public:
PreClusterCommand(string);
PreClusterCommand();
- ~PreClusterCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~PreClusterCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "pre.cluster"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Pre.cluster"; }
+ string getDescription() { return "implements a pseudo-single linkage algorithm with the goal of removing sequences that are likely due to pyrosequencing errors"; }
+
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
int diffs, length;
- bool abort;
- string fastafile, namefile, outputDir;
+ bool abort, bygroup;
+ string fastafile, namefile, outputDir, groupfile;
vector<seqPNode> alignSeqs; //maps the number of identical seqs to a sequence
map<string, string> names; //represents the names file first column maps to second column
map<string, int> sizes; //this map a seq name to the number of identical seqs in the names file
//int readNamesFASTA();
int calcMisMatches(string, string);
void printData(string, string); //fasta filename, names file name
+ int process();
+ int loadSeqs(map<string, string>&, vector<Sequence>&);
};
/************************************************************/