23 namespace Victor {
namespace Align2{
40 const vector<unsigned int> &v1,
const vector<unsigned int> &v2);
77 const vector<unsigned int> &v2,
bool update =
true);
virtual void getMultiMatch()
Return two-element array containing an alignment with maximal score.
Definition: SWAlign.cc:69
Pairwise sequence and profile alignment.
Definition: Align.h:48
virtual ~SWAlign()
Destructor.
Definition: SWAlign.cc:49
Base class for gap functions.
Definition: GapFunction.h:31
AlignmentData * ad
Pointer to AlignmentData.
Definition: Align.h:157
virtual void pCalculateMatrix(bool update=true)
Update/create matrix values.
Definition: SWAlign.cc:112
virtual SWAlign * newCopy()
Construct a new "deep copy" of this object.
Definition: SWAlign.cc:100
virtual void copy(const SWAlign &orig)
Copy orig object to this object ("deep copy").
Definition: SWAlign.cc:92
Base class for printing alignments.
Definition: AlignmentData.h:35
SWAlign(AlignmentData *ad, GapFunction *gf, ScoringScheme *ss)
Default constructor.
Definition: SWAlign.cc:35
SWAlign & operator=(const SWAlign &orig)
Assignment operator.
Definition: SWAlign.cc:56
Implement Smith-Waterman local alignment.
Definition: SWAlign.h:30
ScoringScheme * ss
Pointer to ScoringScheme.
Definition: Align.h:159
Base class for scoring schemes.
Definition: ScoringScheme.h:34
GapFunction * gf
Pointer to GapFunction.
Definition: Align.h:158