Cassiopee
1.0
Suffix indexer and search tool
|
#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 |
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.
TreeNode::TreeNode | ( | char | nc | ) |
Creates a node from a char
nc | character for this node |
TreeNode::TreeNode | ( | char | nc, |
long | pos | ||
) |
Creates a node from a char
nc | character for this node |
pos | position of the character in the sequence |
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