X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mgclustercommand.h;h=f16a8f0c5ebc75bf07039a54d910d266e418b94e;hb=6d12ed0ba66fb35e9e2781fe3ca361e2293f2476;hp=9aa86d4441e5c5f1202a6d552fef31162337c00d;hpb=c82900be3ceed3d9bc491bdc98b1819ef85c1af7;p=mothur.git

diff --git a/mgclustercommand.h b/mgclustercommand.h
index 9aa86d4..f16a8f0 100644
--- a/mgclustercommand.h
+++ b/mgclustercommand.h
@@ -24,7 +24,12 @@ class MGClusterCommand : public Command {
 
 public:
 	MGClusterCommand(string);
+	MGClusterCommand();
 	~MGClusterCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();
 	void help();
 	
@@ -36,20 +41,21 @@ private:
 	HCluster* hcluster;
 	ListVector* list;
 	ListVector oldList;
-	vector<DistNode> overlapMatrix;
-	DistNode next;
-
+	vector<seqDist> overlapMatrix;
+	vector<string> outputNames;
+	map<string, vector<string> > outputTypes;
 	
-	string blastfile, method, namefile, overlapFile, distFile;
+	string blastfile, method, namefile, overlapFile, distFile, outputDir;
 	ofstream sabundFile, rabundFile, listFile;
-	float cutoff, penalty;
+	double cutoff;
+	float penalty;
 	int precision, length, precisionLength;
-	bool abort, minWanted, hclusterWanted, exitedBreak, merge;
+	bool abort, minWanted, hclusterWanted, merge, hard;
 	
 	void printData(ListVector*);
 	ListVector* mergeOPFs(map<string, int>, float);
 	void sortHclusterFiles(string, string);
-	vector<DistNode> getSeqs(ifstream&);
+	vector<seqDist> getSeqs(ifstream&);
 
 };