X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=fullmatrix.h;fp=fullmatrix.h;h=0000000000000000000000000000000000000000;hp=9de7ead566d4d5446b5ea405b5e3c7eb24991cc0;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76

diff --git a/fullmatrix.h b/fullmatrix.h
deleted file mode 100644
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