X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=hclustercommand.h;h=fc0333174a87b111a0cda756dc24ff4669202cc9;hb=09ce41fb228c00d0f49896c66b2f2c5760914769;hp=1dd46b9ad96890c5576e18ae500cff6359270795;hpb=c82900be3ceed3d9bc491bdc98b1819ef85c1af7;p=mothur.git

diff --git a/hclustercommand.h b/hclustercommand.h
index 1dd46b9..fc03331 100644
--- a/hclustercommand.h
+++ b/hclustercommand.h
@@ -29,17 +29,16 @@
 //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();
 	
@@ -52,23 +51,17 @@ private:
 	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&);
 };
 
 /************************************************************/