8 * Created by Pat Schloss on 12/15/08.
9 * Copyright 2008 Patrick D. Schloss. All rights reserved.
11 * There are two types of nodes in a suffix tree as I have implemented it. First, there are the internal nodes that
12 * have children, these are the SuffixBranch objects. There are also the terminal nodes, which are the suffixBranches.
13 * I divided them into two groups to save on memory. A SuffixTree object will be a vector of SuffixNodes; therefore,
14 * the values of parentNode, children nodes, and suffix nodes are stored as ints that correspond to indices in the
20 #include "mothurout.h"
22 //********************************************************************************************************************
27 SuffixNode(int, int, int);
28 virtual ~SuffixNode() {}
29 virtual void print(string, int) = 0;
30 virtual void setChildren(char, int);
31 virtual int getNumChildren();
32 virtual void eraseChild(char);
33 virtual void setSuffixNode(int);
34 virtual int getSuffixNode();
35 virtual int getChild(char);
37 void setParentNode(int);
38 int getStartCharPos();
39 void setStartCharPos(int start);
44 int startCharPosition;
49 //********************************************************************************************************************
51 class SuffixLeaf : public SuffixNode { // most of the methods are already set in the parent class
54 SuffixLeaf(int, int, int); // we just need to define a constructor and
56 void print(string, int); // print method
59 //********************************************************************************************************************
61 class SuffixBranch : public SuffixNode {
64 SuffixBranch(int, int, int);
66 void print(string, int); // need a special method for printing the node because there are children
67 void eraseChild(char); // need a special method for erasing the children
68 void setChildren(char, int); // need a special method for setting children
69 void setSuffixNode(int); // need a special method for setting the suffix node
70 int getSuffixNode(); // need a special method for returning the suffix node
71 int getChild(char); // need a special method for return children
74 vector<int> childNodes; // a suffix branch is unique because it has children and a suffixNode. The
75 int suffixNode; // are stored in a vector for super-fast lookup. If the alphabet were bigger, this
76 }; // might not be practical. Since we only have 5 possible letters, it makes sense
78 //********************************************************************************************************************