X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=fullmatrix.h;h=9de7ead566d4d5446b5ea405b5e3c7eb24991cc0;hp=5912b6ccc0ea323bf905bd0e9f301631276c4490;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=197c6d3303439582502840980d6a85cf3aab2314

diff --git a/fullmatrix.h b/fullmatrix.h
index 5912b6c..9de7ead 100644
--- a/fullmatrix.h
+++ b/fullmatrix.h
@@ -11,10 +11,8 @@
 
 #include "mothur.h"
 #include "groupmap.h"
-#include "globaldata.hpp"
 #include "progress.hpp"
 
-using namespace std;
 
 struct Names {
 	string		seqName;
@@ -24,32 +22,37 @@ struct Names {
 class FullMatrix {
 	
 public:
-	FullMatrix(){};
-	FullMatrix(ifstream&);
+	//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:
 	vector< vector<float> > matrix;  //a 2D distance matrix of all the sequences and their distances to eachother.
-	void readSquareMatrix(ifstream&);  
-	void readLTMatrix(ifstream&);
+	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 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;
-	GlobalData* globaldata;
+	bool sim;
+	MothurOut* m;
 };
 
-#endif
\ No newline at end of file
+#endif