string getOutputPattern(string);
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Primer.design"; }
- string getDescription() { return "design sequence fragments that are specific to particular OTUs"; }
+ string getDescription() { return "identify sequence fragments that are specific to particular OTUs"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
};
bool abort, allLines, large;
- int cutoff, pdiffs, length, otunumber, processors, alignedLength;
- string outputDir, listfile, namefile, countfile, fastafile, label;
+ int cutoff, pdiffs, length, processors, alignedLength;
+ string outputDir, listfile, otulabel, namefile, countfile, fastafile, label;
double minTM, maxTM;
ListVector* list;
vector<string> outputNames;
bool findPrimer(string, string, vector<int>&, vector<int>&, vector<int>&);
int findMeltingPoint(string primer, double&, double&);
- set<int> createProcesses(string, vector<double>&, vector<double>&, set<string>&, vector<Sequence>&);
- set<int> driver(string, vector<double>&, vector<double>&, set<string>&, vector<Sequence>&, int, int, int&);
+ set<int> createProcesses(string, vector<double>&, vector<double>&, set<string>&, vector<Sequence>&, int);
+ set<int> driver(string, vector<double>&, vector<double>&, set<string>&, vector<Sequence>&, int, int, int&, int);
vector< vector< vector<unsigned int> > > driverGetCounts(map<string, int>&, unsigned long int&, vector<unsigned int>&, unsigned long long&, unsigned long long&);
vector<Sequence> createProcessesConSeqs(map<string, int>&, unsigned long int&);
+ int findIndex(string binLabel, vector<string> binLabels);
};
MothurOut* m;
int start;
int end;
- int pdiffs, threadID, otunumber, length;
+ int pdiffs, threadID, length, binIndex;
set<string> primers;
vector<double> minTms, maxTms;
set<int> otusToRemove;
maxTms = max;
primers = pri;
consSeqs = seqs;
- otunumber = otun;
+ binIndex = otun;
length = l;
threadID = tid;
numBinsProcessed = 0;
if (pDataArray->m->control_pressed) { break; }
- if (i != (pDataArray->otunumber-1)) {
+ if (i != (pDataArray->binIndex)) {
int primerIndex = 0;
for (set<string>::iterator it = pDataArray->primers.begin(); it != pDataArray->primers.end(); it++) {
vector<int> primerStarts;