Victor
 All Data Structures Functions Variables Friends Pages
ThreadingSs2.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 __ThreadingSs2_H__
19 #define __ThreadingSs2_H__
20 
21 #include <AlignmentData.h>
22 #include <Ss2Input.h>
23 #include <Structure.h>
24 #include <ThreadingInput.h>
25 
26 namespace Victor { namespace Align2{
27 
34  class ThreadingSs2 : public Structure {
35  public:
36 
37  // CONSTRUCTORS:
38 
41  Ss2Input *psipred1, Ss2Input *psipred2, double cThr, double cSs2);
42 
44  ThreadingSs2(const ThreadingSs2 &orig);
45 
47  virtual ~ThreadingSs2();
48 
49 
50  // OPERATORS:
51 
53  ThreadingSs2& operator =(const ThreadingSs2 &orig);
54 
55 
56  // PREDICATES:
57 
59  virtual double scoringStr(int i, int j);
60 
61 
62  // MODIFIERS:
63 
65  virtual void copy(const ThreadingSs2 &orig);
66 
68  virtual ThreadingSs2* newCopy();
69 
70 
71  protected:
72 
73 
74  private:
75 
76  // ATTRIBUTES:
77 
78  string seq1;
79  string sec1;
80  string sec2;
81  ThreadingInput *thread;
82  Ss2Input *psipred1;
83  Ss2Input *psipred2;
84  double cThr;
85  double cSs2;
86 
87  };
88 
89 }} // namespace
90 
91 #endif
virtual double scoringStr(int i, int j)
Calculate structural scores to create matrix values.
Definition: ThreadingSs2.cc:81
Implement a standard substitution matrix.
Definition: SubMatrix.h:30
Implement I/O objects for handling threading files.
Definition: ThreadingInput.h:32
ThreadingSs2 & operator=(const ThreadingSs2 &orig)
Assignment operator.
Definition: ThreadingSs2.cc:65
Implement I/O objects for handling PSI-PRED files.
Definition: Ss2Input.h:34
ThreadingSs2(SubMatrix *subStr, AlignmentData *ad, ThreadingInput *thread, Ss2Input *psipred1, Ss2Input *psipred2, double cThr, double cSs2)
Default constructor.
Definition: ThreadingSs2.cc:47
Base class for printing alignments.
Definition: AlignmentData.h:35
virtual ~ThreadingSs2()
Destructor.
Definition: ThreadingSs2.cc:58
Base class for structural scores.
Definition: Structure.h:32
virtual void copy(const ThreadingSs2 &orig)
Copy orig object to this object ("deep copy").
Definition: ThreadingSs2.cc:137
SubMatrix * subStr
Structural substitution matrix.
Definition: Structure.h:82
Calculate structural scores with info derived from threading and PSI-PRED.
Definition: ThreadingSs2.h:34
virtual ThreadingSs2 * newCopy()
Construct a new "deep copy" of this object.
Definition: ThreadingSs2.cc:150