//University of Florida, Gainesville, FL 32610-3622 and 3Materials Technology Directorate, Air Force Technical
//Applications Center, 1030 S. Highway A1A, Patrick AFB, FL 32925-3002, USA
//Received January 28, 2009; Revised April 14, 2009; Accepted April 15, 2009
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-/******************************************************************/
-
-
-/************************************************************/
-struct seqDist {
- int seq1;
- int seq2;
- float dist;
-};
/************************************************************/
class HClusterCommand : public Command {
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;
void printData(string label);
- vector<seqDist> getSeqs(ifstream&);
};
/************************************************************/