fixed some bugs and added mgcluster command

[mothur.git] / fullmatrix.h

diff --git a/fullmatrix.h b/fullmatrix.h
index 5912b6ccc0ea323bf905bd0e9f301631276c4490..7cb8b15fedf8c39f06aeaee5ca3fb6e9f3274499 100644 (file)
--- a/fullmatrix.h
+++ b/fullmatrix.h
@@ -14,7 +14,6 @@
 #include "globaldata.hpp"
 #include "progress.hpp"
 
-using namespace std;
 
 struct Names {
        string          seqName;
@@ -31,9 +30,12 @@ public:
        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.
@@ -42,8 +44,9 @@ private:
        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 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;
@@ -52,4 +55,4 @@ private:
        GlobalData* globaldata;
 };
 
-#endif
\ No newline at end of file
+#endif