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

[mothur.git] / suffixnodes.hpp

diff --git a/suffixnodes.hpp b/suffixnodes.hpp
deleted file mode 100644 (file)
index 6a22c4d..0000000
--- a/suffixnodes.hpp
+++ /dev/null
@@ -1,80 +0,0 @@
-#ifndef SUFFIXNODES_H
-#define SUFFIXNODES_H
-
-/*
- *  SuffixNodes.h
- *  
- *
- *  Created by Pat Schloss on 12/15/08.
- *  Copyright 2008 Patrick D. Schloss. All rights reserved.
- *
- *     There are two types of nodes in a suffix tree as I have implemented it.  First, there are the internal nodes that
- *     have children, these are the SuffixBranch objects.  There are also the terminal nodes, which are the suffixBranches.
- *  I divided them into two groups to save on memory.  A SuffixTree object will be a vector of SuffixNodes; therefore,
- *     the values of parentNode, children nodes, and suffix nodes are stored as ints that correspond to indices in the 
- *     vector
- *
- */
-
-#include "mothur.h"
-#include "mothurout.h"
-
-//********************************************************************************************************************
-
-class SuffixNode {
-       
-public:
-       SuffixNode(int, int, int);
-       virtual ~SuffixNode() {}
-       virtual void print(string, int) = 0;
-       virtual void setChildren(char, int);
-       virtual int getNumChildren();
-       virtual void eraseChild(char);
-       virtual void setSuffixNode(int);
-       virtual int getSuffixNode();
-       virtual int getChild(char);
-       int getParentNode();
-       void setParentNode(int);
-       int getStartCharPos();
-       void setStartCharPos(int start);
-       int getEndCharPos();
-       
-protected:
-       int parentNode;
-       int startCharPosition;
-       int endCharPosition;
-       MothurOut* m;
-};
-
-//********************************************************************************************************************
-
-class SuffixLeaf : public SuffixNode { //      most of the methods are already set in the parent class
-       
-public:
-       SuffixLeaf(int, int, int);              //      we just need to define a constructor and
-       ~SuffixLeaf() {}
-       void print(string, int);                //      print method
-};
-
-//********************************************************************************************************************
-
-class SuffixBranch : public SuffixNode {
-       
-public:
-       SuffixBranch(int, int, int);
-       ~SuffixBranch() {}
-       void print(string, int);                //      need a special method for printing the node because there are children
-       void eraseChild(char);                  //      need a special method for erasing the children
-       void setChildren(char, int);    //      need a special method for setting children
-       void setSuffixNode(int);                //      need a special method for setting the suffix node
-       int getSuffixNode();                    //      need a special method for returning the suffix node
-       int getChild(char);                             //      need a special method for return children
-       
-private:
-       vector<int> childNodes;                 //      a suffix branch is unique because it has children and a suffixNode.  The 
-       int suffixNode;                                 //      are stored in a vector for super-fast lookup.  If the alphabet were bigger, this
-};                                                                     //      might not be practical.  Since we only have 5 possible letters, it makes sense
-
-//********************************************************************************************************************
-
-#endif