Victor
 All Data Structures Functions Variables Friends Pages
Prof.h
1 /* This file is part of Victor.
2 
3  Victor is free software: you can redistribute it and/or modify
4  it under the terms of the GNU General Public License as published by
5  the Free Software Foundation, either version 3 of the License, or
6  (at your option) any later version.
7 
8  Victor is distributed in the hope that it will be useful,
9  but WITHOUT ANY WARRANTY; without even the implied warranty of
10  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
11  GNU General Public License for more details.
12 
13  You should have received a copy of the GNU General Public License
14  along with Victor. If not, see <http://www.gnu.org/licenses/>.
15  */
16 
17 
18 #ifndef __Prof_H__
19 #define __Prof_H__
20 
21 #include <ProfInput.h>
22 #include <Structure.h>
23 
24 namespace Victor { namespace Align2{
25 
31  class Prof : public Structure {
32  public:
33 
34  // CONSTRUCTORS:
35 
37  Prof(SubMatrix *subStr, ProfInput *phd1, ProfInput *phd2, double cPrf);
38 
40  Prof(const Prof &orig);
41 
43  virtual ~Prof();
44 
45 
46  // OPERATORS:
47 
49  Prof& operator =(const Prof &orig);
50 
51 
52  // PREDICATES:
53 
55  virtual double scoringStr(int i, int j);
56 
57 
58  // MODIFIERS:
59 
61  virtual void copy(const Prof &orig);
62 
64  virtual Prof* newCopy();
65 
66 
67  protected:
68 
69 
70  private:
71 
72  // ATTRIBUTES:
73 
74  ProfInput *phd1;
75  ProfInput *phd2;
76  double cPrf;
77 
78  };
79 
80 }} // namespace
81 
82 #endif
virtual ~Prof()
Destructor.
Definition: Prof.cc:43
Prof(SubMatrix *subStr, ProfInput *phd1, ProfInput *phd2, double cPrf)
Default constructor.
Definition: Prof.cc:35
Implement a standard substitution matrix.
Definition: SubMatrix.h:30
virtual void copy(const Prof &orig)
Copy orig object to this object ("deep copy").
Definition: Prof.cc:92
Base class for structural scores.
Definition: Structure.h:32
virtual double scoringStr(int i, int j)
Calculate structural scores to create matrix values.
Definition: Prof.cc:70
Calculate structural scores with info derived from PHD.
Definition: Prof.h:31
SubMatrix * subStr
Structural substitution matrix.
Definition: Structure.h:82
Implement I/O objects for handling PHD files.
Definition: ProfInput.h:34
virtual Prof * newCopy()
Construct a new "deep copy" of this object.
Definition: Prof.cc:103
Prof & operator=(const Prof &orig)
Assignment operator.
Definition: Prof.cc:54