Spec
SimpleScoreSimple scoring scheme that has scores for matches, mismatches, opening gaps and extending gaps.
Simple scoring scheme that has scores for matches, mismatches, opening gaps and extending gaps.
Extends | Score |
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All Extended | Score |
All Subcl's | ScoreSimdWrapper |
Defined in | <seqan/score.h> |
Signature |
template <typename TValue>
class Score<TValue, Simple>;
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Template Parameters
TValue |
The score value to use. |
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Member Function Overview
Interface Function Overview
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TValue scoreGap(score);
Set gap score. -
TValue scoreGapExtend(score);
Set gap extension score. -
TValue scoreGapOpen(score);
Set gap open score. -
TValue scoreMatch(score);
Match score -
TValue scoreMismatch(score);
Set mismatch score. -
void setScoreGap(score, value);
Set gap score. -
void setScoreGapExtend(score, value);
Set gap extend score. -
void setScoreGapOpen(score, value);
Set gap open score. -
void setScoreMatch(score, value);
Set match score. -
void setScoreMismatch(score, value);
Set mismatch score.
Interface Functions Inherited From Score
Interface Metafunction Overview
Interface Metafunctions Inherited From Score
Member Functions Detail
Score::Score();
Score::Score(score);
Score::Score(match, mismatch, gap[, gapOpen]);
Constructor
Parameters
score
|
Other SimpleScore object to copy from. |
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match
|
Match score value, type TValue, default 0. |
msmatch
|
Mismatch score value, type TValue, default -1. |
gap
|
Gap extension value, type TValue, default -1. |
gapOpen
|
Gap open value (defaults to gap), type TValue. |
Data Races
Thread safety unknown!
Interface Functions Detail
TValue scoreGap(score);
Set gap score.
Parameters
score
|
The SimpleScore to query for its gap score. |
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Returns
TValue |
The gap score. |
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Data Races
Thread safety unknown!
TValue scoreGapExtend(score);
Set gap extension score.
Parameters
score
|
The SimpleScore to query for its gap extension score. |
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Returns
TValue |
The gap extension score. |
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Data Races
Thread safety unknown!
TValue scoreGapOpen(score);
Set gap open score.
Parameters
score
|
The SimpleScore to query for its gap open score. |
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Returns
TValue |
The gap open score. |
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Data Races
Thread safety unknown!
TValue scoreMatch(score);
Match score
Parameters
score
|
The SimpleScore scoring scheme. |
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Returns
TValue |
The match score. |
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Data Races
Thread safety unknown!
TValue scoreMismatch(score);
Set mismatch score.
Parameters
score
|
The SimpleScore to query for its mismatch score. |
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Returns
TValue |
The mismatch score. |
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Data Races
Thread safety unknown!
void setScoreGap(score, value);
Set gap score.
Parameters
score
|
The SimpleScore scoring scheme to set the gap value for. |
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value
|
The value to set the gap score to. |
Data Races
Thread safety unknown!
void setScoreGapExtend(score, value);
Set gap extend score.
Parameters
score
|
The SimpleScore scoring scheme to set the gap extend value for. |
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value
|
The value to set the gap open score to. |
Data Races
Thread safety unknown!
void setScoreGapOpen(score, value);
Set gap open score.
Parameters
score
|
The SimpleScore scoring scheme to set the gap open value for. |
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value
|
The value to set the gap open score to. |
Data Races
Thread safety unknown!
void setScoreMatch(score, value);
Set match score.
Parameters
score
|
The SimpleScore scoring scheme to set the value for. |
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value
|
The value to set the match score to. |
Data Races
Thread safety unknown!
void setScoreMismatch(score, value);
Set mismatch score.
Parameters
score
|
The SimpleScore scoring scheme to set the mismatch value for. |
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value
|
The value to set the mismatch score to. |
Data Races
Thread safety unknown!