X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fullmatrix.h;h=9de7ead566d4d5446b5ea405b5e3c7eb24991cc0;hb=541bab1dac00688b4c3a8c4a95ab464412663c50;hp=4fe11451ea7bc612e1b50397bd82328bbe2195c3;hpb=8aaea67a29205b8d3fe787d94d0dc5987858d2e6;p=mothur.git

diff --git a/fullmatrix.h b/fullmatrix.h
index 4fe1145..9de7ead 100644
--- a/fullmatrix.h
+++ b/fullmatrix.h
@@ -11,22 +11,48 @@
 
 #include "mothur.h"
 #include "groupmap.h"
+#include "progress.hpp"
+
+
+struct Names {
+	string		seqName;
+	string		groupName;
+};
 
 class FullMatrix {
 	
 public:
-	FullMatrix(){};
-	FullMatrix(ifstream&);
-	~FullMatrix();
+	//FullMatrix(){ m = MothurOut::getInstance(); }
+	FullMatrix(ifstream&, GroupMap*, bool);
+	~FullMatrix(){};
 	
 	int getNumSeqs();
+	vector<int> getSizes();
+	vector<string> getGroups();
+	void setGroups(vector<string> names) { groups = names;  }
+	void setSizes(vector<int> s)		 { sizes = s;		}
+	int getNumGroups();
+	void printMatrix(ostream&);
+	float get(int, int);
+	Names getRowInfo(int row)  {  return index[row];  }
 	
 private:
-	void sortGroups();  //this function sorts the sequences within the matrix.  
 	vector< vector<float> > matrix;  //a 2D distance matrix of all the sequences and their distances to eachother.
+	int readSquareMatrix(ifstream&);  
+	int 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.
+	void swapRows(int, int);
+	
 	GroupMap* groupmap;  //maps sequences to groups they belong to.
 	int numSeqs;
-
+	int numGroups;
+	int numUserGroups;
+	bool sim;
+	MothurOut* m;
 };
 
-#endif
\ No newline at end of file
+#endif