X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fullmatrix.h;h=5912b6ccc0ea323bf905bd0e9f301631276c4490;hb=477e76a8a79b60f6cd4253324dd830bdea25e3e9;hp=43bde963ca3396241a26771771189cb27c2df617;hpb=42b802c0006d8b13bd5b27ea48d032a85d3f2102;p=mothur.git

diff --git a/fullmatrix.h b/fullmatrix.h
index 43bde96..5912b6c 100644
--- a/fullmatrix.h
+++ b/fullmatrix.h
@@ -17,36 +17,39 @@
 using namespace std;
 
 struct Names {
-	string		groupname;
 	string		seqName;
+	string		groupName;
 };
 
-
 class FullMatrix {
 	
-	public:
-		FullMatrix(){};
-		FullMatrix(ifstream&);
-		~FullMatrix(){};
+public:
+	FullMatrix(){};
+	FullMatrix(ifstream&);
+	~FullMatrix(){};
 	
-		int getNumSeqs();
-		void printMatrix(ostream&);
-		void getMinsForRowsVectors();  //requires globaldata->Groups to be filled
+	int getNumSeqs();
+	vector<int> getSizes();
+	vector<string> getGroups();
+	int getNumGroups();
+	void printMatrix(ostream&);
+	float get(int, int);
 	
-	private:
-		void sortGroups(int, int);  //this function sorts the sequences within the matrix.
-		void getBounds(int&, string);
-		void readSquareMatrix(ifstream&);  
-		void readLTMatrix(ifstream&);
-		vector< vector<float> > matrix;  //a 2D distance matrix of all the sequences and their distances to eachother.
-		vector< vector<float> > minsForRows;  //vector< minimum distance for that subrow> -one for each comparison.
-		map<int, Names> index; // row in vector, sequence group.  need to know this so when we sort it can be updated.
-		map<int, Names>::iterator it;
-		GroupMap* groupmap;  //maps sequences to groups they belong to.
-		GlobalData* globaldata;
-		int numSeqs, numGroups, numUserGroups;
-		bool square;
-
+private:
+	vector< vector<float> > matrix;  //a 2D distance matrix of all the sequences and their distances to eachother.
+	void readSquareMatrix(ifstream&);  
+	void readLTMatrix(ifstream&);
+	vector<Names> index; // row in vector, sequence group.  need to know this so when we sort it can be updated.
+	vector<int> sizes;
+	vector<string> groups;
+	void sortGroups(int, int);  //this function sorts the sequences within the matrix.
+	
+	
+	GroupMap* groupmap;  //maps sequences to groups they belong to.
+	int numSeqs;
+	int numGroups;
+	int numUserGroups;
+	GlobalData* globaldata;
 };
 
 #endif
\ No newline at end of file