NCBI C++ ToolKit
cn3d_ba_interface.hpp
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1 /* $Id: cn3d_ba_interface.hpp 33815 2007-05-04 17:18:18Z kazimird $
2 * ===========================================================================
3 *
4 * PUBLIC DOMAIN NOTICE
5 * National Center for Biotechnology Information
6 *
7 * This software/database is a "United States Government Work" under the
8 * terms of the United States Copyright Act. It was written as part of
9 * the author's official duties as a United States Government employee and
10 * thus cannot be copyrighted. This software/database is freely available
11 * to the public for use. The National Library of Medicine and the U.S.
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23 *
24 * ===========================================================================
25 *
26 * Authors: Paul Thiessen
27 *
28 * File Description:
29 * Interface to Alejandro's block alignment algorithm
30 *
31 * ===========================================================================
32 */
33 
34 #ifndef CN3D_BA_INTERFACE__HPP
35 #define CN3D_BA_INTERFACE__HPP
36 
37 #include <corelib/ncbistl.hpp>
38 
39 #include <list>
40 
41 class wxWindow;
42 
43 
44 BEGIN_SCOPE(Cn3D)
45 
47 class SequenceViewer;
48 
50 {
51 public:
52  BlockAligner(void);
53  ~BlockAligner(void) { }
54 
55  typedef std::list < BlockMultipleAlignment * > AlignmentList;
56 
57  // creates new pairwise alignments (as two-row BlockMultipleAlignments), each of which has
58  // the given master and one of the given sequences. If the alignment algorithm fails to
59  // align the new sequence, it will include a null-alignment for that sequence.
61  const AlignmentList& toRealign, AlignmentList *newAlignments,
62  int *nRowsAddedToMultiple, SequenceViewer *sequenceViewer);
63 
64  // brings up a dialog that lets the user set block aligner ; returns false if cancelled
65  bool SetOptions(wxWindow* parent);
66 
68  typedef struct {
70  unsigned int loopExtension;
71  unsigned int loopCutoff;
76 
77 private:
79 };
80 
81 END_SCOPE(Cn3D)
82 
83 #endif // CN3D_BA_INTERFACE__HPP
bool CreateNewPairwiseAlignmentsByBlockAlignment(BlockMultipleAlignment *multiple, const AlignmentList &toRealign, AlignmentList *newAlignments, int *nRowsAddedToMultiple, SequenceViewer *sequenceViewer)
std::list< BlockMultipleAlignment * > AlignmentList
BlockAlignerOptions currentOptions
bool SetOptions(wxWindow *parent)
#define END_SCOPE(ns)
End the previously defined scope.
Definition: ncbistl.hpp:75
#define BEGIN_SCOPE(ns)
Define a new scope.
Definition: ncbistl.hpp:72
The NCBI C++/STL use hints.
Modified on Sat Mar 02 10:54:22 2024 by modify_doxy.py rev. 669887