added alignment code

[mothur.git] / suffixnodes.hpp

diff --git a/suffixnodes.hpp b/suffixnodes.hpp
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+#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"
+
+using namespace std;
+
+//********************************************************************************************************************
+
+class SuffixNode {
+       
+public:
+       SuffixNode(int, int, int);
+       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;
+};
+
+//********************************************************************************************************************
+
+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
+       void print(string, int);                //      print method
+};
+
+//********************************************************************************************************************
+
+class SuffixBranch : public SuffixNode {
+       
+public:
+       SuffixBranch(int, int, int);
+       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