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ncbitree.h
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ncbitree.h
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/***************************************************************************
* Copyright (C) 2009 by BUI Quang Minh *
* minh.bui@univie.ac.at *
* *
* This program is free software; you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation; either version 2 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License *
* along with this program; if not, write to the *
* Free Software Foundation, Inc., *
* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
***************************************************************************/
#ifndef NCBITREE_H
#define NCBITREE_H
#include "mtree.h"
const int MAX_TAXONOMY_ID = 2000000;
/**
Class for processing NCBI Taxonomy tree
@author BUI Quang Minh <minh.bui@univie.ac.at>
*/
class NCBITree : public MTree
{
public:
NCBITree();
~NCBITree();
/********************************************************
READ TREE FROM FILE
********************************************************/
/**
read the tree in nodes.dmp file from NCBI taxonomy
@param infile the input file file.
@param root_id taxon ID of the root
@param taxon_level e.g. "species", "genus"; NULL to take all taxa (incl. subspecies)
*/
Node* readNCBITree(const char *infile, int root_id, const char* taxon_level, const char *ignore_level);
Node* readNCBITree(istream &in, int root_id, const char* taxon_level, const char *ignore_level);
/**
read names.dmp file. You must call readNCBITree() before calling this function
@param infile input file name (typically names.dmp from NCBI)
@param name_type type of the name
*/
void readNCBINames(const char* infile, const char *name_type = "scientific name");
void readNCBINames(ifstream &in, const char *name_type = "scientific name");
protected:
/**
taxonomy rank of the nodes
*/
StrVector node_levels;
/**
vector of all taxonomical nodes
*/
NodeVector nodes;
/**
prune subtree below the taxon_level
@return number of nodes pruned
*/
int pruneTaxa(StrVector &node_levels, const char* taxon_level, Node *node, Node *dad);
/**
prune all nodes that have degree of 2
@return number of nodes pruned
*/
int pruneBridgeNodes(Node *node, Node *dad);
void countNodeNum(Node *node, Node *dad);
/**
release the nemory.
@param node the starting node, NULL to start from the root
@param dad dad of the node, used to direct the search
*/
int freeNode(Node *node = NULL, Node *dad = NULL);
};
#endif