1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
|
/***************************************************************************
* 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 MODELPROTEIN_H
#define MODELPROTEIN_H
#include "modelmarkov.h"
extern const char* builtin_prot_models;
/**
Substitution models for protein sequences
@author BUI Quang Minh <minh.bui@univie.ac.at>
*/
class ModelProtein : public ModelMarkov
{
public:
/**
constructor
@param model_name model name, e.g., JTT, WAG.
@param freq state frequency type
@param tree associated phylogenetic tree
*/
ModelProtein(const char *model_name, string model_params, StateFreqType freq, string freq_params, PhyloTree *tree, ModelsBlock *models_block);
/**
initialization, called automatically by the constructor, no need to call it
@param model_name model name, e.g., JTT, WAG.
@param freq state frequency type
*/
virtual void init(const char *model_name, string model_params, StateFreqType freq, string freq_params);
/**
start structure for checkpointing
*/
virtual void startCheckpoint();
/**
save object into the checkpoint
*/
virtual void saveCheckpoint();
/**
restore object from the checkpoint
*/
virtual void restoreCheckpoint();
/**
read the rates from an input stream. it will throw error messages if failed
@param in input stream
*/
virtual void readRates(istream &in) throw(const char*, string);
/**
* @return model name with parameters in form of e.g. GTR{a,b,c,d,e,f}
*/
virtual string getNameParams() { return name; }
private:
ModelsBlock *models_block;
};
#endif
|
