//Applications Center, 1030 S. Highway A1A, Patrick AFB, FL 32925-3002, USA
//Received January 28, 2009; Revised April 14, 2009; Accepted April 15, 2009
/************************************************************/
-struct seqDist {
- int seq1;
- int seq2;
- float dist;
-};
-/************************************************************/
class HClusterCommand : public Command {
public:
- HClusterCommand(string);
+ HClusterCommand(string);
+ HClusterCommand();
~HClusterCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
ListVector oldList;
ReadCluster* read;
- bool abort;
-
- string method, fileroot, tag, distfile, format, phylipfile, columnfile, namefile, sort;
+ bool abort, sorted, print_start, hard;
+ string method, fileroot, tag, distfile, format, phylipfile, columnfile, namefile, sort, showabund, timing, outputDir;
double cutoff;
- string showabund, timing;
int precision, length;
ofstream sabundFile, rabundFile, listFile;
- //ifstream in;
- seqDist next;
- bool exitedBreak, sorted;
-
- bool print_start;
time_t start;
unsigned long loops;
+ vector<string> outputNames;
+ map<string, vector<string> > outputTypes;
void printData(string label);
- vector<seqDist> getSeqs(ifstream&);
};
/************************************************************/