class PreClusterCommand : public Command {
public:
- PreClusterCommand(string);
- ~PreClusterCommand();
- int execute();
- void help();
+ PreClusterCommand(string);
+ PreClusterCommand();
+ ~PreClusterCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "pre.cluster"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
int diffs, length;
bool abort;
string fastafile, namefile, outputDir;
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
+ 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
+ map<string, int>::iterator itSize;
// map<string, bool> active; //maps sequence name to whether it has already been merged or not.
+ vector<string> outputNames;
+ map<string, vector<string> > outputTypes;
int readFASTA();
- int readNamesFASTA();
+ void readNameFile();
+ //int readNamesFASTA();
int calcMisMatches(string, string);
void printData(string, string); //fasta filename, names file name
};