X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getoturepcommand.h;h=874e43ce5a8f45178a073b9d8e8e00fa8852deb0;hb=d9b668f68b99f92ecdc71dd8cd363cb4e27107f9;hp=0e8a121793823677186d67e5d3cd255dd7ec47d1;hpb=e1cf60b82a48d4d96e3a696a2d221c56cfb0b298;p=mothur.git

diff --git a/getoturepcommand.h b/getoturepcommand.h
index 0e8a121..874e43c 100644
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -39,7 +39,12 @@ class GetOTURepCommand : public Command {
 
 public:
 	GetOTURepCommand(string);
+	GetOTURepCommand();
 	~GetOTURepCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();
 	void help();
 
@@ -53,24 +58,27 @@ private:
 	ReadMatrix* readMatrix;
 	FormatMatrix* formatMatrix;
 	NameAssignment* nameMap;
-	string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, columnfile, distFile, format;
+	string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, columnfile, distFile, format, outputDir, groups;
 	ofstream out;
 	ifstream in, inNames, inRow;
 	bool abort, allLines, groupError, large;
 	set<string> labels; //holds labels to be used
 	map<string, int> nameToIndex;  //maps sequence name to index in sparsematrix
+	vector<string> outputNames, Groups;
+	map<string, string> outputNameFiles;
 	float cutoff;
 	int precision;
 	vector<SeqMap> seqVec;			// contains maps with sequence index and distance
 									// for all distances related to a certain sequence
 	vector<int> rowPositions;
+	map<string, vector<string> > outputTypes;
 
 	void readNamesFile();
 	int process(ListVector*);
 	SeqMap getMap(int);
-	string findRep(int, string&, ListVector*, int&); 	// returns the name of the "representative" sequence of given bin, 
-									// fills a string containing the groups in that bin if a groupfile is given,
-									// and returns the number of sequences in the given bin
+	string findRep(vector<string>); 	// returns the name of the "representative" sequence of given bin or subset of a bin, for groups
+	int processNames(string, string);
+												
 
 };