final fixes for 1.7

[mothur.git] / fullmatrix.h

diff --git a/fullmatrix.h b/fullmatrix.h
index 389816abd70d40ce47ec324ce5d830bee77feff9..a669f70a1aa80428823ada2c40b42e209c6db8f8 100644 (file)
--- a/fullmatrix.h
+++ b/fullmatrix.h
@@ -11,6 +11,14 @@
 
 #include "mothur.h"
 #include "groupmap.h"
+#include "globaldata.hpp"
+#include "progress.hpp"
+
+
+struct Names {
+       string          seqName;
+       string          groupName;
+};
 
 class FullMatrix {
        
@@ -20,13 +28,27 @@ public:
        ~FullMatrix(){};
        
        int getNumSeqs();
+       vector<int> getSizes();
+       vector<string> getGroups();
+       int getNumGroups();
+       void printMatrix(ostream&);
+       float get(int, int);
        
 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.
+       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
+#endif