moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / fullmatrix.h

diff --git a/fullmatrix.h b/fullmatrix.h
deleted file mode 100644 (file)
index 9de7ead..0000000
--- a/fullmatrix.h
+++ /dev/null
@@ -1,58 +0,0 @@
-#ifndef FULLMATRIX_H
-#define FULLMATRIX_H
-/*
- *  fullmatrix.h
- *  Mothur
- *
- *  Created by Sarah Westcott on 3/6/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "mothur.h"
-#include "groupmap.h"
-#include "progress.hpp"
-
-
-struct Names {
-       string          seqName;
-       string          groupName;
-};
-
-class FullMatrix {
-       
-public:
-       //FullMatrix(){ m = MothurOut::getInstance(); }
-       FullMatrix(ifstream&, GroupMap*, bool);
-       ~FullMatrix(){};
-       
-       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.
-       int readSquareMatrix(ifstream&);  
-       int 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.
-       void swapRows(int, int);
-       
-       GroupMap* groupmap;  //maps sequences to groups they belong to.
-       int numSeqs;
-       int numGroups;
-       int numUserGroups;
-       bool sim;
-       MothurOut* m;
-};
-
-#endif