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MASA-Core
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Definition at line 27 of file AlignmentParams.hpp.
#include <AlignmentParams.hpp>
Public Member Functions | |
| AlignmentParams () | |
| virtual | ~AlignmentParams () |
| Sequence * | getSequence (int id) |
| vector< Sequence * > | getSequences () |
| void | addSequence (Sequence *sequence) |
| void | swapSequences () |
| int | getAlignmentMethod () const |
| void | setAlignmentMethod (int alignmentMethod) |
| int | getGapOpen () const |
| int | getGapExtension () const |
| void | setAffineGapPenalties (int gapOpen, int gapExtension) |
| int | getMatch () const |
| int | getMismatch () const |
| void | setMatchMismatchScores (int match, int mismatch) |
| int | getPenaltySystem () const |
| void | setPenaltySystem (int penaltySystem) |
| int | getScoreSystem () const |
| void | setScoreSystem (int scoreSystem) |
| int | getSequencesCount () const |
| void | printParams (FILE *file) |
Private Attributes | |
| vector< Sequence * > | sequences |
| int | alignmentMethod |
| int | penaltySystem |
| int | scoreSystem |
| int | match |
| int | mismatch |
| int | gapOpen |
| int | gapExtension |
Definition at line 27 of file AlignmentParams.cpp.
| AlignmentParams::~AlignmentParams | ( | ) | [virtual] |
Definition at line 31 of file AlignmentParams.cpp.
| void AlignmentParams::addSequence | ( | Sequence * | sequence | ) |
Definition at line 108 of file AlignmentParams.cpp.
| int AlignmentParams::getAlignmentMethod | ( | ) | const |
Definition at line 51 of file AlignmentParams.cpp.
| int AlignmentParams::getGapExtension | ( | ) | const |
Definition at line 70 of file AlignmentParams.cpp.
| int AlignmentParams::getGapOpen | ( | ) | const |
Definition at line 66 of file AlignmentParams.cpp.
| int AlignmentParams::getMatch | ( | ) | const |
Definition at line 80 of file AlignmentParams.cpp.
| int AlignmentParams::getMismatch | ( | ) | const |
Definition at line 84 of file AlignmentParams.cpp.
| int AlignmentParams::getPenaltySystem | ( | ) | const |
Definition at line 88 of file AlignmentParams.cpp.
| int AlignmentParams::getScoreSystem | ( | ) | const |
Definition at line 96 of file AlignmentParams.cpp.
| Sequence * AlignmentParams::getSequence | ( | int | id | ) |
Definition at line 43 of file AlignmentParams.cpp.
| vector< Sequence * > AlignmentParams::getSequences | ( | ) |
Definition at line 47 of file AlignmentParams.cpp.
| int AlignmentParams::getSequencesCount | ( | ) | const |
Definition at line 104 of file AlignmentParams.cpp.
| void AlignmentParams::printParams | ( | FILE * | file | ) |
Definition at line 112 of file AlignmentParams.cpp.
| void AlignmentParams::setAffineGapPenalties | ( | int | gapOpen, |
| int | gapExtension | ||
| ) |
Definition at line 60 of file AlignmentParams.cpp.
| void AlignmentParams::setAlignmentMethod | ( | int | alignmentMethod | ) |
Definition at line 55 of file AlignmentParams.cpp.
| void AlignmentParams::setMatchMismatchScores | ( | int | match, |
| int | mismatch | ||
| ) |
Definition at line 74 of file AlignmentParams.cpp.
| void AlignmentParams::setPenaltySystem | ( | int | penaltySystem | ) |
Definition at line 92 of file AlignmentParams.cpp.
| void AlignmentParams::setScoreSystem | ( | int | scoreSystem | ) |
Definition at line 100 of file AlignmentParams.cpp.
| void AlignmentParams::swapSequences | ( | ) |
Definition at line 35 of file AlignmentParams.cpp.
int AlignmentParams::alignmentMethod [private] |
Definition at line 60 of file AlignmentParams.hpp.
int AlignmentParams::gapExtension [private] |
Definition at line 68 of file AlignmentParams.hpp.
int AlignmentParams::gapOpen [private] |
Definition at line 67 of file AlignmentParams.hpp.
int AlignmentParams::match [private] |
Definition at line 64 of file AlignmentParams.hpp.
int AlignmentParams::mismatch [private] |
Definition at line 65 of file AlignmentParams.hpp.
int AlignmentParams::penaltySystem [private] |
Definition at line 61 of file AlignmentParams.hpp.
int AlignmentParams::scoreSystem [private] |
Definition at line 62 of file AlignmentParams.hpp.
vector<Sequence*> AlignmentParams::sequences [private] |
Definition at line 58 of file AlignmentParams.hpp.
1.7.6.1