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/***************************************************************************
* Copyright (C) 2006 by BUI Quang Minh, Steffen Klaere, Arndt von Haeseler *
* 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 MSETSBLOCK_H
#define MSETSBLOCK_H
#include "ncl/ncl.h"
/**
a taxa set with name
*/
class TaxaSetName {
public:
/**
set name
*/
string name;
/**
string vector of taxa names
*/
vector<string> taxlist;
};
typedef vector<TaxaSetName*> TaxaSetNameVector;
/**
* a charset
*/
class CharSet {
public:
/** charset name */
string name;
/** positions specification, e.g., 1-500\3 501-502 */
string position_spec;
/** name of model associated with charset, e.g., GTR+G */
string model_name;
/** alignment name */
string aln_file;
/** sequence type */
string sequence_type;
/** name of CharPartition where this charset is included*/
string char_partition;
};
/**
Sets Block of Nexus file parser
@author BUI Quang Minh, Steffen Klaere, Arndt von Haeseler
*/
class MSetsBlock : public NxsBlock
{
public:
/**
constructor, assigning an associated splits graph
*/
MSetsBlock();
/**
destructor
*/
virtual ~MSetsBlock();
/**
print info to an output stream
@param out output stream, cout for output to screen
*/
virtual void Report(ostream &out);
/**
reset the block
*/
virtual void Reset();
/**
@return the number of sets
*/
int getNSets() const { return sets.size(); }
/**
@param id set id
@return reference to the corresponding set
*/
inline TaxaSetName *getSet(int id) { return sets[id]; }
/**
@return vector of all taxa set
*/
inline TaxaSetNameVector *getSets() { return &sets; }
/**
@param name an area name
@return ID of the area with that name, -1 if not found
*/
int findArea(string &name);
/** list of charsets with (possible) models */
vector<CharSet* > charsets;
/**
* return CharSet with a name from charsets, NULL if not found
*/
CharSet *findCharSet(string name);
protected:
/**
main method to read block from file
@param token a token reader
*/
virtual void Read(NxsToken &token);
/**
list of taxa set names
*/
TaxaSetNameVector sets;
};
#endif
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