X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=fullmatrix.h;fp=fullmatrix.h;h=5912b6ccc0ea323bf905bd0e9f301631276c4490;hp=078cdb7699f53192b526ab3979036d5144b968e1;hb=197c6d3303439582502840980d6a85cf3aab2314;hpb=3329385a816a97bdde934d98a615865c29eaacad

diff --git a/fullmatrix.h b/fullmatrix.h
index 078cdb7..5912b6c 100644
--- a/fullmatrix.h
+++ b/fullmatrix.h
@@ -17,52 +17,39 @@
 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(){};
+	FullMatrix(ifstream&);
+	~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(string, string);  //shuffles the sequences in the groups passed in.
-		void restore();  //unshuffles the matrix.
+	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&);
-		void printMinsForRows(ostream&);
-		
-		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;
-
+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