class PreClusterCommand : public Command {
public:
- PreClusterCommand(string);
+ PreClusterCommand(string);
+ PreClusterCommand();
~PreClusterCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
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
};