X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fullmatrix.h;h=078cdb7699f53192b526ab3979036d5144b968e1;hb=8770435f2eedcbf4e69daba716144e83da1dd939;hp=389816abd70d40ce47ec324ce5d830bee77feff9;hpb=5589a967aab6b83d826508f4c37a789fb6a2a26e;p=mothur.git

diff --git a/fullmatrix.h b/fullmatrix.h
index 389816a..078cdb7 100644
--- a/fullmatrix.h
+++ b/fullmatrix.h
@@ -11,21 +11,57 @@
 
 #include "mothur.h"
 #include "groupmap.h"
+#include "globaldata.hpp"
+#include "progress.hpp"
+
+using namespace std;
+
+struct Names {
+	string		groupname;
+	string		seqName;
+};
+
+struct Swap {
+	int		a;
+	int		b;
+};
+
 
 class FullMatrix {
 	
-public:
-	FullMatrix(){};
-	FullMatrix(ifstream&);
-	~FullMatrix(){};
+	public:
+		FullMatrix(){};
+		FullMatrix(ifstream&);
+		~FullMatrix(){};
 	
-	int getNumSeqs();
+		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.
 	
-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.
-	GroupMap* groupmap;  //maps sequences to groups they belong to.
-	int numSeqs;
+	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;
 
 };