X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=fullmatrix.h;h=9de7ead566d4d5446b5ea405b5e3c7eb24991cc0;hp=b744490d760d108df3ef7780cb35bcae918b9dd2;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=2d2fbc80f9359b19873ba3e63970b58f4f8f49f3

diff --git a/fullmatrix.h b/fullmatrix.h
index b744490..9de7ead 100644
--- a/fullmatrix.h
+++ b/fullmatrix.h
@@ -11,59 +11,48 @@
 
 #include "mothur.h"
 #include "groupmap.h"
-#include "globaldata.hpp"
 #include "progress.hpp"
 
-using namespace std;
 
 struct Names {
-	string		groupname;
 	string		seqName;
+	string		groupName;
 };
 
-struct Swap {
-	int		a;
-	int		b;
-};
-
-
 class FullMatrix {
 	
-	public:
-		FullMatrix(){};
-		FullMatrix(ifstream&);
-		~FullMatrix(){};
+public:
+	//FullMatrix(){ m = MothurOut::getInstance(); }
+	FullMatrix(ifstream&, GroupMap*, bool);
+	~FullMatrix(){};
 	
-		int getNumSeqs();
-		void printMatrix(ostream&);
-		void setBounds();  //requires globaldata->Groups to be filled
-		vector<float> getMins(int); //returns vector of mins for "box" requested ie. groups A, B, 0 = AA, 1 = AB, 2 = BA, 3 = BB;
-		void getDist(vector<float>&);  //fills a vector with the valid distances for the integral form.
-		void shuffle(int);  //shuffles the sequences in the box passed in.
-		void restore();  //unshuffles the matrix.
-				
-		
-	void printMinsForRows(ostream&);
-	private:
-		void sortGroups(int, int);  //this function sorts the sequences within the matrix.
-		void getBounds(int&, string);
-		void readSquareMatrix(ifstream&);  
-		void readLTMatrix(ifstream&);
-		
-		map<int, Names> index; // row in vector, sequence group.  need to know this so when we sort it can be updated.
-		map<int, Swap> restoreIndex; //a map of the swaps made so you can undo them in restore.
-		map<int, Names>::iterator it;
-		map<int, Swap>::reverse_iterator it2;
-			
-		vector< vector<float> > matrix;  //a 2D distance matrix of all the sequences and their distances to eachother.
-		vector<float> minsForRows;  //vector< minimum distance for that subrow> - one for each comparison.
-		vector<int> bounds;  //bounds[1] = starting row in matrix from group B, bounds[2] = starting row in matrix from group C, bounds[3] = no need to find upper bound of C because its numSeqs.
-								
-		GroupMap* groupmap;  //maps sequences to groups they belong to.
-		GlobalData* globaldata;
-		int numSeqs, numGroups, numUserGroups;
-		bool square;
-
+	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.
+	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