);
+ map<string, string> temp;
+ map<string, string>::iterator it;
+ bool error = false;
+
+ m->readNames(namefile, temp); //use central buffered read
+
+ for (map<string, string>::iterator itTemp = temp.begin(); itTemp != temp.end(); itTemp++) {
+ string thisname, repnames;
+ thisname = itTemp->first;
+ repnames = itTemp->second;
+
+ it = nameMap.find(thisname);
if (it != nameMap.end()) { //then this sequence was in the fastafile
-
+ nameFileMap[thisname] = repnames; //for later when outputting the new namesFile if the list file is unique
+
vector<string> splitRepNames;
m->splitAtComma(repnames, splitRepNames);
- nameFileMap[thisname] = repnames; //for later when outputting the new namesFile if the list file is unique
for (int i = 0; i < splitRepNames.size(); i++) { nameMap[splitRepNames[i]] = thisname; }
}else{ m->mothurOut("[ERROR]: " + thisname + " is not in the fasta file, please correct."); m->mothurOutEndLine(); error = true; }
-
- m->gobble(in);
- }
-
- in.close();
-
+ }
+
if (error) { m->control_pressed = true; }
return 0;