working on libshuff

[mothur.git] / fullmatrix.h

diff --git a/fullmatrix.h b/fullmatrix.h
index 0bd5c873ea4da00bc48d8a3395844f80151bd630..43bde963ca3396241a26771771189cb27c2df617 100644 (file)
--- a/fullmatrix.h
+++ b/fullmatrix.h
@@ -19,7 +19,6 @@ using namespace std;
 struct Names {
        string          groupname;
        string          seqName;
-       float           minDist;
 };
 
 
@@ -32,16 +31,20 @@ class FullMatrix {
        
                int getNumSeqs();
                void printMatrix(ostream&);
+               void getMinsForRowsVectors();  //requires globaldata->Groups to be filled
        
        private:
                void sortGroups(int, int);  //this function sorts the sequences within the matrix.
+               void getBounds(int&, string);
                void readSquareMatrix(ifstream&);  
                void readLTMatrix(ifstream&);
                vector< vector<float> > matrix;  //a 2D distance matrix of all the sequences and their distances to eachother.
+               vector< vector<float> > minsForRows;  //vector< minimum distance for that subrow> -one for each comparison.
                map<int, Names> index; // row in vector, sequence group.  need to know this so when we sort it can be updated.
+               map<int, Names>::iterator it;
                GroupMap* groupmap;  //maps sequences to groups they belong to.
                GlobalData* globaldata;
-               int numSeqs;
+               int numSeqs, numGroups, numUserGroups;
                bool square;
 
 };