#ifndef CONSENSUSSEQSCOMMAND_H
#define CONSENSUSSEQSCOMMAND_H
-
+//test
/*
* consensusseqscommand.h
* Mothur
public:
ConsensusSeqsCommand(string);
ConsensusSeqsCommand();
- ~ConsensusSeqsCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~ConsensusSeqsCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "consensus.seqs"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Consensus.seqs"; }
+ string getDescription() { return "create a consensus sequence for each OTU or for a fasta file"; }
+
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
string fastafile, listfile, namefile, label, outputDir;
set<string> labels;
vector<string> outputNames;
- map<string, vector<string> > outputTypes;
map<string, string> fastaMap;
map<string, string> nameMap;
map<string, string> nameFileMap;
+ int cutoff;
int readFasta();
int readNames();
int processList(ListVector*&);
string getConsSeq(string, ofstream&, string&, int);
- char getBase(vector<int>);
+ char getBase(vector<int>, int);
};
#endif