X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getoturepcommand.h;h=874e43ce5a8f45178a073b9d8e8e00fa8852deb0;hb=d4cd876bd09bfa1bcb137261700eae79f9e41fc0;hp=58fec8d4f3e3aaaf148a9ff8455c4fba93c6b35f;hpb=f27b66ce6415eb14c434f9850019c7cf140e023e;p=mothur.git

diff --git a/getoturepcommand.h b/getoturepcommand.h
index 58fec8d..874e43c 100644
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -18,6 +18,8 @@
 #include "readotu.h"
 #include "fastamap.h"
 #include "groupmap.h"
+#include "readmatrix.hpp"
+#include "formatmatrix.h"
 
 typedef list<PCell>::iterator MatData;
 typedef map<int, float> SeqMap;
@@ -37,7 +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();
 
@@ -48,18 +55,30 @@ private:
 	InputData* input;
 	FastaMap* fasta;
 	GroupMap* groupMap;
-	string filename, fastafile, listfile, namesfile, groupfile, label, sorted, phylipfile, columnfile, namefile;
+	ReadMatrix* readMatrix;
+	FormatMatrix* formatMatrix;
+	NameAssignment* nameMap;
+	string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, columnfile, distFile, format, outputDir, groups;
 	ofstream out;
-	ifstream in, inNames;
-	bool abort, allLines, groupError;
+	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*);
-	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
+	SeqMap getMap(int);
+	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);
+												
 
 };