Cassiopee  1.0
Suffix indexer and search tool
Public Member Functions | Public Attributes | Friends | List of all members
TreeNode Class Reference

#include <Cassiopee.h>

Public Member Functions

 TreeNode (char nc)
 
 TreeNode (char nc, long pos)
 

Public Attributes

char c
 
list< long > positions
 
long next_pos
 
long next_length
 

Friends

class boost::serialization::access
 

Detailed Description

Node in the suffix tree

If tree is reduced (DO_REDUCTION=1), memory usage is highly reduced, keeping in memory only the branching nodes. Search is made after that looking at branch nodes and sequence content between nodes. In addition, data from file are analysed per chunk, limiting again loaded data in memory.

This treatment requires however more disk usage (reads) and tree manipulations, increasing the index and search time for a gain on memory requirements.

Constructor & Destructor Documentation

TreeNode::TreeNode ( char  nc)

Creates a node from a char

Parameters
nccharacter for this node
TreeNode::TreeNode ( char  nc,
long  pos 
)

Creates a node from a char

Parameters
nccharacter for this node
posposition of the character in the sequence

Member Data Documentation

char TreeNode::c

Character to match

long TreeNode::next_length

Length of remaining data to read in sequence file

long TreeNode::next_pos

When tree is reduced, store the location of next characters in input sequence file. Reduction can be made from a branch up to the leaf or between 2 branches. If next_pos is equal to -1, then no reduction is made.

list<long> TreeNode::positions

List of positions in sequence matching this node


The documentation for this class was generated from the following files: